+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=312 WRKLOG=/tmp/bulklog/hisat2-2.2.1nb4/work.log + su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=312 WRKLOG=/tmp/bulklog/hisat2-2.2.1nb4/work.log ===> Building for hisat2-2.2.1nb4 g++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -DCOMPILER_OPTIONS="\"-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I. -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread g++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -DCOMPILER_OPTIONS="\"-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-build-l hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread g++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -DCOMPILER_OPTIONS="\"-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-s hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread g++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -DCOMPILER_OPTIONS="\"-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-l hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread In file included from hisat2_build.cpp:35: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h: In instantiation of 'void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = long unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]': gfm.h:1039:23: required from 'GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 1039 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 1040 | s, | ~~ 1041 | snpfile, | ~~~~~~~~ 1042 | htfile, | ~~~~~~~ 1043 | ssfile, | ~~~~~~~ 1044 | exonfile, | ~~~~~~~~~ 1045 | svfile, | ~~~~~~~ 1046 | repeatfile, | ~~~~~~~~~~~ 1047 | is, | ~~~ 1048 | szs, | ~~~~ 1049 | sztot, | ~~~~~~ 1050 | refparams, | ~~~~~~~~~~ 1051 | fout1, | ~~~~~~ 1052 | fout2, | ~~~~~~ 1053 | outfile, | ~~~~~~~~ 1054 | useBlockwise, | ~~~~~~~~~~~~~ 1055 | bmax, | ~~~~~ 1056 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 1057 | bmaxDivN, | ~~~~~~~~~ 1058 | dcv, | ~~~~ 1059 | parent_szs, | ~~~~~~~~~~~ 1060 | parent_refnames, | ~~~~~~~~~~~~~~~~ 1061 | seed, | ~~~~~ 1062 | verbose); | ~~~~~~~~ hgfm.h:1989:14: required from 'HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; uint32_t = unsigned int]' 1989 | _in6(NULL) | ^ hisat2_build.cpp:535:15: required from 'void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]' 535 | gfm = new HGFM( | ^~~~~~~~~~~~~~~~~~~~~ 536 | s, | ~~ 537 | packed, | ~~~~~~~ 538 | 1, // TODO: maybe not? | ~~~~~~~~~~~~~~~~~~~~~~~ 539 | lineRate, | ~~~~~~~~~ 540 | offRate, // suffix-array sampling rate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 541 | ftabChars, // number of chars in initial arrow-pair calc | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 542 | localOffRate, | ~~~~~~~~~~~~~ 543 | localFtabChars, | ~~~~~~~~~~~~~~~ 544 | nthreads, | ~~~~~~~~~ 545 | snpfile, | ~~~~~~~~ 546 | htfile, | ~~~~~~~ 547 | ssfile, | ~~~~~~~ 548 | exonfile, | ~~~~~~~~~ 549 | svfile, | ~~~~~~~ 550 | repeatfile, | ~~~~~~~~~~~ 551 | outfile, // basename for .?.ht2 files | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 552 | reverse == 0, // fw | ~~~~~~~~~~~~~~~~~~~ 553 | !entireSA, // useBlockwise | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 554 | bmax, // block size for blockwise SA builder | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 555 | bmaxMultSqrt, // block size as multiplier of sqrt(len) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 556 | bmaxDivN, // block size as divisor of len | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 557 | noDc? 0 : dcv,// difference-cover period | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 558 | is, // list of input streams | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 559 | szs, // list of reference sizes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 | (TIndexOffU)sztot.first, // total size of all unambiguous ref chars | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 561 | refparams, // reference read-in parameters | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 562 | localindex, // create local indexes? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 563 | parent_szs, // parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 564 | parent_refnames, // parent refence names | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 565 | seed, // pseudo-random number generator seed | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 566 | -1, // override offRate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 567 | verbose, // be talkative | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 568 | autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 569 | sanityCheck); // verify results and internal consistency | ~~~~~~~~~~~~ hisat2_build.cpp:786:39: required from here 786 | driver >(infile, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ 787 | infiles, | ~~~~~~~~ 788 | snp_fname, | ~~~~~~~~~~ 789 | ht_fname, | ~~~~~~~~~ 790 | ss_fname, | ~~~~~~~~~ 791 | exon_fname, | ~~~~~~~~~~~ 792 | sv_fname, | ~~~~~~~~~ 793 | dummy_fname, | ~~~~~~~~~~~~ 794 | outfile, | ~~~~~~~~ 795 | false, | ~~~~~~ 796 | REF_READ_FORWARD, | ~~~~~~~~~~~~~~~~~ 797 | true, // create local indexes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 798 | NULL, // no parent szs | ~~~~~~~~~~~~~~~~~~~~~~ 799 | NULL, // no parent refnames | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 800 | &parent_szs, // get parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 801 | &parent_refnames); // get parent refnames | ~~~~~~~~~~~~~~~~~ gfm.h:2167:33: warning: variable 'template_len' set but not used [-Wunused-but-set-variable] 2167 | index_t template_len = 0; | ^~~~~~~~~~~~ gfm.h: In instantiation of 'void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]': gfm.h:1039:23: required from 'GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' 1039 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 1040 | s, | ~~ 1041 | snpfile, | ~~~~~~~~ 1042 | htfile, | ~~~~~~~ 1043 | ssfile, | ~~~~~~~ 1044 | exonfile, | ~~~~~~~~~ 1045 | svfile, | ~~~~~~~ 1046 | repeatfile, | ~~~~~~~~~~~ 1047 | is, | ~~~ 1048 | szs, | ~~~~ 1049 | sztot, | ~~~~~~ 1050 | refparams, | ~~~~~~~~~~ 1051 | fout1, | ~~~~~~ 1052 | fout2, | ~~~~~~ 1053 | outfile, | ~~~~~~~~ 1054 | useBlockwise, | ~~~~~~~~~~~~~ 1055 | bmax, | ~~~~~ 1056 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 1057 | bmaxDivN, | ~~~~~~~~~ 1058 | dcv, | ~~~~ 1059 | parent_szs, | ~~~~~~~~~~~ 1060 | parent_refnames, | ~~~~~~~~~~~~~~~~ 1061 | seed, | ~~~~~ 1062 | verbose); | ~~~~~~~~ hgfm.h:1989:14: required from 'HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = unsigned int; uint32_t = unsigned int]' 1989 | _in6(NULL) | ^ hisat2_build.cpp:535:15: required from 'void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]' 535 | gfm = new HGFM( | ^~~~~~~~~~~~~~~~~~~~~ 536 | s, | ~~ 537 | packed, | ~~~~~~~ 538 | 1, // TODO: maybe not? | ~~~~~~~~~~~~~~~~~~~~~~~ 539 | lineRate, | ~~~~~~~~~ 540 | offRate, // suffix-array sampling rate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 541 | ftabChars, // number of chars in initial arrow-pair calc | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 542 | localOffRate, | ~~~~~~~~~~~~~ 543 | localFtabChars, | ~~~~~~~~~~~~~~~ 544 | nthreads, | ~~~~~~~~~ 545 | snpfile, | ~~~~~~~~ 546 | htfile, | ~~~~~~~ 547 | ssfile, | ~~~~~~~ 548 | exonfile, | ~~~~~~~~~ 549 | svfile, | ~~~~~~~ 550 | repeatfile, | ~~~~~~~~~~~ 551 | outfile, // basename for .?.ht2 files | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 552 | reverse == 0, // fw | ~~~~~~~~~~~~~~~~~~~ 553 | !entireSA, // useBlockwise | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 554 | bmax, // block size for blockwise SA builder | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 555 | bmaxMultSqrt, // block size as multiplier of sqrt(len) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 556 | bmaxDivN, // block size as divisor of len | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 557 | noDc? 0 : dcv,// difference-cover period | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 558 | is, // list of input streams | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 559 | szs, // list of reference sizes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 | (TIndexOffU)sztot.first, // total size of all unambiguous ref chars | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 561 | refparams, // reference read-in parameters | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 562 | localindex, // create local indexes? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 563 | parent_szs, // parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 564 | parent_refnames, // parent refence names | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 565 | seed, // pseudo-random number generator seed | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 566 | -1, // override offRate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 567 | verbose, // be talkative | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 568 | autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 569 | sanityCheck); // verify results and internal consistency | ~~~~~~~~~~~~ hisat2_build.cpp:786:39: required from here 786 | driver >(infile, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ 787 | infiles, | ~~~~~~~~ 788 | snp_fname, | ~~~~~~~~~~ 789 | ht_fname, | ~~~~~~~~~ 790 | ss_fname, | ~~~~~~~~~ 791 | exon_fname, | ~~~~~~~~~~~ 792 | sv_fname, | ~~~~~~~~~ 793 | dummy_fname, | ~~~~~~~~~~~~ 794 | outfile, | ~~~~~~~~ 795 | false, | ~~~~~~ 796 | REF_READ_FORWARD, | ~~~~~~~~~~~~~~~~~ 797 | true, // create local indexes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 798 | NULL, // no parent szs | ~~~~~~~~~~~~~~~~~~~~~~ 799 | NULL, // no parent refnames | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 800 | &parent_szs, // get parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 801 | &parent_refnames); // get parent refnames | ~~~~~~~~~~~~~~~~~ gfm.h:2167:33: warning: variable 'template_len' set but not used [-Wunused-but-set-variable] 2167 | index_t template_len = 0; | ^~~~~~~~~~~~ In file included from aligner_sw.h:78, from aligner_sw_driver.h:86, from hi_aligner.h:42, from spliced_aligner.h:23, from hisat2.cpp:46: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' In file included from aligner_sw.h:78, from aligner_sw_driver.h:86, from hi_aligner.h:42, from spliced_aligner.h:23, from hisat2.cpp:46: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' hisat2.cpp: In function 'void parseOptions(int, const char**)': hisat2.cpp:1823:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1823 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: At global scope: hisat2.cpp:2003:20: error: conflicting declaration 'typedef TIndexOffU index_t' 2003 | typedef TIndexOffU index_t; | ^~~~~~~ In file included from /usr/include/sys/wait.h:37, from /usr/include/stdlib.h:46, from /opt/tools/gcc14/include/c++/14.3.0/cstdlib:79, from /opt/tools/gcc14/include/c++/14.3.0/stdlib.h:36, from hisat2.cpp:20: /usr/include/sys/types.h:129:25: note: previous declaration as 'typedef short int index_t' 129 | typedef short index_t; | ^~~~~~~ hisat2.cpp: In function 'void parseOptions(int, const char**)': hisat2.cpp:1823:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1823 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: At global scope: hisat2.cpp:2003:20: error: conflicting declaration 'typedef TIndexOffU index_t' 2003 | typedef TIndexOffU index_t; | ^~~~~~~ In file included from /usr/include/sys/wait.h:37, from /usr/include/stdlib.h:46, from /opt/tools/gcc14/include/c++/14.3.0/cstdlib:79, from /opt/tools/gcc14/include/c++/14.3.0/stdlib.h:36, from hisat2.cpp:20: /usr/include/sys/types.h:129:25: note: previous declaration as 'typedef short int index_t' 129 | typedef short index_t; | ^~~~~~~ hisat2.cpp: In function 'void multiseedSearchWorker_hisat2(void*)': hisat2.cpp:3167:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3168:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3168 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3189:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function 'void multiseedSearchWorker_hisat2(void*)': hisat2.cpp:3167:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3168:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3168 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3189:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function 'void driver(const char*, const std::string&, const std::string&)': hisat2.cpp:4035:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 4035 | auto_ptr refs( | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:4097:19: error: no matching function for call to 'SpliceSiteDB::read(HGFM&, EList, 128>&)' 4097 | ssdb->read(gfm, altdb->alts()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from hisat2.cpp:38: splice_site.h:557:10: note: candidate: 'void SpliceSiteDB::read(std::ifstream&, bool)' 557 | void read(ifstream& in, bool known = false); | ^~~~ splice_site.h:557:25: note: no known conversion for argument 1 from 'HGFM' to 'std::ifstream&' {aka 'std::basic_ifstream&'} 557 | void read(ifstream& in, bool known = false); | ~~~~~~~~~~^~ splice_site.h:547:10: note: candidate: 'bool SpliceSiteDB::read() const' 547 | bool read() const { return _read; } | ^~~~ splice_site.h:547:10: note: candidate expects 0 arguments, 2 provided splice_site.h:556:10: note: candidate: 'void SpliceSiteDB::read(const GFM&, const EList >&)' 556 | void read(const GFM& gfm, const EList >& alts); | ^~~~ splice_site.h:556:38: note: no known conversion for argument 1 from 'HGFM' to 'const GFM&' 556 | void read(const GFM& gfm, const EList >& alts); | ~~~~~~~~~~~~~~~~~~~~~~~^~~ hisat2.cpp: In function 'void driver(const char*, const std::string&, const std::string&)': hisat2.cpp:4035:9: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 4035 | auto_ptr refs( | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:4097:19: error: no matching function for call to 'SpliceSiteDB::read(HGFM&, EList, 128>&)' 4097 | ssdb->read(gfm, altdb->alts()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from hisat2.cpp:38: splice_site.h:557:10: note: candidate: 'void SpliceSiteDB::read(std::ifstream&, bool)' 557 | void read(ifstream& in, bool known = false); | ^~~~ splice_site.h:557:25: note: no known conversion for argument 1 from 'HGFM' to 'std::ifstream&' {aka 'std::basic_ifstream&'} 557 | void read(ifstream& in, bool known = false); | ~~~~~~~~~~^~ splice_site.h:547:10: note: candidate: 'bool SpliceSiteDB::read() const' 547 | bool read() const { return _read; } | ^~~~ splice_site.h:547:10: note: candidate expects 0 arguments, 2 provided splice_site.h:556:10: note: candidate: 'void SpliceSiteDB::read(const GFM&, const EList >&)' 556 | void read(const GFM& gfm, const EList >& alts); | ^~~~ splice_site.h:556:38: note: no known conversion for argument 1 from 'HGFM' to 'const GFM&' 556 | void read(const GFM& gfm, const EList >& alts); | ~~~~~~~~~~~~~~~~~~~~~~~^~~ hi_aligner.h: In instantiation of 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]': hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:4186:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 4186 | for(size_t hi = 0; hi < hit.offsetSize(); hi++) { | ~~~^~~~~~~~~~~~~~~~~~ hi_aligner.h:4188:49: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4188 | if(partialHit.len() >= _minK + 8 && partialHit.size() == 1) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:4198:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 4198 | for(size_t hi = 0; hi < hit2.offsetSize(); hi++) { | ~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:4200:49: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4200 | if(partialHit.len() >= _minK + 8 && partialHit.size() == 1) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:4217:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4217 | for(index_t r = 0; r < rs->size(); r++) { | ~~^~~~~~~~~~~~ hi_aligner.h:4235:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 4235 | for(size_t hi = 0; hi < offsetSize; hi++) { | ~~~^~~~~~~~~~~~ hi_aligner.h:4237:45: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4237 | if(partialHit.len() >= _minK + 8 && partialHit.size() == 1) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:4261:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 4261 | for(size_t hi = 0; hi < offsetSize; hi++) { | ~~~^~~~~~~~~~~~ hi_aligner.h:4263:45: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4263 | if(partialHit.len() >= (_minK << 1)) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ hi_aligner.h:4359:54: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4359 | if(_genomeHits_rep[rdi][i].len() < (_minK << 1)) continue; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:4379:41: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 4379 | for(size_t j = 0; j < prev_align_size[1-rdi]; j++) { | ~~^~~~~~~~~~~~~~~~~~ hi_aligner.h:4464:60: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4464 | if(_genomeHits_rep[1][j].len() < (_minK << 1)) continue; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hisat2.cpp: In instantiation of 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]': hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ hisat2.cpp:3944:37: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 3944 | for(size_t i = 0; i < gfm.nPat(); i++) { | ~~^~~~~~~~~~~~ hi_aligner.h: In instantiation of 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]': hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:4186:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 4186 | for(size_t hi = 0; hi < hit.offsetSize(); hi++) { | ~~~^~~~~~~~~~~~~~~~~~ hi_aligner.h:4188:49: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4188 | if(partialHit.len() >= _minK + 8 && partialHit.size() == 1) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:4198:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 4198 | for(size_t hi = 0; hi < hit2.offsetSize(); hi++) { | ~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:4200:49: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4200 | if(partialHit.len() >= _minK + 8 && partialHit.size() == 1) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:4217:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4217 | for(index_t r = 0; r < rs->size(); r++) { | ~~^~~~~~~~~~~~ hi_aligner.h:4235:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 4235 | for(size_t hi = 0; hi < offsetSize; hi++) { | ~~~^~~~~~~~~~~~ hi_aligner.h:4237:45: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4237 | if(partialHit.len() >= _minK + 8 && partialHit.size() == 1) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:4261:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 4261 | for(size_t hi = 0; hi < offsetSize; hi++) { | ~~~^~~~~~~~~~~~ hi_aligner.h:4263:45: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4263 | if(partialHit.len() >= (_minK << 1)) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ hi_aligner.h:4359:54: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4359 | if(_genomeHits_rep[rdi][i].len() < (_minK << 1)) continue; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:4379:41: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 4379 | for(size_t j = 0; j < prev_align_size[1-rdi]; j++) { | ~~^~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'bool HI_Aligner::pairReads(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]': hi_aligner.h:4088:17: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4088 | pairReads(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, wlm, prm, him, rnd, sink); | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5971:26: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5971 | for(index_t i = 0; i < rs1->size(); i++) { | ~~^~~~~~~~~~~~~ hi_aligner.h:5972:57: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5972 | for(index_t j = (i >= start_i ? 0 : start_j); j < rs2->size(); j++) { | ~~^~~~~~~~~~~~~ hi_aligner.h:4464:60: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4464 | if(_genomeHits_rep[1][j].len() < (_minK << 1)) continue; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]': hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5636:22: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5636 | while(hitoff >= _minK_local - 1) { | ~~~~~~~^~~~~~~~~~~~~~~~~~ hi_aligner.h:5685:40: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5685 | for(index_t ri = 0; ri < coords.size(); ri++) { | ~~~^~~~~~~~~~~~~~~ hi_aligner.h:5688:65: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'short int' [-Wsign-compare] 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'TRefOff' {aka 'long int'} [-Wsign-compare] 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:5714:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const short int' [-Wsign-compare] 5714 | if(_genomeHits.size() > maxsize) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~ hi_aligner.h:5720:28: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5720 | for(index_t hi = 0; hi < _genomeHits.size(); hi++) { | ~~~^~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'index_t HI_Aligner::getRepeatHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const RB_KmerTable&, const BitPairReference&, RandomSource&, index_t, bool, index_t, EList >&, index_t, SharedTempVars&, const Scoring&, SwAligner&, SpliceSiteDB&, SwMetrics&, WalkMetrics&, PerReadMetrics&, HIMetrics&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]': hi_aligner.h:4329:21: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4329 | getRepeatHits(rfm, | ^~~~~~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5236:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5236 | for(index_t i = 0; i < _tmp_alignments.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from gfm.h:59: repeat.h: In instantiation of 'bool RepeatDB::findCoords(index_t, index_t, index_t, index_t, index_t, const EList&, const ALTDB&, EList, RepeatCoord > >&, index_t, index_t) const [with index_t = short int]': hi_aligner.h:4391:44: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4391 | repeatdb.findCoords(joinedOff, | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 4392 | joinedOff + res.refExtent(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4393 | _genomeHits_rep[rdi][i]._tidx, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4394 | _genomeHits_rep[rdi][i]._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4395 | _genomeHits_rep[rdi][i]._joinedOff + _genomeHits_rep[rdi][i].len(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4396 | _snpIDs, | ~~~~~~~~ 4397 | raltdb, | ~~~~~~~ 4398 | positions, | ~~~~~~~~~~ 4399 | rp.khits * 10); | ~~~~~~~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ repeat.h:442:18: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 442 | if(repID >= _repeatMap.size()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~ hisat2.cpp: In instantiation of 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]': hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ hisat2.cpp:3944:37: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 3944 | for(size_t i = 0; i < gfm.nPat(); i++) { | ~~^~~~~~~~~~~~ repeat.h:467:17: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 467 | for(; p < positions.size(); p++) { | ~~^~~~~~~~~~~~~~~~~~ repeat.h:493:38: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 493 | if(near_positions.size() >= max_positions) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ repeat.h: In instantiation of 'bool RepeatDB::findCommonCoords(index_t, index_t, index_t, const EList&, index_t, index_t, index_t, const EList&, const ALTDB&, EList, RepeatCoord > >&, index_t, index_t) const [with index_t = short int]': hi_aligner.h:4471:54: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4471 | repeatdb.findCommonCoords(_genomeHits_rep[0][i]._tidx, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4472 | _genomeHits_rep[0][i]._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4473 | _genomeHits_rep[0][i]._joinedOff + _genomeHits_rep[0][i].len(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4474 | _snpIDs, | ~~~~~~~~ 4475 | _genomeHits_rep[1][j]._tidx, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4476 | _genomeHits_rep[1][j]._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4477 | _genomeHits_rep[1][j]._joinedOff + _genomeHits_rep[1][j].len(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4478 | _snpIDs2, | ~~~~~~~~~ 4479 | raltdb, | ~~~~~~~ 4480 | positions, | ~~~~~~~~~~ 4481 | rp.khits * 10); | ~~~~~~~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ repeat.h:514:18: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 514 | if(repID >= _repeatMap.size() || repID2 >= _repeatMap.size()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~ repeat.h:514:49: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 514 | if(repID >= _repeatMap.size() || repID2 >= _repeatMap.size()) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ repeat.h:554:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 554 | for(index_t i = 0; i < positions.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ repeat.h:559:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 559 | for(index_t j = jsave; j < positions2.