+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=310 WRKLOG=/tmp/bulklog/hisat2-2.2.1nb3/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=310 WRKLOG=/tmp/bulklog/hisat2-2.2.1nb3/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
===> Building for hisat2-2.2.1nb3
g++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.10 -DCOMPILER_OPTIONS="\"-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.10 -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 
In file included from hisat2_build.cpp:35:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h: In instantiation of 'void GFM<index_t>::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, bool) [with TStr = SString<char>; index_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ofstream = std::basic_ofstream<char>; uint32_t = unsigned int]':
gfm.h:1039:23:   required from 'GFM<index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
hgfm.h:1989:14:   required from 'HGFM<index_t, local_index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = unsigned int; uint32_t = unsigned int]'
hisat2_build.cpp:535:15:   required from 'void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, 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<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
hisat2_build.cpp:786:39:   required from here
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 sequence_io.h:30,
                 from hisat2_build.cpp:28:
In member function 'void SString<T>::resize(std::size_t) [with T = char]',
    inlined from 'void SString<T>::install(const T*, std::size_t) [with T = char]' at sstring.h:687:9,
    inlined from 'void SString<T>::install(const T*, std::size_t) [with T = char]' at sstring.h:685:15,
    inlined from 'RFM<index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; 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<T>::resize(std::size_t) [with T = char]',
    inlined from 'RFM<index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; 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<T>::resize(std::size_t) [with T = char]',
    inlined from 'void SString<T>::install(const T*, std::size_t) [with T = char]' at sstring.h:687:9,
    inlined from 'void SString<T>::install(const T*, std::size_t) [with T = char]' at sstring.h:685:15,
    inlined from 'RFM<index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; 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<T>::resize(std::size_t) [with T = char]',
    inlined from 'RFM<index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; 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<T>::resize(std::size_t) [with T = char]',
    inlined from 'void SString<T>::install(const T*, std::size_t) [with T = char]' at sstring.h:687:9,
    inlined from 'void SString<T>::install(const T*, std::size_t) [with T = char]' at sstring.h:685:15,
    inlined from 'HGFM<index_t, local_index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; 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<T>::resize(std::size_t) [with T = char]',
    inlined from 'HGFM<index_t, local_index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; 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<T>::resize(std::size_t) [with T = char]',
    inlined from 'void SString<T>::install(const T*, std::size_t) [with T = char]' at sstring.h:687:9,
    inlined from 'void SString<T>::install(const T*, std::size_t) [with T = char]' at sstring.h:685:15,
    inlined from 'HGFM<index_t, local_index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; 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<T>::resize(std::size_t) [with T = char]',
    inlined from 'HGFM<index_t, local_index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; 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];
      |                               ^~~~~~~~~~~
ref_read.cpp: In function 'std::pair<long unsigned int, long unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, 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<long unsigned int, long unsigned int> fastaRefReadFragsNames(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList<std::__cxx11::basic_string<char> >&)':
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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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;
      |              ^~~~~~~~~~~~~~
g++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.10 -DCOMPILER_OPTIONS="\"-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.10 -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 
In file included from hisat2_build.cpp:35:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h: In instantiation of 'void GFM<index_t>::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, bool) [with TStr = SString<char>; index_t = long unsigned int; std::string = std::__cxx11::basic_string<char>; std::ofstream = std::basic_ofstream<char>; uint32_t = unsigned int]':
gfm.h:1039:23:   required from 'GFM<index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
hgfm.h:1989:14:   required from 'HGFM<index_t, local_index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long unsigned int; uint32_t = unsigned int]'
hisat2_build.cpp:535:15:   required from 'void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, 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<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
hisat2_build.cpp:786:39:   required from here