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~ repeat.h:596:44: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 596 | if(common_positions.size() >= max_positions) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ repeat.h:600:40: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 600 | if(common_positions.size() >= max_positions) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from hisat2.cpp:44: aligner_seed.h: In instantiation of 'void SeedResults::toSeedAlSumm(SeedAlSumm&) const [with index_t = short int]': aln_sink.h:2065:34: required from 'void AlnSinkWrap::finishRead(const SeedResults*, const SeedResults*, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, RandomSource&, ReportingMetrics&, const PerReadMetrics&, const Scoring&, bool, bool, bool) [with index_t = short int]' 2065 | sr1->toSeedAlSumm(ssm1); | ~~~~~~~~~~~~~~~~~^~~~~~ hisat2.cpp:3607:25: required from here 3607 | msinkwrap.finishRead( | ~~~~~~~~~~~~~~~~~~~~^ 3608 | NULL, | ~~~~~ 3609 | NULL, | ~~~~~ 3610 | exhaustive[0], // exhausted seed hits for mate 1? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3611 | exhaustive[1], // exhausted seed hits for mate 2? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3612 | nfilt[0], | ~~~~~~~~~ 3613 | nfilt[1], | ~~~~~~~~~ 3614 | scfilt[0], | ~~~~~~~~~~ 3615 | scfilt[1], | ~~~~~~~~~~ 3616 | lenfilt[0], | ~~~~~~~~~~~ 3617 | lenfilt[1], | ~~~~~~~~~~~ 3618 | qcfilt[0], | ~~~~~~~~~~ 3619 | qcfilt[1], | ~~~~~~~~~~ 3620 | sortByScore, // prioritize by alignment score | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3621 | rnd, // pseudo-random generator | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3622 | rpm, // reporting metrics | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3623 | prm, // per-read metrics | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3624 | sc, // scoring scheme | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3625 | !seedSumm, // suppress seed summaries? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3626 | seedSumm, // suppress alignments? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3627 | templateLenAdjustment); | ~~~~~~~~~~~~~~~~~~~~~~ aligner_seed.h:778:37: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const short int' [-Wsign-compare] 778 | for(size_t i = 0; i < numOffs_; i++) { | ~~^~~~~~~~~~ aligner_seed.h:780:83: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 780 | if(ssum.minNonzEltFw == 0 || hitsFw_[i].numElts() < ssum.minNonzEltFw) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ aligner_seed.h:783:83: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 783 | if(ssum.maxNonzEltFw == 0 || hitsFw_[i].numElts() > ssum.maxNonzEltFw) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ aligner_seed.h:786:87: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 786 | if(ssum.minNonzRangeFw == 0 || hitsFw_[i].numRanges() < ssum.minNonzRangeFw) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ aligner_seed.h:789:87: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 789 | if(ssum.maxNonzRangeFw == 0 || hitsFw_[i].numRanges() > ssum.maxNonzRangeFw) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ aligner_seed.h:794:83: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 794 | if(ssum.minNonzEltRc == 0 || hitsRc_[i].numElts() < ssum.minNonzEltRc) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ aligner_seed.h:797:83: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 797 | if(ssum.maxNonzEltRc == 0 || hitsRc_[i].numElts() > ssum.maxNonzEltRc) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ aligner_seed.h:800:87: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 800 | if(ssum.minNonzRangeRc == 0 || hitsRc_[i].numRanges() < ssum.minNonzRangeRc) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ aligner_seed.h:803:87: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 803 | if(ssum.maxNonzRangeRc == 0 || hitsRc_[i].numRanges() > ssum.maxNonzRangeRc) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ repeat.h: In instantiation of 'void RepeatDB::construct(const index_t*, index_t) [with index_t = short int]': hisat2.cpp:3896:32: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3896 | repeatdb->construct(gfm.rstarts(), gfm.nFrag()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ repeat.h:279:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 279 | for(index_t r = 0; r < _repeats.size(); r++) { | ~~^~~~~~~~~~~~~~~~~ repeat.h:280:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 280 | if(_repeats[r].repID >= _repeatMap.size()) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ repeat.h:295:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 295 | for(index_t r = 0; r < _repeats.size(); r++) { | ~~^~~~~~~~~~~~~~~~~ repeat.h:298:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 298 | for(index_t p = 0; p < positions.size(); p++) { | ~~^~~~~~~~~~~~~~~~~~ repeat.h:312:17: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 312 | while(j < joinedOffList.size() && r < rlen) { | ~~^~~~~~~~~~~~~~~~~~~~~~ repeat.h:335:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 335 | for(index_t r = 0; r < _repeats.size(); r++) { | ~~^~~~~~~~~~~~~~~~~ repeat.h:338:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 338 | for(index_t p = 0; p < positions.size(); p++) { | ~~^~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'bool HI_Aligner::pairReads(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]': hi_aligner.h:4088:17: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4088 | pairReads(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, wlm, prm, him, rnd, sink); | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5971:26: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5971 | for(index_t i = 0; i < rs1->size(); i++) { | ~~^~~~~~~~~~~~~ hi_aligner.h:5972:57: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5972 | for(index_t j = (i >= start_i ? 0 : start_j); j < rs2->size(); j++) { | ~~^~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]': hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5636:22: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5636 | while(hitoff >= _minK_local - 1) { | ~~~~~~~^~~~~~~~~~~~~~~~~~ hi_aligner.h:5685:40: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5685 | for(index_t ri = 0; ri < coords.size(); ri++) { | ~~~^~~~~~~~~~~~~~~ hi_aligner.h:5688:65: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'short int' [-Wsign-compare] 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'TRefOff' {aka 'long int'} [-Wsign-compare] 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:5714:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const short int' [-Wsign-compare] 5714 | if(_genomeHits.size() > maxsize) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~ hi_aligner.h:5720:28: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5720 | for(index_t hi = 0; hi < _genomeHits.size(); hi++) { | ~~~^~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'index_t HI_Aligner::getRepeatHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const RB_KmerTable&, const BitPairReference&, RandomSource&, index_t, bool, index_t, EList >&, index_t, SharedTempVars&, const Scoring&, SwAligner&, SpliceSiteDB&, SwMetrics&, WalkMetrics&, PerReadMetrics&, HIMetrics&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]': hi_aligner.h:4329:21: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4329 | getRepeatHits(rfm, | ^~~~~~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5236:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5236 | for(index_t i = 0; i < _tmp_alignments.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from gfm.h:59: repeat.h: In instantiation of 'bool RepeatDB::findCoords(index_t, index_t, index_t, index_t, index_t, const EList&, const ALTDB&, EList, RepeatCoord > >&, index_t, index_t) const [with index_t = short int]': hi_aligner.h:4391:44: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4391 | repeatdb.findCoords(joinedOff, | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 4392 | joinedOff + res.refExtent(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4393 | _genomeHits_rep[rdi][i]._tidx, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4394 | _genomeHits_rep[rdi][i]._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4395 | _genomeHits_rep[rdi][i]._joinedOff + _genomeHits_rep[rdi][i].len(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4396 | _snpIDs, | ~~~~~~~~ 4397 | raltdb, | ~~~~~~~ 4398 | positions, | ~~~~~~~~~~ 4399 | rp.khits * 10); | ~~~~~~~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ repeat.h:442:18: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 442 | if(repID >= _repeatMap.size()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~ repeat.h:467:17: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 467 | for(; p < positions.size(); p++) { | ~~^~~~~~~~~~~~~~~~~~ repeat.h:493:38: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 493 | if(near_positions.size() >= max_positions) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ repeat.h: In instantiation of 'bool RepeatDB::findCommonCoords(index_t, index_t, index_t, const EList&, index_t, index_t, index_t, const EList&, const ALTDB&, EList, RepeatCoord > >&, index_t, index_t) const [with index_t = short int]': hi_aligner.h:4471:54: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4471 | repeatdb.findCommonCoords(_genomeHits_rep[0][i]._tidx, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4472 | _genomeHits_rep[0][i]._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4473 | _genomeHits_rep[0][i]._joinedOff + _genomeHits_rep[0][i].len(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4474 | _snpIDs, | ~~~~~~~~ 4475 | _genomeHits_rep[1][j]._tidx, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4476 | _genomeHits_rep[1][j]._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4477 | _genomeHits_rep[1][j]._joinedOff + _genomeHits_rep[1][j].len(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4478 | _snpIDs2, | ~~~~~~~~~ 4479 | raltdb, | ~~~~~~~ 4480 | positions, | ~~~~~~~~~~ 4481 | rp.khits * 10); | ~~~~~~~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ repeat.h:514:18: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 514 | if(repID >= _repeatMap.size() || repID2 >= _repeatMap.size()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~ repeat.h:514:49: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 514 | if(repID >= _repeatMap.size() || repID2 >= _repeatMap.size()) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ repeat.h:554:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 554 | for(index_t i = 0; i < positions.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ repeat.h:559:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 559 | for(index_t j = jsave; j < positions2.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~ repeat.h:596:44: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 596 | if(common_positions.size() >= max_positions) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ repeat.h:600:40: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 600 | if(common_positions.size() >= max_positions) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from hisat2.cpp:44: aligner_seed.h: In instantiation of 'void SeedResults::toSeedAlSumm(SeedAlSumm&) const [with index_t = short int]': aln_sink.h:2065:34: required from 'void AlnSinkWrap::finishRead(const SeedResults*, const SeedResults*, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, RandomSource&, ReportingMetrics&, const PerReadMetrics&, const Scoring&, bool, bool, bool) [with index_t = short int]' 2065 | sr1->toSeedAlSumm(ssm1); | ~~~~~~~~~~~~~~~~~^~~~~~ hisat2.cpp:3607:25: required from here 3607 | msinkwrap.finishRead( | ~~~~~~~~~~~~~~~~~~~~^ 3608 | NULL, | ~~~~~ 3609 | NULL, | ~~~~~ 3610 | exhaustive[0], // exhausted seed hits for mate 1? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3611 | exhaustive[1], // exhausted seed hits for mate 2? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3612 | nfilt[0], | ~~~~~~~~~ 3613 | nfilt[1], | ~~~~~~~~~ 3614 | scfilt[0], | ~~~~~~~~~~ 3615 | scfilt[1], | ~~~~~~~~~~ 3616 | lenfilt[0], | ~~~~~~~~~~~ 3617 | lenfilt[1], | ~~~~~~~~~~~ 3618 | qcfilt[0], | ~~~~~~~~~~ 3619 | qcfilt[1], | ~~~~~~~~~~ 3620 | sortByScore, // prioritize by alignment score | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3621 | rnd, // pseudo-random generator | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3622 | rpm, // reporting metrics | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3623 | prm, // per-read metrics | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3624 | sc, // scoring scheme | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3625 | !seedSumm, // suppress seed summaries? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3626 | seedSumm, // suppress alignments? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3627 | templateLenAdjustment); | ~~~~~~~~~~~~~~~~~~~~~~ aligner_seed.h:778:37: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const short int' [-Wsign-compare] 778 | for(size_t i = 0; i < numOffs_; i++) { | ~~^~~~~~~~~~ aligner_seed.h:780:83: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 780 | if(ssum.minNonzEltFw == 0 || hitsFw_[i].numElts() < ssum.minNonzEltFw) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ aligner_seed.h:783:83: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 783 | if(ssum.maxNonzEltFw == 0 || hitsFw_[i].numElts() > ssum.maxNonzEltFw) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ aligner_seed.h:786:87: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 786 | if(ssum.minNonzRangeFw == 0 || hitsFw_[i].numRanges() < ssum.minNonzRangeFw) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ aligner_seed.h:789:87: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 789 | if(ssum.maxNonzRangeFw == 0 || hitsFw_[i].numRanges() > ssum.maxNonzRangeFw) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'index_t HI_Aligner::partialSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, size_t, size_t&, size_t&, ReadBWTHit&, RandomSource&, bool&, bool&, index_t) [with index_t = short int; local_index_t = short unsigned int; size_t = long unsigned int]': hi_aligner.h:4724:13: required from 'bool HI_Aligner::nextBWT(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, index_t&, bool&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4724 | partialSearch( | ^~~~~~~~~~~~~ hi_aligner.h:4077:15: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4077 | while(nextBWT(sc, pepol, tpol, gpol, gfm, altdb, ref, rdi, fw, wlm, prm, him, rnd, sink)) { | ^~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:6515:29: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 6515 | if(dep - offset >= _minK + 8 && node_rangeTemp.second - node_rangeTemp.first >= 4) { | ~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:6531:29: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 6531 | if(dep - offset >= _minK + 12 && range.second - range.first == 1) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43: btypes.h:29:19: warning: overflow in conversion from 'long unsigned int' to 'short int' changes value from '18446744073709551615' to '-1' [-Woverflow] 29 | #define INDEX_MAX 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ hi_aligner.h:6581:37: note: in expansion of macro 'INDEX_MAX' 6581 | partialHits.back().init(INDEX_MAX, | ^~~~~~~~~ btypes.h:29:19: warning: overflow in conversion from 'long unsigned int' to 'short int' changes value from '18446744073709551615' to '-1' [-Woverflow] 29 | #define INDEX_MAX 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ hi_aligner.h:6582:37: note: in expansion of macro 'INDEX_MAX' 6582 | INDEX_MAX, | ^~~~~~~~~ btypes.h:29:19: warning: overflow in conversion from 'long unsigned int' to 'short int' changes value from '18446744073709551615' to '-1' [-Woverflow] 29 | #define INDEX_MAX 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ hi_aligner.h:6583:37: note: in expansion of macro 'INDEX_MAX' 6583 | INDEX_MAX, | ^~~~~~~~~ btypes.h:29:19: warning: overflow in conversion from 'long unsigned int' to 'short int' changes value from '18446744073709551615' to '-1' [-Woverflow] 29 | #define INDEX_MAX 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ hi_aligner.h:6584:37: note: in expansion of macro 'INDEX_MAX' 6584 | INDEX_MAX, | ^~~~~~~~~ hi_aligner.h: In instantiation of 'index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = short int; local_index_t = short unsigned int]': hi_aligner.h:5525:23: required from 'bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5033:31: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 5033 | for(size_t hi = 0; hi < offsetSize; hi++) { | ~~~^~~~~~~~~~~~ hi_aligner.h:5039:39: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5039 | partialHit_j.len() <= _minK + 2) continue; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:5048:39: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5048 | partialHit_k.len() <= _minK + 2) continue; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:5101:32: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5101 | if(edgeIdx < partialHit._node_iedge_count.size()) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5113:29: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 5113 | if(rndi < remainedGenomeHitSize - added) { | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5145:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 5145 | if(genomeHit_size + coords.size() > maxGenomeHitSize) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ hi_aligner.h:5148:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5148 | for(index_t k = 0; k < coords.size(); k++) { | ~~^~~~~~~~~~~~~~~ hi_aligner.h:5187:79: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 5187 | if(partialHit._hit_type == CANDIDATE_HIT && genomeHits.size() >= maxGenomeHitSize) break; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:5189:75: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 5189 | if(partialHit._hit_type == CANDIDATE_HIT && genomeHits.size() >= maxGenomeHitSize) break; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ aligner_seed.h:794:83: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 794 | if(ssum.minNonzEltRc == 0 || hitsRc_[i].numElts() < ssum.minNonzEltRc) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ aligner_seed.h:797:83: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 797 | if(ssum.maxNonzEltRc == 0 || hitsRc_[i].numElts() > ssum.maxNonzEltRc) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ aligner_seed.h:800:87: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 800 | if(ssum.minNonzRangeRc == 0 || hitsRc_[i].numRanges() < ssum.minNonzRangeRc) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ aligner_seed.h:803:87: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 803 | if(ssum.maxNonzRangeRc == 0 || hitsRc_[i].numRanges() > ssum.maxNonzRangeRc) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ hgfm.h: In instantiation of 'const LocalGFM* HGFM::getLocalGFM(index_t, index_t) const [with index_t = short int; local_index_t = short unsigned int]': hi_aligner.h:5619:69: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5619 | const LocalGFM* lGFM = hGFM->getLocalGFM(tidx, toff); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hgfm.h:1717:22: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1717 | if(offsetidx >= localGFMs.size()) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hgfm.h: In instantiation of 'const LocalGFM* HGFM::prevLocalGFM(const LocalGFM*) const [with index_t = short int; local_index_t = short unsigned int]': hi_aligner.h:5631:42: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5631 | lGFM = hGFM->prevLocalGFM(lGFM); | ~~~~~~~~~~~~~~~~~~^~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hgfm.h:1728:19: warning: comparison of integer expressions of different signedness: 'short int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 1728 | if(offset < local_index_interval) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]': hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2270:26: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2270 | for(index_t s = 0; s < ssOffs.size(); s++) { | ~~^~~~~~~~~~~~~~~ hi_aligner.h:2314:51: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const short int' [-Wsign-compare] 2314 | if(offDiffs.size() - single_offDiffs_size > max_offDiffs_size) offDiffs.resize(single_offDiffs_size + max_offDiffs_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:2315:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2315 | for(index_t o = 0; o < offDiffs.size() && !found2; o++) { | ~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2361:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2361 | for(index_t i = 0; i < genomeHits.size() - 1; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2367:42: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2367 | for(index_t e = 0; e < candidate_edits.size(); e++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~ repeat.h: In instantiation of 'void RepeatDB::construct(const index_t*, index_t) [with index_t = short int]': hisat2.cpp:3896:32: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3896 | repeatdb->construct(gfm.rstarts(), gfm.nFrag()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ repeat.h:279:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 279 | for(index_t r = 0; r < _repeats.size(); r++) { | ~~^~~~~~~~~~~~~~~~~ repeat.h:280:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 280 | if(_repeats[r].repID >= _repeatMap.size()) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ repeat.h:295:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 295 | for(index_t r = 0; r < _repeats.size(); r++) { | ~~^~~~~~~~~~~~~~~~~ repeat.h:298:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 298 | for(index_t p = 0; p < positions.size(); p++) { | ~~^~~~~~~~~~~~~~~~~~ repeat.h:312:17: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 312 | while(j < joinedOffList.size() && r < rlen) { | ~~^~~~~~~~~~~~~~~~~~~~~~ repeat.h:335:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 335 | for(index_t r = 0; r < _repeats.size(); r++) { | ~~^~~~~~~~~~~~~~~~~ repeat.h:338:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 338 | for(index_t p = 0; p < positions.size(); p++) { | ~~^~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'bool GenomeHit::extend(const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, PerReadMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, const TranscriptomePolicy&, const GraphPolicy&, index_t&, index_t&, index_t) [with index_t = short int; TAlScore = long int]': hi_aligner.h:5724:25: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5724 | genomeHit.extend( | ~~~~~~~~~~~~~~~~^ 5725 | ord, | ~~~~ 5726 | gfm, | ~~~~ 5727 | ref, | ~~~~ 5728 | altdb, | ~~~~~~ 5729 | repeatdb, | ~~~~~~~~~ 5730 | ssdb, | ~~~~~ 5731 | swa, | ~~~~ 5732 | swm, | ~~~~ 5733 | prm, | ~~~~ 5734 | sc, | ~~~ 5735 | _minsc[ordi], | ~~~~~~~~~~~~~ 5736 | rnd, | ~~~~ 5737 | (index_t)_minK_local, | ~~~~~~~~~~~~~~~~~~~~~ 5738 | tpol, | ~~~~~ 5739 | gpol, | ~~~~~ 5740 | leftext, | ~~~~~~~~ 5741 | rightext); | ~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2132:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2132 | for(index_t i = 0; i < _edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:2158:36: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2158 | for(index_t ei = 0; ei < _edits->size(); ei++) { | ~~~^~~~~~~~~~~~~~~~ repeat.h: In instantiation of 'bool RepeatDB::repeatExist(index_t, index_t, index_t) const [with index_t = short int]': hi_aligner.h:5240:37: required from 'index_t HI_Aligner::getRepeatHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const RB_KmerTable&, const BitPairReference&, RandomSource&, index_t, bool, index_t, EList >&, index_t, SharedTempVars&, const Scoring&, SwAligner&, SpliceSiteDB&, SwMetrics&, WalkMetrics&, PerReadMetrics&, HIMetrics&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 5240 | if(!repeatdb.repeatExist(repID, coord.pos, coord.pos + len)) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4329:21: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4329 | getRepeatHits(rfm, | ^~~~~~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ repeat.h:360:18: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 360 | if(repID >= _repeatMap.size()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~ gfm.h: In instantiation of 'GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short int; std::string = std::__cxx11::basic_string; int32_t = int]': hgfm.h:1604:14: required from 'HGFM::HGFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short int; local_index_t = short unsigned int; std::string = std::__cxx11::basic_string; int32_t = int]' 1604 | _in6(NULL) | ^ hisat2.cpp:3776:31: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3776 | HGFM gfm( | ^~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:772:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 772 | if(alts.size() == numAlts) break; | ~~~~~~~~~~~~^~~~~~~~~~ gfm.h:788:42: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 788 | for(index_t h = 0; h < ht.alts.size(); h++) { | ~~^~~~~~~~~~~~~~~~ gfm.h:791:42: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 791 | if(haplotypes.size() == numHaplotypes) break; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ gfm.h:809:33: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 809 | for(size_t k = 0; k < numRepeatIndex; k++) { | ~~^~~~~~~~~~~~~~~~ gfm.h:822:41: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 822 | while(k < numRepeatIndex && k2 < readLens->size()) { | ~~^~~~~~~~~~~~~~~~ gfm.h:823:65: warning: comparison of integer expressions of different signedness: 'short int' and 'long unsigned int' [-Wsign-compare] 823 | if (repeatLens[k].first >= (*readLens)[k2]) { gfm.h:835:53: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 835 | for(size_t i = 0; i < numRepeatIndex; i++) { | ~~^~~~~~~~~~~~~~~~ gfm.h:850:33: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 850 | for(size_t k = 0; k < numKmertables; k++) { | ~~^~~~~~~~~~~~~~~ gfm.h:853:33: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 853 | for(size_t k = 0; k < numKmertables; k++) { | ~~^~~~~~~~~~~~~~~ gfm.h:888:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 888 | if(alts.size() > 1 && alts.size() > nalts) { | ~~~~~~~~~~~~^~~~~~~ gfm.h:910:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 910 | for(index_t h = 0; h < haplotypes.size(); h++) { | ~~^~~~~~~~~~~~~~~~~~~ gfm.h:912:40: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 912 | for(index_t h2 = 0; h2 < ht.alts.size(); h2++) { | ~~~^~~~~~~~~~~~~~~~ hgfm.h: In instantiation of 'void HGFM::readIntoMemory(int, bool, bool, bool, bool, GFMParams*, bool, bool, bool) [with index_t = short int; local_index_t = short unsigned int]': hgfm.h:1667:3: required from 'void HGFM::loadIntoMemory(int, bool, bool, bool, bool, bool) [with index_t = short int; local_index_t = short unsigned int]' 1667 | readIntoMemory( | ^~~~~~~~~~~~~~ hisat2.cpp:3808:21: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3808 | gfm.loadIntoMemory( | ~~~~~~~~~~~~~~~~~~^ 3809 | -1, // fw index | ~~~~~~~~~~~~~~~ 3810 | true, // load SA sample | ~~~~~~~~~~~~~~~~~~~~~~~ 3811 | true, // load ftab | ~~~~~~~~~~~~~~~~~~ 3812 | true, // load rstarts | ~~~~~~~~~~~~~~~~~~~~~ 3813 | !noRefNames, | ~~~~~~~~~~~~ 3814 | startVerbose); | ~~~~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ hgfm.h:2604:29: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2604 | for(size_t i = 0; i < _nlocalGFMs; i++) { | ~~^~~~~~~~~~~~~ hgfm.h:2637:25: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2637 | if(tidx >= _localGFMs.size()) { | ~~~~~^~~~~~~~~~~~~~~~~~~~ gfm.h: In instantiation of 'void GFM::restore(SString&) const [with index_t = short int]': gfm.h:6926:5: required from 'void GFM::checkOrigs(const EList >&, bool) const [with index_t = short int]' 6926 | restore(rest); | ^~~~~~~ hisat2.cpp:3815:17: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3815 | gfm.checkOrigs(os, false); | ~~~~~~~~~~~~~~^~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:6900:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 6900 | for(index_t j = 0; j < _zOffs.size(); j++) { | ~~^~~~~~~~~~~~~~~ In file included from hisat2.cpp:34: rfm.h: In instantiation of 'void RFM::readIntoMemory(int, bool, bool, bool, bool, GFMParams*, bool, bool, bool) [with index_t = short int]': rfm.h:389:3: required from 'void RFM::loadIntoMemory(int, bool, bool, bool, bool, bool) [with index_t = short int]' 389 | readIntoMemory( | ^~~~~~~~~~~~~~ hisat2.cpp:3888:33: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3888 | rgfm->loadIntoMemory( | ~~~~~~~~~~~~~~~~~~~~^ 3889 | -1, // not the reverse index | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3890 | true, // load SA samp? (yes, need forward index's SA samp) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3891 | true, // load ftab (in forward index) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3892 | true, // load rstarts (in forward index) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3893 | !noRefNames, // load names? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3894 | startVerbose); | ~~~~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ rfm.h:1088:29: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 1088 | for(size_t i = 0; i < nlocalRFMs; i++) { | ~~^~~~~~~~~~~~ hi_aligner.h: In instantiation of 'static void GenomeHit::findSSOffs(const GFM&, const ALTDB&, index_t, index_t, EList >&) [with index_t = short int]': hi_aligner.h:2267:15: required from 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]' 2267 | findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2498:65: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2498 | for(index_t i = (index_t)alts.bsearchLoBound(alt_search); i < alts.size(); i++) { | ~~^~~~~~~~~~~~~ hi_aligner.h:2511:73: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2511 | for(index_t j = (index_t)alts.bsearchLoBound(alt_search); j < alts.size(); j++) { | ~~^~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'static index_t GenomeHit::findOffDiffs(const GFM&, const ALTDB&, index_t, index_t, EList >&) [with index_t = short int]': hi_aligner.h:2298:58: required from 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]' 2298 | const index_t single_offDiffs_size = findOffDiffs(gfm, | ~~~~~~~~~~~~^~~~~ 2299 | altdb, | ~~~~~~ 2300 | (genomeHit._joinedOff >= width ? genomeHit._joinedOff - width : 0), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2301 | genomeHit._joinedOff + width, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2302 | offDiffs); | ~~~~~~~~~ hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2564:66: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2564 | for(alt_range.second = alt_range.first; alt_range.second < alts.size(); alt_range.second++) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2625:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2625 | for(index_t i = 0; i < offDiffs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = short int; BTDnaString = SDnaStringExpandable<1024, 2>]': hi_aligner.h:2337:47: required from 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]' 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:758:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 758 | if(f.pos + extlen == base_rdoff + 1) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:769:36: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'int' [-Wsign-compare] 769 | if(extlen > 0 && b.pos == rdoff - base_rdoff + extlen - 1) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:775:44: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 775 | if(extlen == 0 && edits.size() > nedits) { | ~~~~~~~~~~~~~^~~~~~~~ hi_aligner.h: In instantiation of 'bool GenomeHit::operator==(const GenomeHit&) const [with index_t = short int]': hi_aligner.h:2362:38: required from 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]' 2362 | if(genomeHits[i] == genomeHits.back()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:1167:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1167 | for(index_t i = 0; i < _edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'void GenomeHit::getLeft(index_t&, index_t&, index_t&, int64_t*, const Read*, const Scoring*) const [with index_t = short int; int64_t = long int]': hi_aligner.h:2070:15: required from 'bool GenomeHit::extend(const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, PerReadMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, const TranscriptomePolicy&, const GraphPolicy&, index_t&, index_t&, index_t) [with index_t = short int; TAlScore = long int]' 2070 | this->getLeft(left_rdoff, left_len, left_toff); | ~~~~~~^~~~~~~ hi_aligner.h:5724:25: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5724 | genomeHit.extend( | ~~~~~~~~~~~~~~~~^ 5725 | ord, | ~~~~ 5726 | gfm, | ~~~~ 5727 | ref, | ~~~~ 5728 | altdb, | ~~~~~~ 5729 | repeatdb, | ~~~~~~~~~ 5730 | ssdb, | ~~~~~ 5731 | swa, | ~~~~ 5732 | swm, | ~~~~ 5733 | prm, | ~~~~ 5734 | sc, | ~~~ 5735 | _minsc[ordi], | ~~~~~~~~~~~~~ 5736 | rnd, | ~~~~ 5737 | (index_t)_minK_local, | ~~~~~~~~~~~~~~~~~~~~~ 5738 | tpol, | ~~~~~ 5739 | gpol, | ~~~~~ 5740 | leftext, | ~~~~~~~~ 5741 | rightext); | ~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:935:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 935 | for(index_t i = 0; i < _edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:940:57: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'short int' [-Wsign-compare] 940 | (edit.type == EDIT_TYPE_MM && edit.snpID != (index_t)INDEX_MAX)) { hi_aligner.h:947:35: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'short int' [-Wsign-compare] 947 | if(edit.snpID == (index_t)INDEX_MAX) { hi_aligner.h: In instantiation of 'void GenomeHit::getRight(index_t&, index_t&, index_t&, int64_t*, const Read*, const Scoring*) const [with index_t = short int; int64_t = long int]': hi_aligner.h:2147:15: required from 'bool GenomeHit::extend(const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, PerReadMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, const TranscriptomePolicy&, const GraphPolicy&, index_t&, index_t&, index_t) [with index_t = short int; TAlScore = long int]' 2147 | this->getRight(right_rdoff, right_len, right_toff); | ~~~~~~^~~~~~~~ hi_aligner.h:5724:25: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5724 | genomeHit.extend( | ~~~~~~~~~~~~~~~~^ 5725 | ord, | ~~~~ 5726 | gfm, | ~~~~ 5727 | ref, | ~~~~ 5728 | altdb, | ~~~~~~ 5729 | repeatdb, | ~~~~~~~~~ 5730 | ssdb, | ~~~~~ 5731 | swa, | ~~~~ 5732 | swm, | ~~~~ 5733 | prm, | ~~~~ 5734 | sc, | ~~~ 5735 | _minsc[ordi], | ~~~~~~~~~~~~~ 5736 | rnd, | ~~~~ 5737 | (index_t)_minK_local, | ~~~~~~~~~~~~~~~~~~~~~ 5738 | tpol, | ~~~~~ 5739 | gpol, | ~~~~~ 5740 | leftext, | ~~~~~~~~ 5741 | rightext); | ~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:984:57: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'short int' [-Wsign-compare] 984 | (edit.type == EDIT_TYPE_MM && edit.snpID != (index_t)INDEX_MAX)) { hi_aligner.h:1005:35: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'short int' [-Wsign-compare] 1005 | if(edit.snpID == (index_t)INDEX_MAX) { hi_aligner.h: In instantiation of 'void GenomeHit::leftAlign(const Read&) [with index_t = short int]': hi_aligner.h:2218:21: required from 'bool GenomeHit::extend(const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, PerReadMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, const TranscriptomePolicy&, const GraphPolicy&, index_t&, index_t&, index_t) [with index_t = short int; TAlScore = long int]' 2218 | if(doLeftAlign) leftAlign(rd); | ^~~~~~~~~ hi_aligner.h:5724:25: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5724 | genomeHit.extend( | ~~~~~~~~~~~~~~~~^ 5725 | ord, | ~~~~ 5726 | gfm, | ~~~~ 5727 | ref, | ~~~~ 5728 | altdb, | ~~~~~~ 5729 | repeatdb, | ~~~~~~~~~ 5730 | ssdb, | ~~~~~ 5731 | swa, | ~~~~ 5732 | swm, | ~~~~ 5733 | prm, | ~~~~ 5734 | sc, | ~~~ 5735 | _minsc[ordi], | ~~~~~~~~~~~~~ 5736 | rnd, | ~~~~ 5737 | (index_t)_minK_local, | ~~~~~~~~~~~~~~~~~~~~~ 5738 | tpol, | ~~~~~ 5739 | gpol, | ~~~~~ 5740 | leftext, | ~~~~~~~~ 5741 | rightext); | ~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:3558:28: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3558 | for(index_t ei = 0; ei < _edits->size(); ei++) { | ~~~^~~~~~~~~~~~~~~~ hi_aligner.h:3562:23: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'short int' [-Wsign-compare] 3562 | if(edit.snpID != (index_t)INDEX_MAX) hi_aligner.h:3565:19: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3565 | for(; ei2 < _edits->size(); ei2++) { | ~~~~^~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'int64_t GenomeHit::calculateScore(const Read&, SpliceSiteDB&, const Scoring&, index_t, index_t, index_t, index_t, index_t, const BitPairReference&) [with index_t = short int; int64_t = long int]': hi_aligner.h:2220:5: required from 'bool GenomeHit::extend(const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, PerReadMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, const TranscriptomePolicy&, const GraphPolicy&, index_t&, index_t&, index_t) [with index_t = short int; TAlScore = long int]' 2220 | calculateScore( | ^~~~~~~~~~~~~~ hi_aligner.h:5724:25: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5724 | genomeHit.extend( | ~~~~~~~~~~~~~~~~^ 5725 | ord, | ~~~~ 5726 | gfm, | ~~~~ 5727 | ref, | ~~~~ 5728 | altdb, | ~~~~~~ 5729 | repeatdb, | ~~~~~~~~~ 5730 | ssdb, | ~~~~~ 5731 | swa, | ~~~~ 5732 | swm, | ~~~~ 5733 | prm, | ~~~~ 5734 | sc, | ~~~ 5735 | _minsc[ordi], | ~~~~~~~~~~~~~ 5736 | rnd, | ~~~~ 5737 | (index_t)_minK_local, | ~~~~~~~~~~~~~~~~~~~~~ 5738 | tpol, | ~~~~~ 5739 | gpol, | ~~~~~ 5740 | leftext, | ~~~~~~~~ 5741 | rightext); | ~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:3733:26: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3733 | for(index_t i = 0; i < _edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:3756:42: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3756 | for(index_t j = i + 1; j < _edits->size(); j++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:3770:37: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'short int' [-Wsign-compare] 3770 | if(intronLen_thresh < maxIntronLen) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:3796:50: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3796 | for(index_t j = i + 1; j < _edits->size(); j++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'index_t HI_Aligner::partialSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, size_t, size_t&, size_t&, ReadBWTHit&, RandomSource&, bool&, bool&, index_t) [with index_t = short int; local_index_t = short unsigned int; size_t = long unsigned int]': hi_aligner.h:4724:13: required from 'bool HI_Aligner::nextBWT(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, index_t&, bool&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4724 | partialSearch( | ^~~~~~~~~~~~~ hi_aligner.h:4077:15: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4077 | while(nextBWT(sc, pepol, tpol, gpol, gfm, altdb, ref, rdi, fw, wlm, prm, him, rnd, sink)) { | ^~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:6515:29: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 6515 | if(dep - offset >= _minK + 8 && node_rangeTemp.second - node_rangeTemp.first >= 4) { | ~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:6531:29: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 6531 | if(dep - offset >= _minK + 12 && range.second - range.first == 1) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43: btypes.h:39:19: warning: overflow in conversion from 'unsigned int' to 'short int' changes value from '4294967295' to '-1' [-Woverflow] 39 | #define INDEX_MAX 0xffffffff | ^~~~~~~~~~ hi_aligner.h:6581:37: note: in expansion of macro 'INDEX_MAX' 6581 | partialHits.back().init(INDEX_MAX, | ^~~~~~~~~ btypes.h:39:19: warning: overflow in conversion from 'unsigned int' to 'short int' changes value from '4294967295' to '-1' [-Woverflow] 39 | #define INDEX_MAX 0xffffffff | ^~~~~~~~~~ hi_aligner.h:6582:37: note: in expansion of macro 'INDEX_MAX' 6582 | INDEX_MAX, | ^~~~~~~~~ btypes.h:39:19: warning: overflow in conversion from 'unsigned int' to 'short int' changes value from '4294967295' to '-1' [-Woverflow] 39 | #define INDEX_MAX 0xffffffff | ^~~~~~~~~~ hi_aligner.h:6583:37: note: in expansion of macro 'INDEX_MAX' 6583 | INDEX_MAX, | ^~~~~~~~~ btypes.h:39:19: warning: overflow in conversion from 'unsigned int' to 'short int' changes value from '4294967295' to '-1' [-Woverflow] 39 | #define INDEX_MAX 0xffffffff | ^~~~~~~~~~ hi_aligner.h:6584:37: note: in expansion of macro 'INDEX_MAX' 6584 | INDEX_MAX, | ^~~~~~~~~ hi_aligner.h: In instantiation of 'index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = short int; local_index_t = short unsigned int]': hi_aligner.h:5525:23: required from 'bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:5033:31: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 5033 | for(size_t hi = 0; hi < offsetSize; hi++) { | ~~~^~~~~~~~~~~~ hi_aligner.h:5039:39: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5039 | partialHit_j.len() <= _minK + 2) continue; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:5048:39: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5048 | partialHit_k.len() <= _minK + 2) continue; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:5101:32: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5101 | if(edgeIdx < partialHit._node_iedge_count.size()) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5113:29: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 5113 | if(rndi < remainedGenomeHitSize - added) { | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5145:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 5145 | if(genomeHit_size + coords.size() > maxGenomeHitSize) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ hi_aligner.h:5148:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 5148 | for(index_t k = 0; k < coords.size(); k++) { | ~~^~~~~~~~~~~~~~~ hi_aligner.h:5187:79: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 5187 | if(partialHit._hit_type == CANDIDATE_HIT && genomeHits.size() >= maxGenomeHitSize) break; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:5189:75: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 5189 | if(partialHit._hit_type == CANDIDATE_HIT && genomeHits.size() >= maxGenomeHitSize) break; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hgfm.h: In instantiation of 'const LocalGFM* HGFM::getLocalGFM(index_t, index_t) const [with index_t = short int; local_index_t = short unsigned int]': hi_aligner.h:5619:69: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5619 | const LocalGFM* lGFM = hGFM->getLocalGFM(tidx, toff); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hgfm.h:1717:22: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1717 | if(offsetidx >= localGFMs.size()) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hgfm.h: In instantiation of 'const LocalGFM* HGFM::prevLocalGFM(const LocalGFM*) const [with index_t = short int; local_index_t = short unsigned int]': hi_aligner.h:5631:42: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5631 | lGFM = hGFM->prevLocalGFM(lGFM); | ~~~~~~~~~~~~~~~~~~^~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hgfm.h:1728:19: warning: comparison of integer expressions of different signedness: 'short int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 1728 | if(offset < local_index_interval) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ gfm.h: In instantiation of 'void GFM::readIntoMemory(int, bool, bool, bool, bool, GFMParams*, bool, bool, bool, bool) [with index_t = short int]': gfm.h:694:13: required from 'GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short int; std::string = std::__cxx11::basic_string; int32_t = int]' 694 | readIntoMemory( | ^~~~~~~~~~~~~~ hgfm.h:1604:14: required from 'HGFM::HGFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short int; local_index_t = short unsigned int; std::string = std::__cxx11::basic_string; int32_t = int]' 1604 | _in6(NULL) | ^ hisat2.cpp:3776:31: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3776 | HGFM gfm( | ^~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:6182:37: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 6182 | for(size_t i = 0; i < gh->_numSides; i++) { | ~~^~~~~~~~~~~~~~~ gfm.h:6251:41: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 6251 | for(size_t i = 0; i < gh->_ftabLen; i++) | ~~^~~~~~~~~~~~~~ gfm.h:6281:41: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 6281 | for(size_t i = 0; i < gh->_eftabLen; i++) | ~~^~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]': hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2270:26: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2270 | for(index_t s = 0; s < ssOffs.size(); s++) { | ~~^~~~~~~~~~~~~~~ hi_aligner.h:2314:51: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const short int' [-Wsign-compare] 2314 | if(offDiffs.size() - single_offDiffs_size > max_offDiffs_size) offDiffs.resize(single_offDiffs_size + max_offDiffs_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:2315:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2315 | for(index_t o = 0; o < offDiffs.size() && !found2; o++) { | ~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2361:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2361 | for(index_t i = 0; i < genomeHits.size() - 1; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2367:42: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2367 | for(index_t e = 0; e < candidate_edits.size(); e++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'bool GenomeHit::extend(const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, PerReadMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, const TranscriptomePolicy&, const GraphPolicy&, index_t&, index_t&, index_t) [with index_t = short int; TAlScore = long int]': hi_aligner.h:5724:25: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5724 | genomeHit.extend( | ~~~~~~~~~~~~~~~~^ 5725 | ord, | ~~~~ 5726 | gfm, | ~~~~ 5727 | ref, | ~~~~ 5728 | altdb, | ~~~~~~ 5729 | repeatdb, | ~~~~~~~~~ 5730 | ssdb, | ~~~~~ 5731 | swa, | ~~~~ 5732 | swm, | ~~~~ 5733 | prm, | ~~~~ 5734 | sc, | ~~~ 5735 | _minsc[ordi], | ~~~~~~~~~~~~~ 5736 | rnd, | ~~~~ 5737 | (index_t)_minK_local, | ~~~~~~~~~~~~~~~~~~~~~ 5738 | tpol, | ~~~~~ 5739 | gpol, | ~~~~~ 5740 | leftext, | ~~~~~~~~ 5741 | rightext); | ~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2132:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2132 | for(index_t i = 0; i < _edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:2158:36: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2158 | for(index_t ei = 0; ei < _edits->size(); ei++) { | ~~~^~~~~~~~~~~~~~~~ repeat.h: In instantiation of 'bool RepeatDB::repeatExist(index_t, index_t, index_t) const [with index_t = short int]': hi_aligner.h:5240:37: required from 'index_t HI_Aligner::getRepeatHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const RB_KmerTable&, const BitPairReference&, RandomSource&, index_t, bool, index_t, EList >&, index_t, SharedTempVars&, const Scoring&, SwAligner&, SpliceSiteDB&, SwMetrics&, WalkMetrics&, PerReadMetrics&, HIMetrics&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 5240 | if(!repeatdb.repeatExist(repID, coord.pos, coord.pos + len)) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4329:21: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4329 | getRepeatHits(rfm, | ^~~~~~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ repeat.h:360:18: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 360 | if(repID >= _repeatMap.size()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~ gfm.h: In instantiation of 'index_t GFM::mapLF1(index_t, const SideLocus&, int) const [with index_t = short int]': gfm.h:3967:29: required from 'std::pair<_FIter, _FIter> GFM::mapGLF1(index_t, SideLocus&, int, std::pair<_FIter, _FIter>*) const [with index_t = short int]' 3967 | index_t top = mapLF1(row, l, c); | ~~~~~~^~~~~~~~~~~ hi_aligner.h:6475:40: required from 'index_t HI_Aligner::partialSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, size_t, size_t&, size_t&, ReadBWTHit&, RandomSource&, bool&, bool&, index_t) [with index_t = short int; local_index_t = short unsigned int; size_t = long unsigned int]' 6475 | rangeTemp = gfm.mapGLF1(range.first, tloc, c, &node_rangeTemp); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4724:13: required from 'bool HI_Aligner::nextBWT(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, index_t&, bool&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4724 | partialSearch( | ^~~~~~~~~~~~~ hi_aligner.h:4077:15: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4077 | while(nextBWT(sc, pepol, tpol, gpol, gfm, altdb, ref, rdi, fw, wlm, prm, him, rnd, sink)) { | ^~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ gfm.h:3900:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3900 | for(index_t i = 0; i < _zOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~ gfm.h: In instantiation of 'GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short int; std::string = std::__cxx11::basic_string; int32_t = int]': hgfm.h:1604:14: required from 'HGFM::HGFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short int; local_index_t = short unsigned int; std::string = std::__cxx11::basic_string; int32_t = int]' 1604 | _in6(NULL) | ^ hisat2.cpp:3776:31: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3776 | HGFM gfm( | ^~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:772:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 772 | if(alts.size() == numAlts) break; | ~~~~~~~~~~~~^~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41: group_walk.h: In instantiation of 'std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]': group_walk.h:1517:14: required from 'bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]' 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ hi_aligner.h:5901:34: required from 'bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]' 5901 | _gws_local.advanceElement( | ~~~~~~~~~~~~~~~~~~~~~~~~~^ 5902 | off, | ~~~~ 5903 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5904 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5905 | _sas_local, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5906 | _gwstate_local, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5907 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5908 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5909 | prm); // per-read metrics | ~~~~ hi_aligner.h:5664:17: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1147 | if(new_node_bot - new_node_top < gws.map.