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 sequence_io.h:30,
                 from hisat2_build.cpp:28:
In member function 'void SString<T>::resize(std::size_t) [with T = char]',
    inlined from 'void SString<T>::install(const T*, std::size_t) [with T = char]' at sstring.h:687:9,
    inlined from 'void SString<T>::install(const T*, std::size_t) [with T = char]' at sstring.h:685:15,
    inlined from 'RFM<index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; 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<T>::resize(std::size_t) [with T = char]',
    inlined from 'RFM<index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; 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<T>::resize(std::size_t) [with T = char]',
    inlined from 'void SString<T>::install(const T*, std::size_t) [with T = char]' at sstring.h:687:9,
    inlined from 'void SString<T>::install(const T*, std::size_t) [with T = char]' at sstring.h:685:15,
    inlined from 'RFM<index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; 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<T>::resize(std::size_t) [with T = char]',
    inlined from 'RFM<index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; 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<T>::resize(std::size_t) [with T = char]',
    inlined from 'void SString<T>::install(const T*, std::size_t) [with T = char]' at sstring.h:687:9,
    inlined from 'void SString<T>::install(const T*, std::size_t) [with T = char]' at sstring.h:685:15,
    inlined from 'HGFM<index_t, local_index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; 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<T>::resize(std::size_t) [with T = char]',
    inlined from 'HGFM<index_t, local_index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; 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<T>::resize(std::size_t) [with T = char]',
    inlined from 'void SString<T>::install(const T*, std::size_t) [with T = char]' at sstring.h:687:9,
    inlined from 'void SString<T>::install(const T*, std::size_t) [with T = char]' at sstring.h:685:15,
    inlined from 'HGFM<index_t, local_index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; 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<T>::resize(std::size_t) [with T = char]',
    inlined from 'HGFM<index_t, local_index_t>::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<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; 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];
      |                               ^~~~~~~~~~~
ref_read.cpp: In function 'std::pair<long unsigned int, long unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, 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<long unsigned int, long unsigned int> fastaRefReadFragsNames(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList<std::__cxx11::basic_string<char> >&)':
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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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;
      |              ^~~~~~~~~~~~~~
g++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.10 -DCOMPILER_OPTIONS="\"-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -D_FORTIFY_SOURCE=2 -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.10 -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  
In file included from hgfm.h:24,
                 from hisat2.cpp:33:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp: In function 'void parseOptions(int, const char**)':
hisat2.cpp:1823:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1823 |         auto_ptr<Presets> presets(new PresetsV0());
      |         ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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:45,
                 from /opt/tools/gcc13/include/c++/13.1.0/cstdlib:79,
                 from /opt/tools/gcc13/include/c++/13.1.0/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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 3167 |         auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, tid));
      |         ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp:3168:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 3168 |         auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
      |         ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp:3189:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 3189 |         auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
      |         ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp: In function 'void driver(const char*, const std::string&, const std::string&)':
hisat2.cpp:4035:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 4035 |         auto_ptr<BitPairReference> refs(
      |         ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp:4097:19: error: no matching function for call to 'SpliceSiteDB::read(HGFM<short int>&, EList<ALT<short int>, 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<short int>' to 'std::ifstream&' {aka 'std::basic_ifstream<char>&'}
  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<unsigned int>&, const EList<ALT<unsigned int> >&)'
  556 |     void read(const GFM<TIndexOffU>& gfm, const EList<ALT<TIndexOffU> >& alts);
      |          ^~~~
splice_site.h:556:38: note:   no known conversion for argument 1 from 'HGFM<short int>' to 'const GFM<unsigned int>&'
  556 |     void read(const GFM<TIndexOffU>& gfm, const EList<ALT<TIndexOffU> >& alts);