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~ gfm.h:788:42: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 788 | for(index_t h = 0; h < ht.alts.size(); h++) { | ~~^~~~~~~~~~~~~~~~ gfm.h:791:42: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 791 | if(haplotypes.size() == numHaplotypes) break; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ gfm.h:809:33: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 809 | for(size_t k = 0; k < numRepeatIndex; k++) { | ~~^~~~~~~~~~~~~~~~ group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ gfm.h:822:41: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 822 | while(k < numRepeatIndex && k2 < readLens->size()) { | ~~^~~~~~~~~~~~~~~~ group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ gfm.h:823:65: warning: comparison of integer expressions of different signedness: 'short int' and 'long unsigned int' [-Wsign-compare] 823 | if (repeatLens[k].first >= (*readLens)[k2]) { gfm.h:835:53: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 835 | for(size_t i = 0; i < numRepeatIndex; i++) { | ~~^~~~~~~~~~~~~~~~ gfm.h:850:33: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 850 | for(size_t k = 0; k < numKmertables; k++) { | ~~^~~~~~~~~~~~~~~ gfm.h:853:33: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 853 | for(size_t k = 0; k < numKmertables; k++) { | ~~^~~~~~~~~~~~~~~ gfm.h:888:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 888 | if(alts.size() > 1 && alts.size() > nalts) { | ~~~~~~~~~~~~^~~~~~~ hi_aligner.h: In instantiation of 'static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = short int; BTDnaString = SDnaStringExpandable<1024, 2>]': hi_aligner.h:717:28: required from 'static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = short int; BTDnaString = SDnaStringExpandable<1024, 2>]' 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ hi_aligner.h:2337:47: required from 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]' 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2794:21: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2794 | if(numALTsTried > gpol.maxAltsTried() + dep) return 0; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2797:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2797 | if(ht_llist.size() <= dep) ht_llist.expand(); | ~~~~~~~~~~~~~~~~^~~~~~ hi_aligner.h:2798:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2798 | if(raw_refbufs.size() <= dep) raw_refbufs.expand(); | ~~~~~~~~~~~~~~~~~~~^~~~~~ hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2801 | if(rfoff >= contig_len) return 0; | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2802:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2802 | if(rfoff >= 0 && rfoff + rflen > contig_len) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:2804:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2804 | } else if(rfoff < 0 && rflen > contig_len) { | ~~~~~~^~~~~~~~~~~~ gfm.h:910:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 910 | for(index_t h = 0; h < haplotypes.size(); h++) { | ~~^~~~~~~~~~~~~~~~~~~ gfm.h:912:40: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 912 | for(index_t h2 = 0; h2 < ht.alts.size(); h2++) { | ~~~^~~~~~~~~~~~~~~~ hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2879 | if(alt_range.first >= alts.size()) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:2904:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2904 | for(index_t p = 0; p < ht_prev_list.size(); p++) { | ~~^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2984:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2984 | for(index_t h = 0; h < ht_list.size(); h++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:3032:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3032 | if(raw_refbufs.size() <= dep + 1) raw_refbufs.expand(); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:3165:28: warning: comparison of integer expressions of different signedness: 'const short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3165 | if(orig_nedits < tmp_edits.size()) tmp_edits.erase(0, tmp_edits.size() - orig_nedits); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ hi_aligner.h:3223:32: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3223 | if(alt_range.first >= alts.size()) return 0; | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:3224:36: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3224 | for(; alt_range.second < alts.size(); alt_range.second++) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3257:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3257 | for(index_t p = 0; p < ht_prev_list.size(); p++) { | ~~^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:3260:38: warning: comparison of integer expressions of different signedness: 'const short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3260 | if(ht_ref.second < ht.alts.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ hi_aligner.h:3267:42: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3267 | if(ht_ref.second + 1 >= ht.alts.size() && joinedOff > ht.right) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:3317:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3317 | for(index_t h = 0; h < ht_list.size(); h++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:3320:38: warning: comparison of integer expressions of different signedness: 'const short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3320 | if(ht_ref.second >= ht.alts.size()) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:3374:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3374 | if(raw_refbufs.size() <= dep + 1) raw_refbufs.expand(); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:3542:28: warning: comparison of integer expressions of different signedness: 'const short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3542 | if(orig_nedits < tmp_edits.size()) tmp_edits.resize(orig_nedits); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'index_t GenomeHit::getRightOff() const [with index_t = short int]': hi_aligner.h:999:24: required from 'void GenomeHit::getRight(index_t&, index_t&, index_t&, int64_t*, const Read*, const Scoring*) const [with index_t = short int; int64_t = long int]' 999 | toff = getRightOff() - len; | ^~~~~~~~~~~ hi_aligner.h:2147:15: required from 'bool GenomeHit::extend(const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, PerReadMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, const TranscriptomePolicy&, const GraphPolicy&, index_t&, index_t&, index_t) [with index_t = short int; TAlScore = long int]' 2147 | this->getRight(right_rdoff, right_len, right_toff); | ~~~~~~^~~~~~~~ hi_aligner.h:5724:25: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5724 | genomeHit.extend( | ~~~~~~~~~~~~~~~~^ 5725 | ord, | ~~~~ 5726 | gfm, | ~~~~ 5727 | ref, | ~~~~ 5728 | altdb, | ~~~~~~ 5729 | repeatdb, | ~~~~~~~~~ 5730 | ssdb, | ~~~~~ 5731 | swa, | ~~~~ 5732 | swm, | ~~~~ 5733 | prm, | ~~~~ 5734 | sc, | ~~~ 5735 | _minsc[ordi], | ~~~~~~~~~~~~~ 5736 | rnd, | ~~~~ 5737 | (index_t)_minK_local, | ~~~~~~~~~~~~~~~~~~~~~ 5738 | tpol, | ~~~~~ 5739 | gpol, | ~~~~~ 5740 | leftext, | ~~~~~~~~ 5741 | rightext); | ~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:1023:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1023 | for(index_t i = 0; i < _edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~ hgfm.h: In instantiation of 'void HGFM::readIntoMemory(int, bool, bool, bool, bool, GFMParams*, bool, bool, bool) [with index_t = short int; local_index_t = short unsigned int]': hgfm.h:1667:3: required from 'void HGFM::loadIntoMemory(int, bool, bool, bool, bool, bool) [with index_t = short int; local_index_t = short unsigned int]' 1667 | readIntoMemory( | ^~~~~~~~~~~~~~ hisat2.cpp:3808:21: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3808 | gfm.loadIntoMemory( | ~~~~~~~~~~~~~~~~~~^ 3809 | -1, // fw index | ~~~~~~~~~~~~~~~ 3810 | true, // load SA sample | ~~~~~~~~~~~~~~~~~~~~~~~ 3811 | true, // load ftab | ~~~~~~~~~~~~~~~~~~ 3812 | true, // load rstarts | ~~~~~~~~~~~~~~~~~~~~~ 3813 | !noRefNames, | ~~~~~~~~~~~~ 3814 | startVerbose); | ~~~~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ hgfm.h:2604:29: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2604 | for(size_t i = 0; i < _nlocalGFMs; i++) { | ~~^~~~~~~~~~~~~ hgfm.h:2637:25: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2637 | if(tidx >= _localGFMs.size()) { | ~~~~~^~~~~~~~~~~~~~~~~~~~ gfm.h: In instantiation of 'void GFM::restore(SString&) const [with index_t = short int]': gfm.h:6926:5: required from 'void GFM::checkOrigs(const EList >&, bool) const [with index_t = short int]' 6926 | restore(rest); | ^~~~~~~ hisat2.cpp:3815:17: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3815 | gfm.checkOrigs(os, false); | ~~~~~~~~~~~~~~^~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:6900:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 6900 | for(index_t j = 0; j < _zOffs.size(); j++) { | ~~^~~~~~~~~~~~~~~ In file included from hisat2.cpp:34: rfm.h: In instantiation of 'void RFM::readIntoMemory(int, bool, bool, bool, bool, GFMParams*, bool, bool, bool) [with index_t = short int]': rfm.h:389:3: required from 'void RFM::loadIntoMemory(int, bool, bool, bool, bool, bool) [with index_t = short int]' 389 | readIntoMemory( | ^~~~~~~~~~~~~~ hisat2.cpp:3888:33: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3888 | rgfm->loadIntoMemory( | ~~~~~~~~~~~~~~~~~~~~^ 3889 | -1, // not the reverse index | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3890 | true, // load SA samp? (yes, need forward index's SA samp) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3891 | true, // load ftab (in forward index) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3892 | true, // load rstarts (in forward index) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3893 | !noRefNames, // load names? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3894 | startVerbose); | ~~~~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ rfm.h:1088:29: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 1088 | for(size_t i = 0; i < nlocalRFMs; i++) { | ~~^~~~~~~~~~~~ gfm.h: In instantiation of 'void GFM::postReadInit(const GFMParams&) [with index_t = short int]': gfm.h:6434:11: required from 'void GFM::readIntoMemory(int, bool, bool, bool, bool, GFMParams*, bool, bool, bool, bool) [with index_t = short int]' 6434 | this->postReadInit(*gh); // Initialize fields of Ebwt not read from file | ~~~~~~^~~~~~~~~~~~ gfm.h:694:13: required from 'GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short int; std::string = std::__cxx11::basic_string; int32_t = int]' 694 | readIntoMemory( | ^~~~~~~~~~~~~~ hgfm.h:1604:14: required from 'HGFM::HGFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short int; local_index_t = short unsigned int; std::string = std::__cxx11::basic_string; int32_t = int]' 1604 | _in6(NULL) | ^ hisat2.cpp:3776:31: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3776 | HGFM gfm( | ^~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:2786:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2786 | for(index_t i = 0; i < _zOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~ gfm.h: In instantiation of 'void GFM::print(std::ostream&, const GFMParams&) const [with index_t = short int; std::ostream = std::basic_ostream]': gfm.h:6435:39: required from 'void GFM::readIntoMemory(int, bool, bool, bool, bool, GFMParams*, bool, bool, bool, bool) [with index_t = short int]' 6435 | if(_verbose || startVerbose) print(cerr, *gh); | ~~~~~^~~~~~~~~~~ gfm.h:694:13: required from 'GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short int; std::string = std::__cxx11::basic_string; int32_t = int]' 694 | readIntoMemory( | ^~~~~~~~~~~~~~ hgfm.h:1604:14: required from 'HGFM::HGFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short int; local_index_t = short unsigned int; std::string = std::__cxx11::basic_string; int32_t = int]' 1604 | _in6(NULL) | ^ hisat2.cpp:3776:31: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3776 | HGFM gfm( | ^~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:2858:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2858 | for(index_t i = 0; i < _zOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~ gfm.h: In instantiation of 'index_t GFM::countBt2Side(const SideLocus&, int) const [with index_t = short int]': gfm.h:3692:9: required from 'index_t GFM::mapLF(const SideLocus&) const [with index_t = short int]' 3692 | ret = countBt2Side(l, c); | ^~~~~~~~~~~~ gfm.h:6906:29: required from 'void GFM::restore(SString&) const [with index_t = short int]' 6906 | index_t newi = mapLF(l ASSERT_ONLY(, false)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:6926:5: required from 'void GFM::checkOrigs(const EList >&, bool) const [with index_t = short int]' 6926 | restore(rest); | ^~~~~~~ hisat2.cpp:3815:17: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3815 | gfm.checkOrigs(os, false); | ~~~~~~~~~~~~~~^~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:2967:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2967 | for(index_t i = 0; i < _zGbwtByteOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ group_walk.h: In instantiation of 'std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short int; T = EListSlice]': group_walk.h:1517:14: required from 'bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short int; T = EListSlice; int S = 16]' 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ hi_aligner.h:5816:28: required from 'bool HI_Aligner::getGenomeCoords(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList >&, bool, index_t, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]' 5816 | _gws.advanceElement( | ~~~~~~~~~~~~~~~~~~~^ 5817 | off, | ~~~~ 5818 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5819 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5820 | _sas, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5821 | _gwstate, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5822 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5823 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5824 | prm); // per-read metrics | ~~~~ hi_aligner.h:5074:17: required from 'index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = short int; local_index_t = short unsigned int]' 5074 | getGenomeCoords( | ^~~~~~~~~~~~~~~ hi_aligner.h:5525:23: required from 'bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:1066:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1066 | for(index_t e = 0; e < node_iedge_count.size() + 1; e++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1067:22: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1067 | if(e >= node_iedge_count.size()) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1147 | if(new_node_bot - new_node_top < gws.map.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1152:54: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1152 | for(index_t c = 0; c < gws.masks[i].size(); c++) { | ~~^~~~~~~~~~~~~~~~~~~~~ group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1159:63: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1159 | for(index_t c = j1 + 1; c < gws.masks[i].size(); c++) { | ~~^~~~~~~~~~~~~~~~~~~~~ group_walk.h:1178:54: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1178 | for(index_t j = 0; j < gws.map.size();) { | ~~^~~~~~~~~~~~~~~~ group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1218:54: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1218 | for(index_t c = 0; c < gws.masks[i].size(); c++) { | ~~^~~~~~~~~~~~~~~~~~~~~ group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1225:63: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1225 | for(index_t c = j1 + 1; c < gws.masks[i].size(); c++) { | ~~^~~~~~~~~~~~~~~~~~~~~ group_walk.h:1244:54: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1244 | for(index_t j = 0; j < st.back().map_.size();) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'static void GenomeHit::findSSOffs(const GFM&, const ALTDB&, index_t, index_t, EList >&) [with index_t = short int]': hi_aligner.h:2267:15: required from 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]' 2267 | findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2498:65: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2498 | for(index_t i = (index_t)alts.bsearchLoBound(alt_search); i < alts.size(); i++) { | ~~^~~~~~~~~~~~~ hi_aligner.h:2511:73: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2511 | for(index_t j = (index_t)alts.bsearchLoBound(alt_search); j < alts.size(); j++) { | ~~^~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'static index_t GenomeHit::findOffDiffs(const GFM&, const ALTDB&, index_t, index_t, EList >&) [with index_t = short int]': hi_aligner.h:2298:58: required from 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]' 2298 | const index_t single_offDiffs_size = findOffDiffs(gfm, | ~~~~~~~~~~~~^~~~~ 2299 | altdb, | ~~~~~~ 2300 | (genomeHit._joinedOff >= width ? genomeHit._joinedOff - width : 0), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2301 | genomeHit._joinedOff + width, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2302 | offDiffs); | ~~~~~~~~~ hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2564:66: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2564 | for(alt_range.second = alt_range.first; alt_range.second < alts.size(); alt_range.second++) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ group_walk.h: In instantiation of 'std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]': group_walk.h:494:14: required from 'std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]' 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1453:18: required from 'void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]' 1453 | st_.back().init( | ~~~~~~~~~~~~~~~^ 1454 | gfmFw, // Bowtie index | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1455 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1456 | sa, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1457 | st_, // EList | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1458 | hit_, // GWHit | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1459 | 0, // range 0 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1460 | false, // put resolved elements into res_? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1461 | NULL, // put resolved elements here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1462 | top, // GBW row at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1463 | bot, // GBW row at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1464 | node_top, // node at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1465 | node_bot, // node at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1466 | sa.node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~ 1467 | 0, // # steps taken | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1468 | met); // update metrics here | ~~~~ hi_aligner.h:5896:20: required from 'bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]' 5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5664:17: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:785:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:789:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 789 | if(new_top - top == tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:795:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 795 | if(i + 1 < tmp_zOffs.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:801:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2625:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2625 | for(index_t i = 0; i < offDiffs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = short int; BTDnaString = SDnaStringExpandable<1024, 2>]': hi_aligner.h:2337:47: required from 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]' 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:758:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 758 | if(f.pos + extlen == base_rdoff + 1) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:769:36: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'int' [-Wsign-compare] 769 | if(extlen > 0 && b.pos == rdoff - base_rdoff + extlen - 1) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:775:44: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 775 | if(extlen == 0 && edits.size() > nedits) { | ~~~~~~~~~~~~~^~~~~~~~ hi_aligner.h: In instantiation of 'bool GenomeHit::operator==(const GenomeHit&) const [with index_t = short int]': hi_aligner.h:2362:38: required from 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]' 2362 | if(genomeHits[i] == genomeHits.back()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:1167:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1167 | for(index_t i = 0; i < _edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'void GenomeHit::getLeft(index_t&, index_t&, index_t&, int64_t*, const Read*, const Scoring*) const [with index_t = short int; int64_t = long int]': hi_aligner.h:2070:15: required from 'bool GenomeHit::extend(const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, PerReadMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, const TranscriptomePolicy&, const GraphPolicy&, index_t&, index_t&, index_t) [with index_t = short int; TAlScore = long int]' 2070 | this->getLeft(left_rdoff, left_len, left_toff); | ~~~~~~^~~~~~~ hi_aligner.h:5724:25: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5724 | genomeHit.extend( | ~~~~~~~~~~~~~~~~^ 5725 | ord, | ~~~~ 5726 | gfm, | ~~~~ 5727 | ref, | ~~~~ 5728 | altdb, | ~~~~~~ 5729 | repeatdb, | ~~~~~~~~~ 5730 | ssdb, | ~~~~~ 5731 | swa, | ~~~~ 5732 | swm, | ~~~~ 5733 | prm, | ~~~~ 5734 | sc, | ~~~ 5735 | _minsc[ordi], | ~~~~~~~~~~~~~ 5736 | rnd, | ~~~~ 5737 | (index_t)_minK_local, | ~~~~~~~~~~~~~~~~~~~~~ 5738 | tpol, | ~~~~~ 5739 | gpol, | ~~~~~ 5740 | leftext, | ~~~~~~~~ 5741 | rightext); | ~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:935:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 935 | for(index_t i = 0; i < _edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:940:57: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'short int' [-Wsign-compare] 940 | (edit.type == EDIT_TYPE_MM && edit.snpID != (index_t)INDEX_MAX)) { hi_aligner.h:947:35: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'short int' [-Wsign-compare] 947 | if(edit.snpID == (index_t)INDEX_MAX) { hi_aligner.h: In instantiation of 'void GenomeHit::getRight(index_t&, index_t&, index_t&, int64_t*, const Read*, const Scoring*) const [with index_t = short int; int64_t = long int]': hi_aligner.h:2147:15: required from 'bool GenomeHit::extend(const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, PerReadMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, const TranscriptomePolicy&, const GraphPolicy&, index_t&, index_t&, index_t) [with index_t = short int; TAlScore = long int]' 2147 | this->getRight(right_rdoff, right_len, right_toff); | ~~~~~~^~~~~~~~ hi_aligner.h:5724:25: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5724 | genomeHit.extend( | ~~~~~~~~~~~~~~~~^ 5725 | ord, | ~~~~ 5726 | gfm, | ~~~~ 5727 | ref, | ~~~~ 5728 | altdb, | ~~~~~~ 5729 | repeatdb, | ~~~~~~~~~ 5730 | ssdb, | ~~~~~ 5731 | swa, | ~~~~ 5732 | swm, | ~~~~ 5733 | prm, | ~~~~ 5734 | sc, | ~~~ 5735 | _minsc[ordi], | ~~~~~~~~~~~~~ 5736 | rnd, | ~~~~ 5737 | (index_t)_minK_local, | ~~~~~~~~~~~~~~~~~~~~~ 5738 | tpol, | ~~~~~ 5739 | gpol, | ~~~~~ 5740 | leftext, | ~~~~~~~~ 5741 | rightext); | ~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:984:57: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'short int' [-Wsign-compare] 984 | (edit.type == EDIT_TYPE_MM && edit.snpID != (index_t)INDEX_MAX)) { hi_aligner.h: In instantiation of 'void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = short int]': hi_aligner.h:2915:39: required from 'static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = short int; BTDnaString = SDnaStringExpandable<1024, 2>]' 2915 | add_haplotypes(alts, | ~~~~~~~~~~~~~~^~~~~~ 2916 | haplotypes, | ~~~~~~~~~~~ 2917 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 2918 | cmp_ht, | ~~~~~~~ 2919 | ht_list, | ~~~~~~~~ 2920 | rdlen); | ~~~~~~ hi_aligner.h:717:28: required from 'static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = short int; BTDnaString = SDnaStringExpandable<1024, 2>]' 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ hi_aligner.h:2337:47: required from 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]' 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2660 | if(ht_range.first >= haplotypes.size()) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2674:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2674 | for(index_t h = 0; h < ht_list.size(); h++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:2697:42: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2697 | if(ht_list.back().second == ht.alts.size()) { | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2712:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2712 | for(index_t h = 0; h < ht_list.size(); h++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:2723:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2723 | for(index_t a = 0; a < ht.alts.size(); a++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:2731:42: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2731 | if(ht_list.back().second == ht.alts.size()) { | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:2743:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2743 | for(index_t h = 0; h < ht_list.size(); h++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:1005:35: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'short int' [-Wsign-compare] 1005 | if(edit.snpID == (index_t)INDEX_MAX) { hi_aligner.h: In instantiation of 'void GenomeHit::leftAlign(const Read&) [with index_t = short int]': hi_aligner.h:2218:21: required from 'bool GenomeHit::extend(const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, PerReadMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, const