      |               ~~~~~~~~~~~~~~~~~~~~~~~^~~
In file included from spliced_aligner.h:23,
                 from hisat2.cpp:46:
hi_aligner.h: In instantiation of 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]':
hisat2.cpp:3537:48:   required from here
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<char>; std::string = std::__cxx11::basic_string<char>]':
hisat2.cpp:4351:26:   required from here
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 'bool HI_Aligner<index_t, local_index_t>::pairReads(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]':
hi_aligner.h:4088:17:   required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t, local_index_t>::getRepeatHits(const GFM<index_t>&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const RB_KmerTable&, const BitPairReference&, RandomSource&, index_t, bool, index_t, EList<GenomeHit<index_t> >&, index_t, SharedTempVars<index_t>&, const Scoring&, SwAligner&, SpliceSiteDB&, SwMetrics&, WalkMetrics&, PerReadMetrics&, HIMetrics&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]':
hi_aligner.h:4329:21:   required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::findCoords(index_t, index_t, index_t, index_t, index_t, const EList<T>&, const ALTDB<index_t>&, EList<std::pair<RepeatCoord<index_t>, RepeatCoord<index_t> > >&, index_t, index_t) const [with index_t = short int]':
hi_aligner.h:4391:44:   required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::findCommonCoords(index_t, index_t, index_t, const EList<T>&, index_t, index_t, index_t, const EList<T>&, const ALTDB<index_t>&, EList<std::pair<RepeatCoord<index_t>, RepeatCoord<index_t> > >&, index_t, index_t) const [with index_t = short int]':
hi_aligner.h:4471:54:   required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::toSeedAlSumm(SeedAlSumm&) const [with index_t = short int]':
aln_sink.h:2065:34:   required from 'void AlnSinkWrap<index_t>::finishRead(const SeedResults<index_t>*, const SeedResults<index_t>*, 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]'
hisat2.cpp:3607:25:   required from here
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<index_t>::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<char>; std::string = std::__cxx11::basic_string<char>]'
hisat2.cpp:4351:26:   required from here
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 'index_t HI_Aligner<index_t, local_index_t>::partialSearch(const GFM<index_t>&, const Read&, const Scoring&, const ReportingParams&, bool, size_t, size_t&, size_t&, ReadBWTHit<index_t>&, 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<index_t, local_index_t>::nextBWT(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, index_t&, bool&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:4077:15:   required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t, local_index_t>::getAnchorHits(const GFM<index_t>&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, RandomSource&, index_t, bool, EList<GenomeHit<index_t> >&, index_t, SharedTempVars<index_t>&, 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<index_t, local_index_t>::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:4080:31:   required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<local_index_t, index_t>* HGFM<index_t, local_index_t>::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<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<local_index_t, index_t>* HGFM<index_t, local_index_t>::prevLocalGFM(const LocalGFM<local_index_t, index_t>*) const [with index_t = short int; local_index_t = short unsigned int]':
hi_aligner.h:5631:42:   required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]':
hi_aligner.h:5692:54:   required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::extend(const Read&, const GFM<index_t>&, const BitPairReference&, const ALTDB<index_t>&, const RepeatDB<index_t>&, 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<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::repeatExist(index_t, index_t, index_t) const [with index_t = short int]':
hi_aligner.h:5240:37:   required from 'index_t HI_Aligner<index_t, local_index_t>::getRepeatHits(const GFM<index_t>&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const RB_KmerTable&, const BitPairReference&, RandomSource&, index_t, bool, index_t, EList<GenomeHit<index_t> >&, index_t, SharedTempVars<index_t>&, const Scoring&, SwAligner&, SpliceSiteDB&, SwMetrics&, WalkMetrics&, PerReadMetrics&, HIMetrics&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:4329:21:   required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::GFM(const std::string&, ALTDB<index_t>*, RepeatDB<index_t>*, EList<long unsigned int>*, 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<char>; int32_t = int]':
hgfm.h:1604:14:   required from 'HGFM<index_t, local_index_t>::HGFM(const std::string&, ALTDB<index_t>*, RepeatDB<index_t>*, EList<long unsigned int>*, 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<char>; int32_t = int]'
hisat2.cpp:3776:31:   required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
hisat2.cpp:4351:26:   required from here
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<index_t, local_index_t>::readIntoMemory(int, bool, bool, bool, bool, GFMParams<index_t>*, bool, bool, bool) [with index_t = short int; local_index_t = short unsigned int]':
hgfm.h:1667:3:   required from 'void HGFM<index_t, local_index_t>::loadIntoMemory(int, bool, bool, bool, bool, bool) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3808:21:   required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
hisat2.cpp:4351:26:   required from here
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<index_t>::restore(SString<char>&) const [with index_t = short int]':
gfm.h:6926:5:   required from 'void GFM<index_t>::checkOrigs(const EList<SString<char> >&, bool) const [with index_t = short int]'
hisat2.cpp:3815:17:   required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
hisat2.cpp:4351:26:   required from here
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<index_t>::readIntoMemory(int, bool, bool, bool, bool, GFMParams<index_t>*, bool, bool, bool) [with index_t = short int]':
rfm.h:389:3:   required from 'void RFM<index_t>::loadIntoMemory(int, bool, bool, bool, bool, bool) [with index_t = short int]'
hisat2.cpp:3888:33:   required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
hisat2.cpp:4351:26:   required from here
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<index_t>::findSSOffs(const GFM<index_t>&, const ALTDB<index_t>&, index_t, index_t, EList<std::pair<index_t, int> >&) [with index_t = short int]':
hi_aligner.h:2267:15:   required from 'static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]'
hi_aligner.h:5692:54:   required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::findOffDiffs(const GFM<index_t>&, const ALTDB<index_t>&, index_t, index_t, EList<std::pair<index_t, int> >&) [with index_t = short int]':
hi_aligner.h:2298:58:   required from 'static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]'
hi_aligner.h:5692:54:   required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::alignWithALTs(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars<index_t>&, index_t, int, index_t, bool, const GraphPolicy&, EList<Edit>&, ELList<std::pair<_FIter, _FIter> >&, EList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*) [with index_t = short int; BTDnaString = SDnaStringExpandable<1024, 2>]':
hi_aligner.h:2337:47:   required from 'static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]'
hi_aligner.h:5692:54:   required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::operator==(const GenomeHit<index_t>&) const [with index_t = short int]':
hi_aligner.h:2362:38:   required from 'static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]'
hi_aligner.h:5692:54:   required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::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<index_t>::extend(const Read&, const GFM<index_t>&, const BitPairReference&, const ALTDB<index_t>&, const RepeatDB<index_t>&, 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<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::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<index_t>::extend(const Read&, const GFM<index_t>&, const BitPairReference&, const ALTDB<index_t>&, const RepeatDB<index_t>&, 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<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::leftAlign(const Read&) [with index_t = short int]':
hi_aligner.h:2218:21:   required from 'bool GenomeHit<index_t>::extend(const Read&, const GFM<index_t>&, const BitPairReference&, const ALTDB<index_t>&, const RepeatDB<index_t>&, 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<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::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<index_t>::extend(const Read&, const GFM<index_t>&, const BitPairReference&, const ALTDB<index_t>&, const RepeatDB<index_t>&, 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<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::readIntoMemory(int, bool, bool, bool, bool, GFMParams<index_t>*, bool, bool, bool, bool) [with index_t = short int]':
gfm.h:694:13:   required from 'GFM<index_t>::GFM(const std::string&, ALTDB<index_t>*, RepeatDB<index_t>*, EList<long unsigned int>*, 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<char>; int32_t = int]'
hgfm.h:1604:14:   required from 'HGFM<index_t, local_index_t>::HGFM(const std::string&, ALTDB<index_t>*, RepeatDB<index_t>*, EList<long unsigned int>*, 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<char>; int32_t = int]'
hisat2.cpp:3776:31:   required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
hisat2.cpp:4351:26:   required from here
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<index_t>::mapLF1(index_t, const SideLocus<index_t>&, int) const [with index_t = short int]':
gfm.h:3967:29:   required from 'std::pair<_FIter, _FIter> GFM<index_t>::mapGLF1(index_t, SideLocus<index_t>&, int, std::pair<_FIter, _FIter>*) const [with index_t = short int]'
hi_aligner.h:6475:40:   required from 'index_t HI_Aligner<index_t, local_index_t>::partialSearch(const GFM<index_t>&, const Read&, const Scoring&, const ReportingParams&, bool, size_t, size_t&, size_t&, ReadBWTHit<index_t>&, 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<index_t, local_index_t>::nextBWT(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, index_t&, bool&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:4077:15:   required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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++) {
      |                            ~~^~~~~~~~~~~~~~~
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<int, int> GWState<index_t, T>::advance(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, EList<GWState<index_t, T>, S>&, GroupWalkState<index_t>&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]':