TranscriptomePolicy&, const GraphPolicy&, index_t&, index_t&, index_t) [with index_t = short int; TAlScore = long int]' 2218 | if(doLeftAlign) leftAlign(rd); | ^~~~~~~~~ hi_aligner.h:5724:25: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5724 | genomeHit.extend( | ~~~~~~~~~~~~~~~~^ 5725 | ord, | ~~~~ 5726 | gfm, | ~~~~ 5727 | ref, | ~~~~ 5728 | altdb, | ~~~~~~ 5729 | repeatdb, | ~~~~~~~~~ 5730 | ssdb, | ~~~~~ 5731 | swa, | ~~~~ 5732 | swm, | ~~~~ 5733 | prm, | ~~~~ 5734 | sc, | ~~~ 5735 | _minsc[ordi], | ~~~~~~~~~~~~~ 5736 | rnd, | ~~~~ 5737 | (index_t)_minK_local, | ~~~~~~~~~~~~~~~~~~~~~ 5738 | tpol, | ~~~~~ 5739 | gpol, | ~~~~~ 5740 | leftext, | ~~~~~~~~ 5741 | rightext); | ~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:3558:28: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3558 | for(index_t ei = 0; ei < _edits->size(); ei++) { | ~~~^~~~~~~~~~~~~~~~ hi_aligner.h:3562:23: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'short int' [-Wsign-compare] 3562 | if(edit.snpID != (index_t)INDEX_MAX) hi_aligner.h:3565:19: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3565 | for(; ei2 < _edits->size(); ei2++) { | ~~~~^~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'int64_t GenomeHit::calculateScore(const Read&, SpliceSiteDB&, const Scoring&, index_t, index_t, index_t, index_t, index_t, const BitPairReference&) [with index_t = short int; int64_t = long int]': hi_aligner.h:2220:5: required from 'bool GenomeHit::extend(const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, PerReadMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, const TranscriptomePolicy&, const GraphPolicy&, index_t&, index_t&, index_t) [with index_t = short int; TAlScore = long int]' 2220 | calculateScore( | ^~~~~~~~~~~~~~ hi_aligner.h:5724:25: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5724 | genomeHit.extend( | ~~~~~~~~~~~~~~~~^ 5725 | ord, | ~~~~ 5726 | gfm, | ~~~~ 5727 | ref, | ~~~~ 5728 | altdb, | ~~~~~~ 5729 | repeatdb, | ~~~~~~~~~ 5730 | ssdb, | ~~~~~ 5731 | swa, | ~~~~ 5732 | swm, | ~~~~ 5733 | prm, | ~~~~ 5734 | sc, | ~~~ 5735 | _minsc[ordi], | ~~~~~~~~~~~~~ 5736 | rnd, | ~~~~ 5737 | (index_t)_minK_local, | ~~~~~~~~~~~~~~~~~~~~~ 5738 | tpol, | ~~~~~ 5739 | gpol, | ~~~~~ 5740 | leftext, | ~~~~~~~~ 5741 | rightext); | ~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:3733:26: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3733 | for(index_t i = 0; i < _edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:3756:42: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3756 | for(index_t j = i + 1; j < _edits->size(); j++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:3770:37: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'short int' [-Wsign-compare] 3770 | if(intronLen_thresh < maxIntronLen) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:3796:50: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3796 | for(index_t j = i + 1; j < _edits->size(); j++) { | ~~^~~~~~~~~~~~~~~~ gfm.h: In instantiation of 'void GFM::readIntoMemory(int, bool, bool, bool, bool, GFMParams*, bool, bool, bool, bool) [with index_t = short int]': gfm.h:694:13: required from 'GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short int; std::string = std::__cxx11::basic_string; int32_t = int]' 694 | readIntoMemory( | ^~~~~~~~~~~~~~ hgfm.h:1604:14: required from 'HGFM::HGFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short int; local_index_t = short unsigned int; std::string = std::__cxx11::basic_string; int32_t = int]' 1604 | _in6(NULL) | ^ hisat2.cpp:3776:31: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3776 | HGFM gfm( | ^~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:6182:37: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 6182 | for(size_t i = 0; i < gh->_numSides; i++) { | ~~^~~~~~~~~~~~~~~ gfm.h:6251:41: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 6251 | for(size_t i = 0; i < gh->_ftabLen; i++) | ~~^~~~~~~~~~~~~~ gfm.h:6281:41: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 6281 | for(size_t i = 0; i < gh->_eftabLen; i++) | ~~^~~~~~~~~~~~~~~ gfm.h: In instantiation of 'index_t GFM::mapLF1(index_t, const SideLocus&, int) const [with index_t = short int]': gfm.h:3967:29: required from 'std::pair<_FIter, _FIter> GFM::mapGLF1(index_t, SideLocus&, int, std::pair<_FIter, _FIter>*) const [with index_t = short int]' 3967 | index_t top = mapLF1(row, l, c); | ~~~~~~^~~~~~~~~~~ hi_aligner.h:6475:40: required from 'index_t HI_Aligner::partialSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, size_t, size_t&, size_t&, ReadBWTHit&, RandomSource&, bool&, bool&, index_t) [with index_t = short int; local_index_t = short unsigned int; size_t = long unsigned int]' 6475 | rangeTemp = gfm.mapGLF1(range.first, tloc, c, &node_rangeTemp); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4724:13: required from 'bool HI_Aligner::nextBWT(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, index_t&, bool&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4724 | partialSearch( | ^~~~~~~~~~~~~ hi_aligner.h:4077:15: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4077 | while(nextBWT(sc, pepol, tpol, gpol, gfm, altdb, ref, rdi, fw, wlm, prm, him, rnd, sink)) { | ^~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ gfm.h:3900:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3900 | for(index_t i = 0; i < _zOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~ group_walk.h: In instantiation of 'std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short int; T = EListSlice]': group_walk.h:494:14: required from 'std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short int; T = EListSlice]' 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1453:18: required from 'void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short int; T = EListSlice; int S = 16]' 1453 | st_.back().init( | ~~~~~~~~~~~~~~~^ 1454 | gfmFw, // Bowtie index | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1455 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1456 | sa, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1457 | st_, // EList | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1458 | hit_, // GWHit | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1459 | 0, // range 0 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1460 | false, // put resolved elements into res_? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1461 | NULL, // put resolved elements here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1462 | top, // GBW row at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1463 | bot, // GBW row at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1464 | node_top, // node at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1465 | node_bot, // node at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1466 | sa.node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~ 1467 | 0, // # steps taken | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1468 | met); // update metrics here | ~~~~ hi_aligner.h:5811:14: required from 'bool HI_Aligner::getGenomeCoords(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList >&, bool, index_t, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]' 5811 | _gws.init(gfm, ref, _sas, rnd, met); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5074:17: required from 'index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = short int; local_index_t = short unsigned int]' 5074 | getGenomeCoords( | ^~~~~~~~~~~~~~~ hi_aligner.h:5525:23: required from 'bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:545:25: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 545 | while(e < node_iedge_count.size()) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:546:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 546 | if(i <= node_iedge_count[e].first) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:686:21: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 686 | for(; e < node_iedge_count.size(); e++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:692:26: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 692 | for(e = 0; e < node_iedge_count.size(); e++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:746:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 746 | for(index_t i = 0; i < gfm._zOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~ group_walk.h:768:22: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 768 | if(e < node_iedge_count.size()) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:781:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 781 | for(index_t i = 0; i < tmp_zOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ group_walk.h:785:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:789:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 789 | if(new_top - top == tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:795:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 795 | if(i + 1 < tmp_zOffs.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:801:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:856:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 856 | for(index_t e = 0; e < node_iedge_count.size(); e++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h: In instantiation of 'std::pair<_FIter, _FIter> GFM::mapGLF1(index_t, SideLocus&, std::pair<_FIter, _FIter>*) const [with index_t = short int]': group_walk.h:1306:46: required from 'std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short int; T = EListSlice]' 1306 | pair range = gfm.mapGLF1(top, tloc, &node_range); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1517:14: required from 'bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short int; T = EListSlice; int S = 16]' 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ hi_aligner.h:5816:28: required from 'bool HI_Aligner::getGenomeCoords(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList >&, bool, index_t, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]' 5816 | _gws.advanceElement( | ~~~~~~~~~~~~~~~~~~~^ 5817 | off, | ~~~~ 5818 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5819 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5820 | _sas, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5821 | _gwstate, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5822 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5823 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5824 | prm); // per-read metrics | ~~~~ hi_aligner.h:5074:17: required from 'index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = short int; local_index_t = short unsigned int]' 5074 | getGenomeCoords( | ^~~~~~~~~~~~~~~ hi_aligner.h:5525:23: required from 'bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ gfm.h:4036:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4036 | for(index_t i = 0; i < _zOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41: group_walk.h: In instantiation of 'std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]': group_walk.h:1517:14: required from 'bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]' 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ hi_aligner.h:5901:34: required from 'bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]' 5901 | _gws_local.advanceElement( | ~~~~~~~~~~~~~~~~~~~~~~~~~^ 5902 | off, | ~~~~ 5903 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5904 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5905 | _sas_local, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5906 | _gwstate_local, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5907 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5908 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5909 | prm); // per-read metrics | ~~~~ hi_aligner.h:5664:17: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1147 | if(new_node_bot - new_node_top < gws.map.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = short int; BTDnaString = SDnaStringExpandable<1024, 2>]': hi_aligner.h:717:28: required from 'static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = short int; BTDnaString = SDnaStringExpandable<1024, 2>]' 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ hi_aligner.h:2337:47: required from 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]' 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2794:21: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2794 | if(numALTsTried > gpol.maxAltsTried() + dep) return 0; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2797:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2797 | if(ht_llist.size() <= dep) ht_llist.expand(); | ~~~~~~~~~~~~~~~~^~~~~~ hi_aligner.h:2798:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2798 | if(raw_refbufs.size() <= dep) raw_refbufs.expand(); | ~~~~~~~~~~~~~~~~~~~^~~~~~ hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2801 | if(rfoff >= contig_len) return 0; | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2802:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2802 | if(rfoff >= 0 && rfoff + rflen > contig_len) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:2804:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2804 | } else if(rfoff < 0 && rflen > contig_len) { | ~~~~~~^~~~~~~~~~~~ hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2879 | if(alt_range.first >= alts.size()) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:2904:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2904 | for(index_t p = 0; p < ht_prev_list.size(); p++) { | ~~^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2984:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2984 | for(index_t h = 0; h < ht_list.size(); h++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:3032:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3032 | if(raw_refbufs.size() <= dep + 1) raw_refbufs.expand(); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ gfm.h: In instantiation of 'index_t GFM::tryOffset(index_t, index_t) const [with index_t = short int]': group_walk.h:555:33: required from 'std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short int; T = EListSlice]' 555 | index_t toff = gfm.tryOffset(bwrow, node); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ group_walk.h:494:14: required from 'std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short int; T = EListSlice]' 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1453:18: required from 'void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short int; T = EListSlice; int S = 16]' 1453 | st_.back().init( | ~~~~~~~~~~~~~~~^ 1454 | gfmFw, // Bowtie index | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1455 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1456 | sa, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1457 | st_, // EList | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1458 | hit_, // GWHit | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1459 | 0, // range 0 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1460 | false, // put resolved elements into res_? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1461 | NULL, // put resolved elements here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1462 | top, // GBW row at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1463 | bot, // GBW row at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1464 | node_top, // node at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1465 | node_bot, // node at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1466 | sa.node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~ 1467 | 0, // # steps taken | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1468 | met); // update metrics here | ~~~~ hi_aligner.h:5811:14: required from 'bool HI_Aligner::getGenomeCoords(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList >&, bool, index_t, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]' 5811 | _gws.init(gfm, ref, _sas, rnd, met); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5074:17: required from 'index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = short int; local_index_t = short unsigned int]' 5074 | getGenomeCoords( | ^~~~~~~~~~~~~~~ hi_aligner.h:5525:23: required from 'bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ gfm.h:2721:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2721 | for(index_t i = 0; i < _zOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~ gfm.h: In instantiation of 'void GFM::countBt2SideRange(const SideLocus&, index_t, index_t*, index_t*, EList*) const [with index_t = short int]': gfm.h:3653:3: required from 'void GFM::mapLFRange(const SideLocus&, const SideLocus&, index_t, index_t*, index_t*, EList*) const [with index_t = short int]' 3653 | countBt2SideRange(ltop, num, cntsUpto, cntsIn, masks); | ^~~~~~~~~~~~~~~~~ group_walk.h:1105:31: required from 'std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short int; T = EListSlice]' 1105 | gfm.mapLFRange(curtloc, curbloc, curbot-curtop, upto, in, gws.masks); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1517:14: required from 'bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short int; T = EListSlice; int S = 16]' 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ hi_aligner.h:5816:28: required from 'bool HI_Aligner::getGenomeCoords(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList >&, bool, index_t, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]' 5816 | _gws.advanceElement( | ~~~~~~~~~~~~~~~~~~~^ 5817 | off, | ~~~~ 5818 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5819 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5820 | _sas, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5821 | _gwstate, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5822 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5823 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5824 | prm); // per-read metrics | ~~~~ hi_aligner.h:5074:17: required from 'index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = short int; local_index_t = short unsigned int]' 5074 | getGenomeCoords( | ^~~~~~~~~~~~~~~ hi_aligner.h:5525:23: required from 'bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ gfm.h:3027:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3027 | for(index_t i = 0; i < _zGbwtByteOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ gfm.h: In instantiation of 'int GFM::mapLF1(index_t&, const SideLocus&) const [with index_t = short int]': gfm.h:4040:15: required from 'std::pair<_FIter, _FIter> GFM::mapGLF1(index_t, SideLocus&, std::pair<_FIter, _FIter>*) const [with index_t = short int]' 4040 | mapLF1(row, l); | ~~~~~~^~~~~~~~ group_walk.h:1306:46: required from 'std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short int; T = EListSlice]' 1306 | pair range = gfm.mapGLF1(top, tloc, &node_range); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1517:14: required from 'bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short int; T = EListSlice; int S = 16]' 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ hi_aligner.h:5816:28: required from 'bool HI_Aligner::getGenomeCoords(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList >&, bool, index_t, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]' 5816 | _gws.advanceElement( | ~~~~~~~~~~~~~~~~~~~^ 5817 | off, | ~~~~ 5818 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5819 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5820 | _sas, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5821 | _gwstate, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5822 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5823 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5824 | prm); // per-read metrics | ~~~~ hi_aligner.h:5074:17: required from 'index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = short int; local_index_t = short unsigned int]' 5074 | getGenomeCoords( | ^~~~~~~~~~~~~~~ hi_aligner.h:5525:23: required from 'bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ gfm.h:3932:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3932 | for(index_t i = 0; i < _zOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~ spliced_aligner.h: In instantiation of 'void SplicedAligner::hybridSearch(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]': spliced_aligner.h:112:6: required from here 112 | void SplicedAligner::hybridSearch( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:141:28: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 141 | for(index_t hi = 0; hi < this->_genomeHits.size(); hi++) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ btypes.h:29:19: warning: overflow in conversion from 'long unsigned int' to 'short int' changes value from '18446744073709551615' to '-1' [-Woverflow] 29 | #define INDEX_MAX 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ spliced_aligner.h:157:26: note: in expansion of macro 'INDEX_MAX' 157 | INDEX_MAX, | ^~~~~~~~~ spliced_aligner.h:169:18: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 169 | for(; hj < this->_genomeHits.size(); hj++) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:172:15: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 172 | if(hj >= this->_genomeHits.size()) break; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:173:37: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 173 | for(index_t hk = hj + 1; hk < this->_genomeHits.size(); hk++) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:220:42: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 220 | bool found = genomeHit.len() >= rd.length(); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ spliced_aligner.h: In instantiation of 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]': spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:378:29: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 378 | if(this->_coords.size() <= dep) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ spliced_aligner.h:433:47: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 433 | if(left + fraglen - 1 < ss.right()) continue; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ spliced_aligner.h:437:49: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 437 | if(fragoff + ss.right() < left + 1) continue; | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ spliced_aligner.h:555:38: warning: comparison of integer expressions of different signedness: 'short int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 555 | if(right > ss.left()) continue; | ~~~~~~^~~~~~~~~~~ hi_aligner.h:3165:28: warning: comparison of integer expressions of different signedness: 'const short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3165 | if(orig_nedits < tmp_edits.size()) tmp_edits.erase(0, tmp_edits.size() - orig_nedits); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ hi_aligner.h:3223:32: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3223 | if(alt_range.first >= alts.size()) return 0; | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:3224:36: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3224 | for(; alt_range.second < alts.size(); alt_range.second++) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ spliced_aligner.h:700:43: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 700 | if(left + fraglen - 1 < ss.right()) continue; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ spliced_aligner.h:701:45: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 701 | if(fragoff + ss.right() < left + 1) continue; | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:3257:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3257 | for(index_t p = 0; p < ht_prev_list.size(); p++) { | ~~^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:3260:38: warning: comparison of integer expressions of different signedness: 'const short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3260 | if(ht_ref.second < ht.alts.