group_walk.h:1517:14:   required from 'bool GroupWalk2S<index_t, T, S>::advanceElement(index_t, const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GroupWalkState<index_t>&, WalkResult<index_t>&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice<short unsigned int, 16>; int S = 16]'
hi_aligner.h:5901:34:   required from 'bool HI_Aligner<index_t, local_index_t>::getGenomeCoords_local(const GFM<local_index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList<std::pair<index_t, index_t> >&, bool, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:5664:17:   required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::alignWithALTs_recur(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList<SStringExpandable<char, 1024, 2> >&, EList<Edit>&, int&, const char*, index_t, int, index_t, bool, EList<Edit>&, index_t, ELList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, 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<index_t>::alignWithALTs(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars<index_t>&, index_t, int, index_t, bool, const GraphPolicy&, EList<Edit>&, ELList<std::pair<_FIter, _FIter> >&, EList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*) [with index_t = short int; BTDnaString = SDnaStringExpandable<1024, 2>]'
hi_aligner.h:2337:47:   required from 'static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]'
hi_aligner.h:5692:54:   required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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();
      |                            ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
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<index_t>::getRightOff() const [with index_t = short int]':
hi_aligner.h:999:24:   required from 'void GenomeHit<index_t>::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<index_t>::extend(const Read&, const GFM<index_t>&, const BitPairReference&, const ALTDB<index_t>&, const RepeatDB<index_t>&, 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<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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++) {
      |                            ~~^~~~~~~~~~~~~~~~
gfm.h: In instantiation of 'void GFM<index_t>::postReadInit(const GFMParams<index_t>&) [with index_t = short int]':
gfm.h:6434:11:   required from 'void GFM<index_t>::readIntoMemory(int, bool, bool, bool, bool, GFMParams<index_t>*, bool, bool, bool, bool) [with index_t = short int]'
gfm.h:694:13:   required from 'GFM<index_t>::GFM(const std::string&, ALTDB<index_t>*, RepeatDB<index_t>*, EList<long unsigned int>*, 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<char>; int32_t = int]'
hgfm.h:1604:14:   required from 'HGFM<index_t, local_index_t>::HGFM(const std::string&, ALTDB<index_t>*, RepeatDB<index_t>*, EList<long unsigned int>*, 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<char>; int32_t = int]'
hisat2.cpp:3776:31:   required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
hisat2.cpp:4351:26:   required from here
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<index_t>::print(std::ostream&, const GFMParams<index_t>&) const [with index_t = short int; std::ostream = std::basic_ostream<char>]':
gfm.h:6435:39:   required from 'void GFM<index_t>::readIntoMemory(int, bool, bool, bool, bool, GFMParams<index_t>*, bool, bool, bool, bool) [with index_t = short int]'
gfm.h:694:13:   required from 'GFM<index_t>::GFM(const std::string&, ALTDB<index_t>*, RepeatDB<index_t>*, EList<long unsigned int>*, 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<char>; int32_t = int]'
hgfm.h:1604:14:   required from 'HGFM<index_t, local_index_t>::HGFM(const std::string&, ALTDB<index_t>*, RepeatDB<index_t>*, EList<long unsigned int>*, 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<char>; int32_t = int]'
hisat2.cpp:3776:31:   required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
hisat2.cpp:4351:26:   required from here
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<index_t>::countBt2Side(const SideLocus<index_t>&, int) const [with index_t = short int]':
gfm.h:3692:9:   required from 'index_t GFM<index_t>::mapLF(const SideLocus<index_t>&) const [with index_t = short int]'
gfm.h:6906:29:   required from 'void GFM<index_t>::restore(SString<char>&) const [with index_t = short int]'
gfm.h:6926:5:   required from 'void GFM<index_t>::checkOrigs(const EList<SString<char> >&, bool) const [with index_t = short int]'
hisat2.cpp:3815:17:   required from 'void driver(const char*, const std::string&, const std::string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
hisat2.cpp:4351:26:   required from here
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<int, int> GWState<index_t, T>::advance(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, EList<GWState<index_t, T>, S>&, GroupWalkState<index_t>&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short int; T = EListSlice<short int, 16>]':
group_walk.h:1517:14:   required from 'bool GroupWalk2S<index_t, T, S>::advanceElement(index_t, const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GroupWalkState<index_t>&, WalkResult<index_t>&, WalkMetrics&, PerReadMetrics&) [with index_t = short int; T = EListSlice<short int, 16>; int S = 16]'
hi_aligner.h:5816:28:   required from 'bool HI_Aligner<index_t, local_index_t>::getGenomeCoords(const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList<std::pair<_FIter, _FIter> >&, bool, index_t, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:5074:17:   required from 'index_t HI_Aligner<index_t, local_index_t>::getAnchorHits(const GFM<index_t>&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, RandomSource&, index_t, bool, EList<GenomeHit<index_t> >&, index_t, SharedTempVars<index_t>&, 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<index_t, local_index_t>::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:4080:31:   required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]':
group_walk.h:494:14:   required from 'std::pair<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, index_t, index_t, index_t, index_t, const EList<std::pair<_FIter, _FIter> >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]'
group_walk.h:1453:18:   required from 'void GroupWalk2S<index_t, T, S>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice<short unsigned int, 16>; int S = 16]'
hi_aligner.h:5896:20:   required from 'bool HI_Aligner<index_t, local_index_t>::getGenomeCoords_local(const GFM<local_index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList<std::pair<index_t, index_t> >&, bool, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:5664:17:   required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, Haplotype<index_t>&, EList<std::pair<_FIter, _FIter> >&, index_t, bool, bool) [with index_t = short int]':
hi_aligner.h:2915:39:   required from 'static index_t GenomeHit<index_t>::alignWithALTs_recur(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList<SStringExpandable<char, 1024, 2> >&, EList<Edit>&, int&, const char*, index_t, int, index_t, bool, EList<Edit>&, index_t, ELList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, 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<index_t>::alignWithALTs(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars<index_t>&, index_t, int, index_t, bool, const GraphPolicy&, EList<Edit>&, ELList<std::pair<_FIter, _FIter> >&, EList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*) [with index_t = short int; BTDnaString = SDnaStringExpandable<1024, 2>]'
hi_aligner.h:2337:47:   required from 'static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]'
hi_aligner.h:5692:54:   required from 'bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, WalkMetrics&) [with int S = 16; index_t = short int; T = EListSlice<short int, 16>]':
group_walk.h:494:14:   required from 'std::pair<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, index_t, index_t, index_t, index_t, const EList<std::pair<_FIter, _FIter> >&, index_t, WalkMetrics&) [with int S = 16; index_t = short int; T = EListSlice<short int, 16>]'
group_walk.h:1453:18:   required from 'void GroupWalk2S<index_t, T, S>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, RandomSource&, WalkMetrics&) [with index_t = short int; T = EListSlice<short int, 16>; int S = 16]'
hi_aligner.h:5811:14:   required from 'bool HI_Aligner<index_t, local_index_t>::getGenomeCoords(const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList<std::pair<_FIter, _FIter> >&, bool, index_t, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:5074:17:   required from 'index_t HI_Aligner<index_t, local_index_t>::getAnchorHits(const GFM<index_t>&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, RandomSource&, index_t, bool, EList<GenomeHit<index_t> >&, index_t, SharedTempVars<index_t>&, 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<index_t, local_index_t>::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:4080:31:   required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::mapGLF1(index_t, SideLocus<index_t>&, std::pair<_FIter, _FIter>*) const [with index_t = short int]':
group_walk.h:1306:46:   required from 'std::pair<int, int> GWState<index_t, T>::advance(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, EList<GWState<index_t, T>, S>&, GroupWalkState<index_t>&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short int; T = EListSlice<short int, 16>]'
group_walk.h:1517:14:   required from 'bool GroupWalk2S<index_t, T, S>::advanceElement(index_t, const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GroupWalkState<index_t>&, WalkResult<index_t>&, WalkMetrics&, PerReadMetrics&) [with index_t = short int; T = EListSlice<short int, 16>; int S = 16]'
hi_aligner.h:5816:28:   required from 'bool HI_Aligner<index_t, local_index_t>::getGenomeCoords(const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList<std::pair<_FIter, _FIter> >&, bool, index_t, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:5074:17:   required from 'index_t HI_Aligner<index_t, local_index_t>::getAnchorHits(const GFM<index_t>&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, RandomSource&, index_t, bool, EList<GenomeHit<index_t> >&, index_t, SharedTempVars<index_t>&, 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<index_t, local_index_t>::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:4080:31:   required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::tryOffset(index_t, index_t) const [with index_t = short int]':
group_walk.h:555:33:   required from 'std::pair<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, WalkMetrics&) [with int S = 16; index_t = short int; T = EListSlice<short int, 16>]'
group_walk.h:494:14:   required from 'std::pair<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, index_t, index_t, index_t, index_t, const EList<std::pair<_FIter, _FIter> >&, index_t, WalkMetrics&) [with int S = 16; index_t = short int; T = EListSlice<short int, 16>]'