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ hi_aligner.h:3267:42: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3267 | if(ht_ref.second + 1 >= ht.alts.size() && joinedOff > ht.right) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:3317:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3317 | for(index_t h = 0; h < ht_list.size(); h++) { | ~~^~~~~~~~~~~~~~~~ spliced_aligner.h:815:44: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 815 | if(hitoff == hit.rdoff() && hitoff <= this->_minK) { | ~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:3320:38: warning: comparison of integer expressions of different signedness: 'const short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3320 | if(ht_ref.second >= ht.alts.size()) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ spliced_aligner.h:866:23: warning: comparison of integer expressions of different signedness: 'short int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 866 | if(extoff < tpol.minAnchorLen()) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:906:23: warning: comparison of integer expressions of different signedness: 'short int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 906 | extlen >= tpol.minAnchorLen() && | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:3374:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3374 | if(raw_refbufs.size() <= dep + 1) raw_refbufs.expand(); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ spliced_aligner.h:1039:40: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1039 | for(index_t ti = 0; ti < this->_local_genomeHits[dep].size(); ti++) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:1077:23: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1077 | if(hitoff > this->_minK && | ~~~~~~~^~~~~~~~~~~~~ spliced_aligner.h:1101:52: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1101 | if(nelt > 0 && nelt <= 5 && extlen >= this->_minK) { | ~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:3542:28: warning: comparison of integer expressions of different signedness: 'const short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3542 | if(orig_nedits < tmp_edits.size()) tmp_edits.resize(orig_nedits); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ spliced_aligner.h:1272:23: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1272 | if(hitoff <= this->_minK_local) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:1326:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1326 | } else if(hitoff > this->_minK_local) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~ spliced_aligner.h:1328:42: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1328 | index_t jumplen = hitoff > this->_minK ? (index_t)this->_minK : (index_t)this->_minK_local; | ~~~~~~~^~~~~~~~~~~~~ spliced_aligner.h:1381:30: warning: comparison of integer expressions of different signedness: 'short int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 1381 | if(right > ss.left()) continue; | ~~~~~~^~~~~~~~~~~ hi_aligner.h: In instantiation of 'index_t GenomeHit::getRightOff() const [with index_t = short int]': hi_aligner.h:999:24: required from 'void GenomeHit::getRight(index_t&, index_t&, index_t&, int64_t*, const Read*, const Scoring*) const [with index_t = short int; int64_t = long int]' 999 | toff = getRightOff() - len; | ^~~~~~~~~~~ hi_aligner.h:2147:15: required from 'bool GenomeHit::extend(const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, PerReadMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, const TranscriptomePolicy&, const GraphPolicy&, index_t&, index_t&, index_t) [with index_t = short int; TAlScore = long int]' 2147 | this->getRight(right_rdoff, right_len, right_toff); | ~~~~~~^~~~~~~~ hi_aligner.h:5724:25: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5724 | genomeHit.extend( | ~~~~~~~~~~~~~~~~^ 5725 | ord, | ~~~~ 5726 | gfm, | ~~~~ 5727 | ref, | ~~~~ 5728 | altdb, | ~~~~~~ 5729 | repeatdb, | ~~~~~~~~~ 5730 | ssdb, | ~~~~~ 5731 | swa, | ~~~~ 5732 | swm, | ~~~~ 5733 | prm, | ~~~~ 5734 | sc, | ~~~ 5735 | _minsc[ordi], | ~~~~~~~~~~~~~ 5736 | rnd, | ~~~~ 5737 | (index_t)_minK_local, | ~~~~~~~~~~~~~~~~~~~~~ 5738 | tpol, | ~~~~~ 5739 | gpol, | ~~~~~ 5740 | leftext, | ~~~~~~~~ 5741 | rightext); | ~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:1023:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1023 | for(index_t i = 0; i < _edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~ spliced_aligner.h:1497:65: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 1497 | if(hit.len() == hitlen && hitoff + hitlen + this->_minK > rdlen) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ spliced_aligner.h:1595:23: warning: comparison of integer expressions of different signedness: 'short int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 1595 | extlen >= tpol.minAnchorLen() && | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:1622:40: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1622 | for(index_t ri = 0; ri < coords.size(); ri++) { | ~~~^~~~~~~~~~~~~~~ spliced_aligner.h:1726:40: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1726 | for(index_t ti = 0; ti < this->_local_genomeHits[dep].size(); ti++) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:1765:50: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 1765 | if(hitoff + hitlen + this->_minK + 1 < rdlen && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ spliced_aligner.h:1788:52: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1788 | if(nelt > 0 && nelt <= 5 && extlen >= this->_minK) { | ~~~~~~~^~~~~~~~~~~~~~ spliced_aligner.h:1813:44: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1813 | for(index_t ri = 0; ri < coords.size(); ri++) { | ~~~^~~~~~~~~~~~~~~ spliced_aligner.h:1959:40: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1959 | if(rdlen - hitoff - hitlen <= this->_minK_local) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:2014:59: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2014 | } else if(hitoff + hitlen + this->_minK_local < rdlen) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ spliced_aligner.h:2016:65: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2016 | index_t jumplen = hitoff + hitlen + this->_minK < rdlen ? (index_t)this->_minK : (index_t)this->_minK_local; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ hi_aligner.h: In instantiation of 'void GenomeHit::replace_edits_with_alts(const Read&, const EList >&, SpliceSiteDB&, const Scoring&, index_t, index_t, index_t, index_t, index_t, const BitPairReference&) [with index_t = short int]': spliced_aligner.h:282:58: required from 'void SplicedAligner::hybridSearch(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 282 | genomeHit.replace_edits_with_alts(rd, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 283 | altdb.alts(), | ~~~~~~~~~~~~~ 284 | ssdb, | ~~~~~ 285 | sc, | ~~~ 286 | this->_minK_local, | ~~~~~~~~~~~~~~~~~~ 287 | (index_t)tpol.minIntronLen(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | (index_t)tpol.maxIntronLen(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 289 | (index_t)tpol.minAnchorLen(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 290 | (index_t)tpol.minAnchorLen_noncan(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 291 | ref); | ~~~~ spliced_aligner.h:112:6: required from here 112 | void SplicedAligner::hybridSearch( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1260:25: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'short int' [-Wsign-compare] 1260 | if(ed.snpID == (index_t)INDEX_MAX) { hi_aligner.h:1264:29: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1264 | for(; alt_i < alts.size(); alt_i++) { | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:1277:40: warning: comparison of integer expressions of different signedness: 'const short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1277 | if(alt.len == gap) { | ~~~~~~~~^~~~~~ hi_aligner.h:1287:40: warning: comparison of integer expressions of different signedness: 'const short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1287 | if(alt.len == gap) { | ~~~~~~~~^~~~~~ hi_aligner.h: In instantiation of 'bool HI_Aligner::isSearched(const GenomeHit&, index_t) [with index_t = short int; local_index_t = short unsigned int]': spliced_aligner.h:373:28: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]' 373 | if(this->isSearched(hit, rdi)) return maxsc; | ~~~~~~~~~~~~~~~~^~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:6904:26: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 6904 | for(index_t i = 0; i < searchedHits.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'bool HI_Aligner::redundant(AlnSinkWrap&, index_t, const GenomeHit&) [with index_t = short int; local_index_t = short unsigned int]': spliced_aligner.h:407:28: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]' 407 | if(!this->redundant(sink, rdi, hit)) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:6323:26: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 6323 | for(index_t i = 0; i < rs->size(); i++) { | ~~^~~~~~~~~~~~ hi_aligner.h: In instantiation of 'bool GenomeHit::combineWith(const GenomeHit&, const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = short int; TAlScore = long int]': spliced_aligner.h:494:60: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]' 494 | bool combined = tempHit.combineWith( | ~~~~~~~~~~~~~~~~~~~^ 495 | hit, | ~~~~ 496 | rd, | ~~~ 497 | gfm, | ~~~~ 498 | ref, | ~~~~ 499 | altdb, | ~~~~~~ 500 | repeatdb, | ~~~~~~~~~ 501 | ssdb, | ~~~~~ 502 | swa, | ~~~~ 503 | swm, | ~~~~ 504 | sc, | ~~~ 505 | minsc, | ~~~~~~ 506 | rnd, | ~~~~ 507 | (index_t)this->_minK_local, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 508 | (index_t)tpol.minIntronLen(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 509 | (index_t)tpol.maxIntronLen(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 510 | 1, | ~~ 511 | 1, | ~~ 512 | gpol.maxAltsTried(), | ~~~~~~~~~~~~~~~~~~~~ 513 | &ss, | ~~~~ 514 | tpol.no_spliced_alignment()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1508:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1508 | for(index_t i = 0; i < otherHit._edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1801:39: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'short int' [-Wsign-compare] 1801 | if(shorter_anchor_len < minAnchorLen_noncan) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1807:39: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'short int' [-Wsign-compare] 1807 | if(shorter_anchor_len < minAnchorLen) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:1824:53: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'short int' [-Wsign-compare] 1824 | (edit.type == EDIT_TYPE_MM && edit.snpID != (index_t)INDEX_MAX)) { hi_aligner.h:1922:29: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1922 | for(; alt_i < altdb.alts().size(); alt_i++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1926:32: warning: comparison of integer expressions of different signedness: 'const uint64_t' {aka 'const long unsigned int'} and 'char' [-Wsign-compare] 1926 | if(alt.seq == rdc) { | ~~~~~~~~^~~~~~ hi_aligner.h:1970:26: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1970 | for(index_t i = 0; i < otherHit._edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1975:53: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'short int' [-Wsign-compare] 1975 | (edit.type == EDIT_TYPE_MM && edit.snpID != (index_t)INDEX_MAX)) { hi_aligner.h:1982:28: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1982 | for(index_t i = fsi; i < otherHit._edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'void GenomeHit::getLeftAnchor(index_t&, index_t&) const [with index_t = short int]': spliced_aligner.h:518:46: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]' 518 | tempHit.getLeftAnchor(leftAnchorLen, nedits); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1046:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1046 | for(index_t i = 0; i < _edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~ gfm.h: In instantiation of 'void GFM::postReadInit(const GFMParams&) [with index_t = short int]': gfm.h:6434:11: required from 'void GFM::readIntoMemory(int, bool, bool, bool, bool, GFMParams*, bool, bool, bool, bool) [with index_t = short int]' 6434 | this->postReadInit(*gh); // Initialize fields of Ebwt not read from file | ~~~~~~^~~~~~~~~~~~ gfm.h:694:13: required from 'GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short int; std::string = std::__cxx11::basic_string; int32_t = int]' 694 | readIntoMemory( | ^~~~~~~~~~~~~~ hgfm.h:1604:14: required from 'HGFM::HGFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short int; local_index_t = short unsigned int; std::string = std::__cxx11::basic_string; int32_t = int]' 1604 | _in6(NULL) | ^ hisat2.cpp:3776:31: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3776 | HGFM gfm( | ^~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:2786:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2786 | for(index_t i = 0; i < _zOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~ gfm.h: In instantiation of 'void GFM::print(std::ostream&, const GFMParams&) const [with index_t = short int; std::ostream = std::basic_ostream]': gfm.h:6435:39: required from 'void GFM::readIntoMemory(int, bool, bool, bool, bool, GFMParams*, bool, bool, bool, bool) [with index_t = short int]' 6435 | if(_verbose || startVerbose) print(cerr, *gh); | ~~~~~^~~~~~~~~~~ gfm.h:694:13: required from 'GFM::GFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short int; std::string = std::__cxx11::basic_string; int32_t = int]' 694 | readIntoMemory( | ^~~~~~~~~~~~~~ hgfm.h:1604:14: required from 'HGFM::HGFM(const std::string&, ALTDB*, RepeatDB*, EList*, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = short int; local_index_t = short unsigned int; std::string = std::__cxx11::basic_string; int32_t = int]' 1604 | _in6(NULL) | ^ hisat2.cpp:3776:31: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3776 | HGFM gfm( | ^~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:2858:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2858 | for(index_t i = 0; i < _zOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'bool GenomeHit::adjustWithALT(const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]': spliced_aligner.h:946:46: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]' 946 | if(!tempHit.adjustWithALT(*this->_rds[rdi], gfm, altdb, ref, gpol)) continue; | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2424:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const short int' [-Wsign-compare] 2424 | if(offDiffs.size() - single_offDiffs_size > max_offDiffs_size) offDiffs.resize(single_offDiffs_size + max_offDiffs_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:2425:26: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2425 | for(index_t o = 0; o < offDiffs.size() && !found; o++) { | ~~^~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'index_t HI_Aligner::globalGFMSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList >&, RandomSource&, bool&, index_t) [with index_t = short int; local_index_t = short unsigned int]': spliced_aligner.h:1086:53: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]' 1086 | index_t nelt = this->globalGFMSearch( | ~~~~~~~~~~~~~~~~~~~~~^ 1087 | gfm, // GFM index | ~~~~~~~~~~~~~~~~~~~~ 1088 | rd, // read to align | ~~~~~~~~~~~~~~~~~~~~~~~~ 1089 | sc, // scoring scheme | ~~~~~~~~~~~~~~~~~~~~~~~~~ 1090 | sink.reportingParams(), | ~~~~~~~~~~~~~~~~~~~~~~~ 1091 | hit.fw(), | ~~~~~~~~~ 1092 | extoff, | ~~~~~~~ 1093 | extlen, | ~~~~~~~ 1094 | top, | ~~~~ 1095 | bot, | ~~~~ 1096 | node_top, | ~~~~~~~~~ 1097 | node_bot, | ~~~~~~~~~ 1098 | this->_node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~~~~~ 1099 | rnd, | ~~~~ 1100 | uniqueStop); | ~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:6709:64: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 6709 | if(range.second - range.first == 1 && dep - offset >= _minK) { | ~~~~~~~~~~~~~^~~~~~~~ sam.h: In instantiation of 'void SamConfig::printAlignedOptFlags(BTString&, bool, const Read&, AlnRes&, StackedAln&, const AlnFlags&, const AlnSetSumm&, const SeedAlSumm&, const PerReadMetrics&, const Scoring&, const char*, const ALTDB*) const [with index_t = short int; BTString = SStringExpandable]': aln_sink.h:3225:29: required from 'void AlnSinkSam::appendMate(BTString&, StackedAln&, const Read&, const Read*, TReadId, AlnRes*, AlnRes*, const AlnSetSumm&, const SeedAlSumm&, const SeedAlSumm&, const AlnFlags&, const PerReadMetrics&, const Mapq&, const Scoring&) [with index_t = short int; BTString = SStringExpandable; TReadId = long unsigned int]' 3225 | samc_.printAlignedOptFlags( | ~~~~~~~~~~~~~~~~~~~~~~~~~~^ 3226 | o, // output buffer | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3227 | true, // first opt flag printed is first overall? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3228 | rd, // read | ~~~~~~~~~~~~~~~~~~~~ 3229 | *rs, // individual alignment result | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3230 | staln, // stacked alignment | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3231 | flags, // alignment flags | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3232 | summ, // summary of alignments for this read | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3233 | ssm, // seed alignment summary | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3234 | prm, // per-read metrics | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3235 | sc, // scoring scheme | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3236 | mapqInps, // inputs to MAPQ calculation | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3237 | this->altdb_); | ~~~~~~~~~~~~~ aln_sink.h:1569:4: required from 'void AlnSinkSam::append(BTString&, StackedAln&, size_t, const Read*, const Read*, TReadId, AlnRes*, AlnRes*, const AlnSetSumm&, const SeedAlSumm&, const SeedAlSumm&, const AlnFlags*, const AlnFlags*, const PerReadMetrics&, const Mapq&, const Scoring&, bool) [with index_t = short int; BTString = SStringExpandable; size_t = long unsigned int; TReadId = long unsigned int]' 1569 | appendMate(o, staln, *rd1, rd2, rdid, rs1, rs2, summ, ssm1, ssm2, | ^~~~~~~~~~ aln_sink.h:1547:15: required from here 1547 | virtual void append( | ^~~~~~ btypes.h:29:19: warning: overflow in conversion from 'long unsigned int' to 'short int' changes value from '18446744073709551615' to '-1' [-Woverflow] 29 | #define INDEX_MAX 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ sam.h:984:28: note: in expansion of macro 'INDEX_MAX' 984 | index_t prev_snp_idx = INDEX_MAX; | ^~~~~~~~~ hi_aligner.h: In instantiation of 'std::pair GenomeHit::spliced() const [with index_t = short int]': hi_aligner.h:6100:43: required from 'bool HI_Aligner::reportHit(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, const SpliceSiteDB&, AlnSinkWrap&, index_t, const GenomeHit&, bool, const GenomeHit*) [with index_t = short int; local_index_t = short unsigned int]' 6100 | pair spliced = hit.spliced(); // pair | ~~~~~~~~~~~^~ spliced_aligner.h:672:40: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]' 672 | this->reportHit(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, ssdb, sink, rdi, canHit, alignMate); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1088:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1088 | for(index_t i = 0; i < _edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'int GenomeHit::splicing_dir() const [with index_t = short int]': hi_aligner.h:6102:28: required from 'bool HI_Aligner::reportHit(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, const SpliceSiteDB&, AlnSinkWrap&, index_t, const GenomeHit&, bool, const GenomeHit*) [with index_t = short int; local_index_t = short unsigned int]' 6102 | if(hit.splicing_dir() == SPL_UNKNOWN) | ~~~~~~~~~~~~~~~~^~ spliced_aligner.h:672:40: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]' 672 | this->reportHit(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, ssdb, sink, rdi, canHit, alignMate); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1130:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1130 | for(index_t i = 0; i < _edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~ gfm.h: In instantiation of 'index_t GFM::countBt2Side(const SideLocus&, int) const [with index_t = short int]': gfm.h:3692:9: required from 'index_t GFM::mapLF(const SideLocus&) const [with index_t = short int]' 3692 | ret = countBt2Side(l, c); | ^~~~~~~~~~~~ gfm.h:6906:29: required from 'void GFM::restore(SString&) const [with index_t = short int]' 6906 | index_t newi = mapLF(l ASSERT_ONLY(, false)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:6926:5: required from 'void GFM::checkOrigs(const EList >&, bool) const [with index_t = short int]' 6926 | restore(rest); | ^~~~~~~ hisat2.cpp:3815:17: required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]' 3815 | gfm.checkOrigs(os, false); | ~~~~~~~~~~~~~~^~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h:2967:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2967 | for(index_t i = 0; i < _zGbwtByteOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ group_walk.h: In instantiation of 'std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short int; T = EListSlice]': group_walk.h:1517:14: required from 'bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short int; T = EListSlice; int S = 16]' 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ hi_aligner.h:5816:28: required from 'bool HI_Aligner::getGenomeCoords(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList >&, bool, index_t, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]' 5816 | _gws.advanceElement( | ~~~~~~~~~~~~~~~~~~~^ 5817 | off, | ~~~~ 5818 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5819 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5820 | _sas, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5821 | _gwstate, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5822 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5823 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5824 | prm); // per-read metrics | ~~~~ hi_aligner.h:5074:17: required from 'index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = short int; local_index_t = short unsigned int]' 5074 | getGenomeCoords( | ^~~~~~~~~~~~~~~ hi_aligner.h:5525:23: required from 'bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:1066:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1066 | for(index_t e = 0; e < node_iedge_count.size() + 1; e++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1067:22: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1067 | if(e >= node_iedge_count.size()) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1147 | if(new_node_bot - new_node_top < gws.map.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1152:54: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1152 | for(index_t c = 0; c < gws.masks[i].size(); c++) { | ~~^~~~~~~~~~~~~~~~~~~~~ group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1159:63: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1159 | for(index_t c = j1 + 1; c < gws.masks[i].size(); c++) { | ~~^~~~~~~~~~~~~~~~~~~~~ group_walk.h:1178:54: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1178 | for(index_t j = 0; j < gws.map.size();) { | ~~^~~~~~~~~~~~~~~~ group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1218:54: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1218 | for(index_t c = 0; c < gws.masks[i].size(); c++) { | ~~^~~~~~~~~~~~~~~~~~~~~ group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1225:63: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1225 | for(index_t c = j1 + 1; c < gws.masks[i].size(); c++) { | ~~^~~~~~~~~~~~~~~~~~~~~ group_walk.h:1244:54: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1244 | for(index_t j = 0; j < st.back().map_.size();) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ group_walk.h: In instantiation of 'std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]': group_walk.h:494:14: required from 'std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]' 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1453:18: required from 'void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]' 1453 | st_.back().init( | ~~~~~~~~~~~~~~~^ 1454 | gfmFw, // Bowtie index | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1455 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1456 | sa, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1457 | st_, // EList | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1458 | hit_, // GWHit | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1459 | 0, // range 0 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1460 | false, // put resolved elements into res_? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1461 | NULL, // put resolved elements here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1462 | top, // GBW row at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1463 | bot, // GBW row at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1464 | node_top, // node at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1465 | node_bot, // node at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1466 | sa.node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~ 1467 | 0, // # steps taken | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1468 | met); // update metrics here | ~~~~ hi_aligner.h:5896:20: required from 'bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]' 5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5664:17: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:785:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:789:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 789 | if(new_top - top == tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:795:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 795 | if(i + 1 < tmp_zOffs.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:801:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = short int]': hi_aligner.h:2915:39: required from 'static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = short int; BTDnaString = SDnaStringExpandable<1024, 2>]' 2915 | add_haplotypes(alts, | ~~~~~~~~~~~~~~^~~~~~ 2916 | haplotypes, | ~~~~~~~~~~~ 2917 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 2918 | cmp_ht, | ~~~~~~~ 2919 | ht_list, | ~~~~~~~~ 2920 | rdlen); | ~~~~~~ hi_aligner.h:717:28: required from 'static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = short int; BTDnaString = SDnaStringExpandable<1024, 2>]' 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ hi_aligner.h:2337:47: required from 'static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]' 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ hi_aligner.h:5692:54: required from 'bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = short int; local_index_t = short unsigned int]' 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ hi_aligner.h:4107:39: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2660 | if(ht_range.first >= haplotypes.size()) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2674:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2674 | for(index_t h = 0; h < ht_list.size(); h++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:2697:42: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2697 | if(ht_list.back().second == ht.alts.size()) { | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2712:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2712 | for(index_t h = 0; h < ht_list.size(); h++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:2723:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2723 | for(index_t a = 0; a < ht.alts.size(); a++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h:2731:42: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2731 | if(ht_list.back().second == ht.alts.size()) { | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:2743:38: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2743 | for(index_t h = 0; h < ht_list.size(); h++) { | ~~^~~~~~~~~~~~~~~~ group_walk.h: In instantiation of 'std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short int; T = EListSlice]': group_walk.h:494:14: required from 'std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short int; T = EListSlice]' 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1453:18: required from 'void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short int; T = EListSlice; int S = 16]' 1453 | st_.back().init( | ~~~~~~~~~~~~~~~^ 1454 | gfmFw, // Bowtie index | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1455 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1456 | sa, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1457 | st_, // EList | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1458 | hit_, // GWHit | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1459 | 0, // range 0 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1460 | false, // put resolved elements into res_? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1461 | NULL, // put resolved elements here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1462 | top, // GBW row at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1463 | bot, // GBW row at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1464 | node_top, // node at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1465 | node_bot, // node at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1466 | sa.node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~ 1467 | 0, // # steps taken | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1468 | met); // update metrics here | ~~~~ hi_aligner.h:5811:14: required from 'bool HI_Aligner::getGenomeCoords(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList >&, bool, index_t, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]' 5811 | _gws.init(gfm, ref, _sas, rnd, met); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5074:17: required from 'index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = short int; local_index_t = short unsigned int]' 5074 | getGenomeCoords( | ^~~~~~~~~~~~~~~ hi_aligner.h:5525:23: required from 'bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ group_walk.h:545:25: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 545 | while(e < node_iedge_count.size()) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:546:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 546 | if(i <= node_iedge_count[e].first) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:686:21: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 686 | for(; e < node_iedge_count.size(); e++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:692:26: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 692 | for(e = 0; e < node_iedge_count.size(); e++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:746:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 746 | for(index_t i = 0; i < gfm._zOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~ group_walk.h:768:22: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 768 | if(e < node_iedge_count.size()) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:781:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 781 | for(index_t i = 0; i < tmp_zOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ group_walk.h:785:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:789:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 789 | if(new_top - top == tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:795:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 795 | if(i + 1 < tmp_zOffs.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:801:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:856:34: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 856 | for(index_t e = 0; e < node_iedge_count.size(); e++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ gfm.h: In instantiation of 'std::pair<_FIter, _FIter> GFM::mapGLF1(index_t, SideLocus&, std::pair<_FIter, _FIter>*) const [with index_t = short int]': group_walk.h:1306:46: required from 'std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short int; T = EListSlice]' 1306 | pair range = gfm.mapGLF1(top, tloc, &node_range); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1517:14: required from 'bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short int; T = EListSlice; int S = 16]' 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ hi_aligner.h:5816:28: required from 'bool HI_Aligner::getGenomeCoords(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList >&, bool, index_t, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]' 5816 | _gws.advanceElement( | ~~~~~~~~~~~~~~~~~~~^ 5817 | off, | ~~~~ 5818 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5819 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5820 | _sas, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5821 | _gwstate, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5822 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5823 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5824 | prm); // per-read metrics | ~~~~ hi_aligner.h:5074:17: required from 'index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = short int; local_index_t = short unsigned int]' 5074 | getGenomeCoords( | ^~~~~~~~~~~~~~~ hi_aligner.h:5525:23: required from 'bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ gfm.h:4036:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 4036 | for(index_t i = 0; i < _zOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~ gfm.h: In instantiation of 'index_t GFM::tryOffset(index_t, index_t) const [with index_t = short int]': group_walk.h:555:33: required from 'std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short int; T = EListSlice]' 555 | index_t toff = gfm.tryOffset(bwrow, node); | ~~~~~~~~~~~~~^~~~~~~~~~~~~ group_walk.h:494:14: required from 'std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short int; T = EListSlice]' 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1453:18: required from 'void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short int; T = EListSlice; int S = 16]' 1453 | st_.back().init( | ~~~~~~~~~~~~~~~^ 1454 | gfmFw, // Bowtie index | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1455 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1456 | sa, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1457 | st_, // EList | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1458 | hit_, // GWHit | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1459 | 0, // range 0 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1460 | false, // put resolved elements into res_? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1461 | NULL, // put resolved elements here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1462 | top, // GBW row at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1463 | bot, // GBW row at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1464 | node_top, // node at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1465 | node_bot, // node at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1466 | sa.node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~ 1467 | 0, // # steps taken | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1468 | met); // update metrics here | ~~~~ hi_aligner.h:5811:14: required from 'bool HI_Aligner::getGenomeCoords(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList >&, bool, index_t, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]' 5811 | _gws.init(gfm, ref, _sas, rnd, met); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:5074:17: required from 'index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = short int; local_index_t = short unsigned int]' 5074 | getGenomeCoords( | ^~~~~~~~~~~~~~~ hi_aligner.h:5525:23: required from 'bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ gfm.h:2721:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2721 | for(index_t i = 0; i < _zOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~ gfm.h: In instantiation of 'void GFM::countBt2SideRange(const SideLocus&, index_t, index_t*, index_t*, EList*) const [with index_t = short int]': gfm.h:3653:3: required from 'void GFM::mapLFRange(const SideLocus&, const SideLocus&, index_t, index_t*, index_t*, EList*) const [with index_t = short int]' 3653 | countBt2SideRange(ltop, num, cntsUpto, cntsIn, masks); | ^~~~~~~~~~~~~~~~~ group_walk.h:1105:31: required from 'std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short int; T = EListSlice]' 1105 | gfm.mapLFRange(curtloc, curbloc, curbot-curtop, upto, in, gws.masks); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1517:14: required from 'bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short int; T = EListSlice; int S = 16]' 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ hi_aligner.h:5816:28: required from 'bool HI_Aligner::getGenomeCoords(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList >&, bool, index_t, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]' 5816 | _gws.advanceElement( | ~~~~~~~~~~~~~~~~~~~^ 5817 | off, | ~~~~ 5818 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5819 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5820 | _sas, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5821 | _gwstate, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5822 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5823 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5824 | prm); // per-read metrics | ~~~~ hi_aligner.h:5074:17: required from 'index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = short int; local_index_t = short unsigned int]' 5074 | getGenomeCoords( | ^~~~~~~~~~~~~~~ hi_aligner.h:5525:23: required from 'bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ gfm.h:3027:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3027 | for(index_t i = 0; i < _zGbwtByteOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ gfm.h: In instantiation of 'int GFM::mapLF1(index_t&, const SideLocus&) const [with index_t = short int]': gfm.h:4040:15: required from 'std::pair<_FIter, _FIter> GFM::mapGLF1(index_t, SideLocus&, std::pair<_FIter, _FIter>*) const [with index_t = short int]' 4040 | mapLF1(row, l); | ~~~~~~^~~~~~~~ group_walk.h:1306:46: required from 'std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short int; T = EListSlice]' 1306 | pair range = gfm.mapGLF1(top, tloc, &node_range); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1517:14: required from 'bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short int; T = EListSlice; int S = 16]' 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ hi_aligner.h:5816:28: required from 'bool HI_Aligner::getGenomeCoords(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList >&, bool, index_t, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]' 5816 | _gws.advanceElement( | ~~~~~~~~~~~~~~~~~~~^ 5817 | off, | ~~~~ 5818 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5819 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5820 | _sas, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5821 | _gwstate, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5822 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5823 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5824 | prm); // per-read metrics | ~~~~ hi_aligner.h:5074:17: required from 'index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = short int; local_index_t = short unsigned int]' 5074 | getGenomeCoords( | ^~~~~~~~~~~~~~~ hi_aligner.h:5525:23: required from 'bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ hi_aligner.h:4080:31: required from 'int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ gfm.h:3932:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3932 | for(index_t i = 0; i < _zOffs.size(); i++) { | ~~^~~~~~~~~~~~~~~ spliced_aligner.h: In instantiation of 'void SplicedAligner::hybridSearch(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]': spliced_aligner.h:112:6: required from here 112 | void SplicedAligner::hybridSearch( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:141:28: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 141 | for(index_t hi = 0; hi < this->_genomeHits.size(); hi++) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ btypes.h:39:19: warning: overflow in conversion from 'unsigned int' to 'short int' changes value from '4294967295' to '-1' [-Woverflow] 39 | #define INDEX_MAX 0xffffffff | ^~~~~~~~~~ spliced_aligner.h:157:26: note: in expansion of macro 'INDEX_MAX' 157 | INDEX_MAX, | ^~~~~~~~~ spliced_aligner.h:169:18: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 169 | for(; hj < this->_genomeHits.size(); hj++) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:172:15: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 172 | if(hj >= this->_genomeHits.size()) break; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:173:37: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 173 | for(index_t hk = hj + 1; hk < this->_genomeHits.size(); hk++) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:220:42: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 220 | bool found = genomeHit.len() >= rd.length(); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ spliced_aligner.h: In instantiation of 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]': spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:378:29: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 378 | if(this->_coords.size() <= dep) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ spliced_aligner.h:433:47: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 433 | if(left + fraglen - 1 < ss.right()) continue; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ spliced_aligner.h:437:49: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 437 | if(fragoff + ss.right() < left + 1) continue; | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ spliced_aligner.h:555:38: warning: comparison of integer expressions of different signedness: 'short int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 555 | if(right > ss.left()) continue; | ~~~~~~^~~~~~~~~~~ spliced_aligner.h:700:43: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 700 | if(left + fraglen - 1 < ss.right()) continue; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ spliced_aligner.h:701:45: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 701 | if(fragoff + ss.right() < left + 1) continue; | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ spliced_aligner.h:815:44: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 815 | if(hitoff == hit.rdoff() && hitoff <= this->_minK) { | ~~~~~~~^~~~~~~~~~~~~~ spliced_aligner.h:866:23: warning: comparison of integer expressions of different signedness: 'short int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 866 | if(extoff < tpol.minAnchorLen()) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:906:23: warning: comparison of integer expressions of different signedness: 'short int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 906 | extlen >= tpol.minAnchorLen() && | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:1039:40: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1039 | for(index_t ti = 0; ti < this->_local_genomeHits[dep].size(); ti++) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:1077:23: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1077 | if(hitoff > this->_minK && | ~~~~~~~^~~~~~~~~~~~~ spliced_aligner.h:1101:52: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1101 | if(nelt > 0 && nelt <= 5 && extlen >= this->_minK) { | ~~~~~~~^~~~~~~~~~~~~~ spliced_aligner.h:1272:23: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1272 | if(hitoff <= this->_minK_local) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:1326:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1326 | } else if(hitoff > this->_minK_local) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~ spliced_aligner.h:1328:42: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1328 | index_t jumplen = hitoff > this->_minK ? (index_t)this->_minK : (index_t)this->_minK_local; | ~~~~~~~^~~~~~~~~~~~~ spliced_aligner.h:1381:30: warning: comparison of integer expressions of different signedness: 'short int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 1381 | if(right > ss.left()) continue; | ~~~~~~^~~~~~~~~~~ spliced_aligner.h:1497:65: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 1497 | if(hit.len() == hitlen && hitoff + hitlen + this->_minK > rdlen) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ spliced_aligner.h:1595:23: warning: comparison of integer expressions of different signedness: 'short int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 1595 | extlen >= tpol.minAnchorLen() && | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:1622:40: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1622 | for(index_t ri = 0; ri < coords.size(); ri++) { | ~~~^~~~~~~~~~~~~~~ spliced_aligner.h:1726:40: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1726 | for(index_t ti = 0; ti < this->_local_genomeHits[dep].size(); ti++) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:1765:50: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 1765 | if(hitoff + hitlen + this->_minK + 1 < rdlen && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ spliced_aligner.h:1788:52: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1788 | if(nelt > 0 && nelt <= 5 && extlen >= this->_minK) { | ~~~~~~~^~~~~~~~~~~~~~ spliced_aligner.h:1813:44: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1813 | for(index_t ri = 0; ri < coords.size(); ri++) { | ~~~^~~~~~~~~~~~~~~ spliced_aligner.h:1959:40: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1959 | if(rdlen - hitoff - hitlen <= this->_minK_local) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:2014:59: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2014 | } else if(hitoff + hitlen + this->_minK_local < rdlen) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ spliced_aligner.h:2016:65: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2016 | index_t jumplen = hitoff + hitlen + this->_minK < rdlen ? (index_t)this->_minK : (index_t)this->_minK_local; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ hi_aligner.h: In instantiation of 'void GenomeHit::replace_edits_with_alts(const Read&, const EList >&, SpliceSiteDB&, const Scoring&, index_t, index_t, index_t, index_t, index_t, const BitPairReference&) [with index_t = short int]': spliced_aligner.h:282:58: required from 'void SplicedAligner::hybridSearch(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = short int; local_index_t = short unsigned int]' 282 | genomeHit.replace_edits_with_alts(rd, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 283 | altdb.alts(), | ~~~~~~~~~~~~~ 284 | ssdb, | ~~~~~ 285 | sc, | ~~~ 286 | this->_minK_local, | ~~~~~~~~~~~~~~~~~~ 287 | (index_t)tpol.minIntronLen(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | (index_t)tpol.maxIntronLen(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 289 | (index_t)tpol.minAnchorLen(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 290 | (index_t)tpol.minAnchorLen_noncan(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 291 | ref); | ~~~~ spliced_aligner.h:112:6: required from here 112 | void SplicedAligner::hybridSearch( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1260:25: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'short int' [-Wsign-compare] 1260 | if(ed.snpID == (index_t)INDEX_MAX) { hi_aligner.h:1264:29: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1264 | for(; alt_i < alts.size(); alt_i++) { | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:1277:40: warning: comparison of integer expressions of different signedness: 'const short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1277 | if(alt.len == gap) { | ~~~~~~~~^~~~~~ hi_aligner.h:1287:40: warning: comparison of integer expressions of different signedness: 'const short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1287 | if(alt.len == gap) { | ~~~~~~~~^~~~~~ hi_aligner.h: In instantiation of 'bool HI_Aligner::isSearched(const GenomeHit&, index_t) [with index_t = short int; local_index_t = short unsigned int]': spliced_aligner.h:373:28: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]' 373 | if(this->isSearched(hit, rdi)) return maxsc; | ~~~~~~~~~~~~~~~~^~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:6904:26: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 6904 | for(index_t i = 0; i < searchedHits.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'bool HI_Aligner::redundant(AlnSinkWrap&, index_t, const GenomeHit&) [with index_t = short int; local_index_t = short unsigned int]': spliced_aligner.h:407:28: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]' 407 | if(!this->redundant(sink, rdi, hit)) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:6323:26: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 6323 | for(index_t i = 0; i < rs->size(); i++) { | ~~^~~~~~~~~~~~ hi_aligner.h: In instantiation of 'bool GenomeHit::combineWith(const GenomeHit&, const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = short int; TAlScore = long int]': spliced_aligner.h:494:60: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]' 494 | bool combined = tempHit.combineWith( | ~~~~~~~~~~~~~~~~~~~^ 495 | hit, | ~~~~ 496 | rd, | ~~~ 497 | gfm, | ~~~~ 498 | ref, | ~~~~ 499 | altdb, | ~~~~~~ 500 | repeatdb, | ~~~~~~~~~ 501 | ssdb, | ~~~~~ 502 | swa, | ~~~~ 503 | swm, | ~~~~ 504 | sc, | ~~~ 505 | minsc, | ~~~~~~ 506 | rnd, | ~~~~ 507 | (index_t)this->_minK_local, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 508 | (index_t)tpol.minIntronLen(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 509 | (index_t)tpol.maxIntronLen(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 510 | 1, | ~~ 511 | 1, | ~~ 512 | gpol.maxAltsTried(), | ~~~~~~~~~~~~~~~~~~~~ 513 | &ss, | ~~~~ 514 | tpol.no_spliced_alignment()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1508:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1508 | for(index_t i = 0; i < otherHit._edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1801:39: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'short int' [-Wsign-compare] 1801 | if(shorter_anchor_len < minAnchorLen_noncan) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1807:39: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'short int' [-Wsign-compare] 1807 | if(shorter_anchor_len < minAnchorLen) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:1824:53: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'short int' [-Wsign-compare] 1824 | (edit.type == EDIT_TYPE_MM && edit.snpID != (index_t)INDEX_MAX)) { hi_aligner.h:1922:29: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1922 | for(; alt_i < altdb.alts().size(); alt_i++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1926:32: warning: comparison of integer expressions of different signedness: 'const uint64_t' {aka 'const long unsigned int'} and 'char' [-Wsign-compare] 1926 | if(alt.seq == rdc) { | ~~~~~~~~^~~~~~ hi_aligner.h:1970:26: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1970 | for(index_t i = 0; i < otherHit._edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1975:53: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'short int' [-Wsign-compare] 1975 | (edit.type == EDIT_TYPE_MM && edit.snpID != (index_t)INDEX_MAX)) { hi_aligner.h:1982:28: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1982 | for(index_t i = fsi; i < otherHit._edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'void GenomeHit::getLeftAnchor(index_t&, index_t&) const [with index_t = short int]': spliced_aligner.h:518:46: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]' 518 | tempHit.getLeftAnchor(leftAnchorLen, nedits); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1046:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1046 | for(index_t i = 0; i < _edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'bool GenomeHit::adjustWithALT(const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]': spliced_aligner.h:946:46: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]' 946 | if(!tempHit.adjustWithALT(*this->_rds[rdi], gfm, altdb, ref, gpol)) continue; | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2424:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const short int' [-Wsign-compare] 2424 | if(offDiffs.size() - single_offDiffs_size > max_offDiffs_size) offDiffs.resize(single_offDiffs_size + max_offDiffs_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:2425:26: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 2425 | for(index_t o = 0; o < offDiffs.size() && !found; o++) { | ~~^~~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'index_t HI_Aligner::globalGFMSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList >&, RandomSource&, bool&, index_t) [with index_t = short int; local_index_t = short unsigned int]': spliced_aligner.h:1086:53: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]' 1086 | index_t nelt = this->globalGFMSearch( | ~~~~~~~~~~~~~~~~~~~~~^ 1087 | gfm, // GFM index | ~~~~~~~~~~~~~~~~~~~~ 1088 | rd, // read to align | ~~~~~~~~~~~~~~~~~~~~~~~~ 1089 | sc, // scoring scheme | ~~~~~~~~~~~~~~~~~~~~~~~~~ 1090 | sink.reportingParams(), | ~~~~~~~~~~~~~~~~~~~~~~~ 1091 | hit.fw(), | ~~~~~~~~~ 1092 | extoff, | ~~~~~~~ 1093 | extlen, | ~~~~~~~ 1094 | top, | ~~~~ 1095 | bot, | ~~~~ 1096 | node_top, | ~~~~~~~~~ 1097 | node_bot, | ~~~~~~~~~ 1098 | this->_node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~~~~~ 1099 | rnd, | ~~~~ 1100 | uniqueStop); | ~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:6709:64: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 6709 | if(range.second - range.first == 1 && dep - offset >= _minK) { | ~~~~~~~~~~~~~^~~~~~~~ sam.h: In instantiation of 'void SamConfig::printAlignedOptFlags(BTString&, bool, const Read&, AlnRes&, StackedAln&, const AlnFlags&, const AlnSetSumm&, const SeedAlSumm&, const PerReadMetrics&, const Scoring&, const char*, const ALTDB*) const [with index_t = short int; BTString = SStringExpandable]': aln_sink.h:3225:29: required from 'void AlnSinkSam::appendMate(BTString&, StackedAln&, const Read&, const Read*, TReadId, AlnRes*, AlnRes*, const AlnSetSumm&, const SeedAlSumm&, const SeedAlSumm&, const AlnFlags&, const PerReadMetrics&, const Mapq&, const Scoring&) [with index_t = short int; BTString = SStringExpandable; TReadId = long unsigned int]' 3225 | samc_.printAlignedOptFlags( | ~~~~~~~~~~~~~~~~~~~~~~~~~~^ 3226 | o, // output buffer | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3227 | true, // first opt flag printed is first overall? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3228 | rd, // read | ~~~~~~~~~~~~~~~~~~~~ 3229 | *rs, // individual alignment result | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3230 | staln, // stacked alignment | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3231 | flags, // alignment flags | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3232 | summ, // summary of alignments for this read | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3233 | ssm, // seed alignment summary | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3234 | prm, // per-read metrics | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3235 | sc, // scoring scheme | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3236 | mapqInps, // inputs to MAPQ calculation | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3237 | this->altdb_); | ~~~~~~~~~~~~~ aln_sink.h:1569:4: required from 'void AlnSinkSam::append(BTString&, StackedAln&, size_t, const Read*, const Read*, TReadId, AlnRes*, AlnRes*, const AlnSetSumm&, const SeedAlSumm&, const SeedAlSumm&, const AlnFlags*, const AlnFlags*, const PerReadMetrics&, const Mapq&, const Scoring&, bool) [with index_t = short int; BTString = SStringExpandable; size_t = long unsigned int; TReadId = long unsigned int]' 1569 | appendMate(o, staln, *rd1, rd2, rdid, rs1, rs2, summ, ssm1, ssm2, | ^~~~~~~~~~ aln_sink.h:1547:15: required from here 1547 | virtual void append( | ^~~~~~ btypes.h:39:19: warning: overflow in conversion from 'unsigned int' to 'short int' changes value from '4294967295' to '-1' [-Woverflow] 39 | #define INDEX_MAX 0xffffffff | ^~~~~~~~~~ sam.h:984:28: note: in expansion of macro 'INDEX_MAX' 984 | index_t prev_snp_idx = INDEX_MAX; | ^~~~~~~~~ hi_aligner.h: In instantiation of 'std::pair GenomeHit::spliced() const [with index_t = short int]': hi_aligner.h:6100:43: required from 'bool HI_Aligner::reportHit(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, const SpliceSiteDB&, AlnSinkWrap&, index_t, const GenomeHit&, bool, const GenomeHit*) [with index_t = short int; local_index_t = short unsigned int]' 6100 | pair spliced = hit.spliced(); // pair | ~~~~~~~~~~~^~ spliced_aligner.h:672:40: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]' 672 | this->reportHit(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, ssdb, sink, rdi, canHit, alignMate); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1088:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1088 | for(index_t i = 0; i < _edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~ hi_aligner.h: In instantiation of 'int GenomeHit::splicing_dir() const [with index_t = short int]': hi_aligner.h:6102:28: required from 'bool HI_Aligner::reportHit(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, const SpliceSiteDB&, AlnSinkWrap&, index_t, const GenomeHit&, bool, const GenomeHit*) [with index_t = short int; local_index_t = short unsigned int]' 6102 | if(hit.splicing_dir() == SPL_UNKNOWN) | ~~~~~~~~~~~~~~~~^~ spliced_aligner.h:672:40: required from 'int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = short int; local_index_t = short unsigned int; int64_t = long int]' 672 | this->reportHit(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, ssdb, sink, rdi, canHit, alignMate); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:1130:30: warning: comparison of integer expressions of different signedness: 'short int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1130 | for(index_t i = 0; i < _edits->size(); i++) { | ~~^~~~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)': ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)': ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, std::size_t, std::size_t, std::size_t) const': reference.cpp:522:26: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, std::size_t, std::size_t, std::size_t) const': reference.cpp:522:26: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from sequence_io.h:30, from hisat2_build.cpp:28: In member function 'void SString::resize(std::size_t) [with T = char]', inlined from 'void SString::install(const T*, std::size_t) [with T = char]' at sstring.h:687:9, inlined from 'void SString::install(const T*, std::size_t) [with T = char]' at sstring.h:685:15, inlined from 'RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]' at rfm.h:768:29: sstring.h:602:25: warning: 'void operator delete(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function 'void SString::resize(std::size_t) [with T = char]', inlined from 'RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]' at rfm.h:764:24: sstring.h:610:31: note: returned from 'void* operator new [](std::size_t)' 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function 'void SString::resize(std::size_t) [with T = char]', inlined from 'void SString::install(const T*, std::size_t) [with T = char]' at sstring.h:687:9, inlined from 'void SString::install(const T*, std::size_t) [with T = char]' at sstring.h:685:15, inlined from 'RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]' at rfm.h:766:29: sstring.h:602:25: warning: 'void operator delete(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function 'void SString::resize(std::size_t) [with T = char]', inlined from 'RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]' at rfm.h:764:24: sstring.h:610:31: note: returned from 'void* operator new [](std::size_t)' 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In file included from sequence_io.h:30, from hisat2_build.cpp:28: In member function 'void SString::resize(std::size_t) [with T = char]', inlined from 'void SString::install(const T*, std::size_t) [with T = char]' at sstring.h:687:9, inlined from 'void SString::install(const T*, std::size_t) [with T = char]' at sstring.h:685:15, inlined from 'RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]' at rfm.h:768:29: sstring.h:602:25: warning: 'void operator delete(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function 'void SString::resize(std::size_t) [with T = char]', inlined from 'RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]' at rfm.h:764:24: sstring.h:610:31: note: returned from 'void* operator new [](std::size_t)' 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function 'void SString::resize(std::size_t) [with T = char]', inlined from 'void SString::install(const T*, std::size_t) [with T = char]' at sstring.h:687:9, inlined from 'void SString::install(const T*, std::size_t) [with T = char]' at sstring.h:685:15, inlined from 'RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]' at rfm.h:766:29: sstring.h:602:25: warning: 'void operator delete(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function 'void SString::resize(std::size_t) [with T = char]', inlined from 'RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]' at rfm.h:764:24: sstring.h:610:31: note: returned from 'void* operator new [](std::size_t)' 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function 'void SString::resize(std::size_t) [with T = char]', inlined from 'void SString::install(const T*, std::size_t) [with T = char]' at sstring.h:687:9, inlined from 'void SString::install(const T*, std::size_t) [with T = char]' at sstring.h:685:15, inlined from 'HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]' at hgfm.h:2259:41: sstring.h:602:25: warning: 'void operator delete(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function 'void SString::resize(std::size_t) [with T = char]', inlined from 'HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]' at hgfm.h:2255:36: sstring.h:610:31: note: returned from 'void* operator new [](std::size_t)' 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function 'void SString::resize(std::size_t) [with T = char]', inlined from 'void SString::install(const T*, std::size_t) [with T = char]' at sstring.h:687:9, inlined from 'void SString::install(const T*, std::size_t) [with T = char]' at sstring.h:685:15, inlined from 'HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]' at hgfm.h:2257:41: sstring.h:602:25: warning: 'void operator delete(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function 'void SString::resize(std::size_t) [with T = char]', inlined from 'HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]' at hgfm.h:2255:36: sstring.h:610:31: note: returned from 'void* operator new [](std::size_t)' 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function 'void SString::resize(std::size_t) [with T = char]', inlined from 'void SString::install(const T*, std::size_t) [with T = char]' at sstring.h:687:9, inlined from 'void SString::install(const T*, std::size_t) [with T = char]' at sstring.h:685:15, inlined from 'HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]' at hgfm.h:2259:41: sstring.h:602:25: warning: 'void operator delete(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function 'void SString::resize(std::size_t) [with T = char]', inlined from 'HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]' at hgfm.h:2255:36: sstring.h:610:31: note: returned from 'void* operator new [](std::size_t)' 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function 'void SString::resize(std::size_t) [with T = char]', inlined from 'void SString::install(const T*, std::size_t) [with T = char]' at sstring.h:687:9, inlined from 'void SString::install(const T*, std::size_t) [with T = char]' at sstring.h:685:15, inlined from 'HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]' at hgfm.h:2257:41: sstring.h:602:25: warning: 'void operator delete(void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function 'void SString::resize(std::size_t) [with T = char]', inlined from 'HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]' at hgfm.h:2255:36: sstring.h:610:31: note: returned from 'void* operator new [](std::size_t)' 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)': ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)': ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from aligner_sw.cpp:25: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from aligner_sw.cpp:25: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' In file included from gfm.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, std::size_t, std::size_t, std::size_t) const': reference.cpp:522:26: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, std::size_t, std::size_t, std::size_t) const': reference.cpp:522:26: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ g++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 \ -DCOMPILER_OPTIONS="\"-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \ -I. -I third_party -I . \ -o hisat2-inspect-s hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread g++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 \ -DCOMPILER_OPTIONS="\"-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \ -I. -I third_party -I . \ -o hisat2-inspect-l hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread In file included from hisat2_inspect.cpp:25: alt.h: In member function 'bool ALT::repOk() const': assert_helpers.h:227:18: warning: comparison of constant '1' with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro 'assert_leq' 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from hisat2_inspect.cpp:25: alt.h: In member function 'bool ALT::repOk() const': assert_helpers.h:227:18: warning: comparison of constant '1' with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro 'assert_leq' 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)': ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)': ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' In file included from edit.h:26, from edit.cpp:21: alt.h: In member function 'bool ALT::repOk() const': assert_helpers.h:227:18: warning: comparison of constant '1' with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro 'assert_leq' 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function 'bool ALT::repOk() const': assert_helpers.h:227:18: warning: comparison of constant '1' with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro 'assert_leq' 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: alt.h: In member function 'bool ALT::repOk() const': assert_helpers.h:227:18: warning: comparison of constant '1' with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro 'assert_leq' 180 | assert_leq(fw, 1); | ^~~~~~~~~~ gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: alt.h: In member function 'bool ALT::repOk() const': assert_helpers.h:227:18: warning: comparison of constant '1' with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro 'assert_leq' 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ splice_site.cpp: In member function 'void SpliceSiteDB::read(const GFM&, const EList >&)': splice_site.cpp:717:59: warning: '?:' using integer constants in boolean context, the expression will always evaluate to 'true' [-Wint-in-bool-context] 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29: ds.h: In instantiation of 'void EList::push_back_array(const T*, std::size_t) [with T = Exon; int S = 128; std::size_t = long unsigned int]': splice_site.cpp:722:31: required from here 722 | _exons.push_back_array(exons.begin(), exons.size()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ds.h:663:28: warning: 'void* std::memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class Exon'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 663 | std::memcpy(list_ + cur_, l, bytes); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ splice_site.h:377:7: note: 'class Exon' declared here 377 | class Exon { | ^~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ splice_site.cpp: In member function 'void SpliceSiteDB::read(const GFM&, const EList >&)': splice_site.cpp:717:59: warning: '?:' using integer constants in boolean context, the expression will always evaluate to 'true' [-Wint-in-bool-context] 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29: ds.h: In instantiation of 'void EList::push_back_array(const T*, std::size_t) [with T = Exon; int S = 128; std::size_t = long unsigned int]': splice_site.cpp:722:31: required from here 722 | _exons.push_back_array(exons.begin(), exons.size()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ds.h:663:28: warning: 'void* std::memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'class Exon'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 663 | std::memcpy(list_ + cur_, l, bytes); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ splice_site.h:377:7: note: 'class Exon' declared here 377 | class Exon { | ^~~~ g++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -DCOMPILER_OPTIONS="\"-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-repeat hisat2_repeat.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp mask.cpp qual.cpp aligner_bt.cpp scoring.cpp simple_func.cpp dp_framer.cpp aligner_result.cpp aligner_sw_driver.cpp aligner_sw.cpp aligner_swsse_ee_i16.cpp aligner_swsse_ee_u8.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse.cpp bit_packed_array.cpp repeat_builder.cpp diff_sample.cpp hisat2_repeat_main.cpp \ -lpthread In file included from hisat2_repeat.cpp:36: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:78, from hisat2_repeat.cpp:37: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' gmake: *** [Makefile:370: hisat2-align-l] Error 1 gmake: *** Waiting for unfinished jobs.... gmake: *** [Makefile:362: hisat2-align-s] Error 1 ref_read.cpp: In function 'std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)': ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function 'std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)': ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function 'int BitPairReference::getStretch(uint32_t*, std::size_t, std::size_t, std::size_t) const': reference.cpp:522:26: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from aligner_sw.cpp:25: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from bit_packed_array.cpp:24: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:77, from repeat_builder.cpp:26: gfm.h: In static member function 'static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)': gfm.h:1185:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /opt/tools/gcc14/include/c++/14.3.0/memory:78, from gfm.h:28: /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /opt/tools/gcc14/include/c++/14.3.0/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:78: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the '< >' repeat_builder.cpp: In function 'std::string reverse_complement(const std::string&)': repeat_builder.cpp:88:30: warning: array subscript has type 'char' [-Wchar-subscripts] 88 | rev[i] = asc2dnacomp[nt]; | ^~ repeat_builder.cpp: In function 'std::string reverseComplement(const std::string&)': repeat_builder.cpp:200:53: warning: array subscript has type 'char' [-Wchar-subscripts] 200 | rc.push_back(asc2dnacomp[str[si - 1]]); | ^ repeat_builder.cpp: In member function 'int CoordHelper::mapJoinedOffToSeq(TIndexOffU)': repeat_builder.cpp:403:29: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 403 | for(size_t i = 0; i < num_cached_; i++) { | ~~^~~~~~~~~~~~~ repeat_builder.cpp: In function 'std::size_t extract_kmer(const std::string&, std::size_t, std::size_t)': repeat_builder.cpp:1217:53: warning: array subscript has type 'char' [-Wchar-subscripts] 1217 | kmer = (kmer << 2) | asc2dna[seq[offset + i]]; | ^ repeat_builder.cpp: In function 'std::size_t next_kmer(std::size_t, char, std::size_t)': repeat_builder.cpp:1225:34: warning: array subscript has type 'char' [-Wchar-subscripts] 1225 | kmer = (kmer << 2) | asc2dna[base]; | ^~~~ repeat_builder.cpp: In function 'void find_gap_pos(const std::string&, const std::string&, EList&, EList&, bool, std::size_t, std::size_t, std::size_t&, std::size_t&, bool)': repeat_builder.cpp:1275:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare] 1275 | for(int i = seq_len - 1; i >= gap_len; i--) { | ~~^~~~~~~~~~ repeat_builder.cpp:1277:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare] 1277 | if(i == seq_len - 1) ed2[i] = add; | ~~^~~~~~~~~~~~~~ repeat_builder.cpp: In member function 'void RB_SWAligner::makePadString(const std::string&, const std::string&, std::string&, std::size_t)': repeat_builder.cpp:2915:39: warning: array subscript has type 'char' [-Wchar-subscripts] 2915 | pad[i] = "CGTA"[asc2dna[ref[i]]]; | ^ repeat_builder.cpp:2919:43: warning: array subscript has type 'char' [-Wchar-subscripts] 2919 | pad[i] = "CGTA"[asc2dna[pad[i]]]; | ^ repeat_builder.cpp:2926:25: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 2926 | for(size_t i = 0; i < head_len; i++) { | ~~^~~~~~~~~~ repeat_builder.cpp:2929:67: warning: array subscript has type 'char' [-Wchar-subscripts] 2929 | pad[pad_start + i] = "CGTA"[asc2dna[pad[pad_start + i]]]; | ^ repeat_builder.cpp: In member function 'int RB_SWAligner::alignStrings(const std::string&, const std::string&, EList&, Coord&)': repeat_builder.cpp:3065:13: warning: variable 'max_match_len' set but not used [-Wunused-but-set-variable] 3065 | int max_match_len = 0; | ^~~~~~~~~~~~~ In file included from repeat_builder.cpp:31: repeat_builder.cpp: In instantiation of 'RepeatBuilder::RepeatBuilder(TStr&, const EList&, const EList >&, bool, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]': repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.h:947:17: warning: 'RepeatBuilder >::coordHelper_' will be initialized after [-Wreorder] 947 | CoordHelper coordHelper_; | ^~~~~~~~~~~~ repeat_builder.h:940:10: warning: 'bool RepeatBuilder >::forward_only_' [-Wreorder] 940 | bool forward_only_; | ^~~~~~~~~~~~~ repeat_builder.cpp:3167:1: warning: when initialized here [-Wreorder] 3167 | RepeatBuilder::RepeatBuilder(TStr& s, | ^~~~~~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of 'void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]': repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:3396:29: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long unsigned int'} [-Wsign-compare] 3396 | if(spos != string::npos) { | ~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3426:29: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long unsigned int'} [-Wsign-compare] 3426 | if(spos != string::npos) { | ~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3553:24: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long unsigned int'} [-Wsign-compare] 3553 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3563:24: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long unsigned int'} [-Wsign-compare] 3563 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of 'void RepeatBuilder::saveConsensus(const RepeatParameter&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]': repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4114:34: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare] 4114 | if((oskip + out_len) == output_width) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of 'void dump_tstr(const TStr&) [with TStr = SString]': repeat_builder.cpp:4754:46: required from here 4754 | template void dump_tstr(const SString& ); | ^ repeat_builder.cpp:309:38: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 309 | for(size_t j = 0; (j < print_width) && (i + j < s_len); j++) { | ~~~^~~~~~~~~~~~~~ repeat_builder.cpp:310:46: warning: array subscript has type 'char' [-Wchar-subscripts] 310 | buf.push_back("ACGTN"[s[i + j]]); | ~~~~~~~^ repeat_builder.cpp: In instantiation of 'std::string getString(const TStr&, TIndexOffU, std::size_t) [with TStr = SString; std::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; std::size_t = long unsigned int]': repeat_builder.cpp:3312:30: required from 'void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]' 3312 | query = getString(s_, i, rp.min_repeat_len); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:272:33: warning: array subscript has type 'char' [-Wchar-subscripts] 272 | char nt = "ACGT"[ref[start + i]]; | ~~~~~~^ repeat_builder.cpp: In instantiation of 'void getString(const TStr&, TIndexOffU, std::size_t, std::string&) [with TStr = SString; TIndexOffU = long unsigned int; std::size_t = long unsigned int; std::string = std::__cxx11::basic_string]': repeat_builder.cpp:3545:22: required from 'void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]' 3545 | getString(s_, saElt, rp.min_repeat_len, query); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:286:25: warning: array subscript has type 'char' [-Wchar-subscripts] 286 | char nt = "ACGT"[ref[start + i]]; | ~~~~~~^ In file included from /opt/tools/gcc14/include/c++/14.3.0/iostream:41, from repeat_builder.cpp:21: In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char; _Traits = std::char_traits]', inlined from 'void RepeatBuilder::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList&, std::ostream&) [with TStr = SString]' at repeat_builder.cpp:3678:31: /opt/tools/gcc14/include/c++/14.3.0/ostream:179:25: warning: 'pos_in_chr' may be used uninitialized [-Wmaybe-uninitialized] 179 | { return _M_insert(__n); } | ~~~~~~~~~^~~~~ repeat_builder.cpp: In member function 'void RepeatBuilder::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList&, std::ostream&) [with TStr = SString]': repeat_builder.cpp:3664:20: note: 'pos_in_chr' was declared here 3664 | TIndexOffU pos_in_chr; | ^~~~~~~~~~ *** Error code 2 Stop. bmake[1]: stopped making "all" in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/hisat2 *** Error code 1 Stop. bmake: stopped making "all" in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/hisat2