group_walk.h:1453:18:   required from 'void GroupWalk2S<index_t, T, S>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, RandomSource&, WalkMetrics&) [with index_t = short int; T = EListSlice<short int, 16>; int S = 16]'
hi_aligner.h:5811:14:   required from 'bool HI_Aligner<index_t, local_index_t>::getGenomeCoords(const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList<std::pair<_FIter, _FIter> >&, bool, index_t, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:5074:17:   required from 'index_t HI_Aligner<index_t, local_index_t>::getAnchorHits(const GFM<index_t>&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, RandomSource&, index_t, bool, EList<GenomeHit<index_t> >&, index_t, SharedTempVars<index_t>&, 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<index_t, local_index_t>::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:4080:31:   required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::countBt2SideRange(const SideLocus<index_t>&, index_t, index_t*, index_t*, EList<bool>*) const [with index_t = short int]':
gfm.h:3653:3:   required from 'void GFM<index_t>::mapLFRange(const SideLocus<index_t>&, const SideLocus<index_t>&, index_t, index_t*, index_t*, EList<bool>*) const [with index_t = short int]'
group_walk.h:1105:31:   required from 'std::pair<int, int> GWState<index_t, T>::advance(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, EList<GWState<index_t, T>, S>&, GroupWalkState<index_t>&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short int; T = EListSlice<short int, 16>]'
group_walk.h:1517:14:   required from 'bool GroupWalk2S<index_t, T, S>::advanceElement(index_t, const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GroupWalkState<index_t>&, WalkResult<index_t>&, WalkMetrics&, PerReadMetrics&) [with index_t = short int; T = EListSlice<short int, 16>; int S = 16]'
hi_aligner.h:5816:28:   required from 'bool HI_Aligner<index_t, local_index_t>::getGenomeCoords(const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList<std::pair<_FIter, _FIter> >&, bool, index_t, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:5074:17:   required from 'index_t HI_Aligner<index_t, local_index_t>::getAnchorHits(const GFM<index_t>&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, RandomSource&, index_t, bool, EList<GenomeHit<index_t> >&, index_t, SharedTempVars<index_t>&, 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<index_t, local_index_t>::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:4080:31:   required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t>::mapLF1(index_t&, const SideLocus<index_t>&) const [with index_t = short int]':
gfm.h:4040:15:   required from 'std::pair<_FIter, _FIter> GFM<index_t>::mapGLF1(index_t, SideLocus<index_t>&, std::pair<_FIter, _FIter>*) const [with index_t = short int]'
group_walk.h:1306:46:   required from 'std::pair<int, int> GWState<index_t, T>::advance(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, EList<GWState<index_t, T>, S>&, GroupWalkState<index_t>&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short int; T = EListSlice<short int, 16>]'
group_walk.h:1517:14:   required from 'bool GroupWalk2S<index_t, T, S>::advanceElement(index_t, const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GroupWalkState<index_t>&, WalkResult<index_t>&, WalkMetrics&, PerReadMetrics&) [with index_t = short int; T = EListSlice<short int, 16>; int S = 16]'
hi_aligner.h:5816:28:   required from 'bool HI_Aligner<index_t, local_index_t>::getGenomeCoords(const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, index_t, index_t, index_t, index_t, const EList<std::pair<_FIter, _FIter> >&, bool, index_t, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:5074:17:   required from 'index_t HI_Aligner<index_t, local_index_t>::getAnchorHits(const GFM<index_t>&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, RandomSource&, index_t, bool, EList<GenomeHit<index_t> >&, index_t, SharedTempVars<index_t>&, 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<index_t, local_index_t>::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hi_aligner.h:4080:31:   required from 'int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
hisat2.cpp:3537:48:   required from here
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<index_t, local_index_t>::hybridSearch(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]':
spliced_aligner.h:112:6:   required from here
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<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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
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<index_t>::replace_edits_with_alts(const Read&, const EList<ALT<index_t> >&, 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<index_t, local_index_t>::hybridSearch(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = short int; local_index_t = short unsigned int]'
spliced_aligner.h:112:6:   required from here
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<index_t, local_index_t>::isSearched(const GenomeHit<index_t>&, index_t) [with index_t = short int; local_index_t = short unsigned int]':
spliced_aligner.h:373:28:   required from 'int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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
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<index_t, local_index_t>::redundant(AlnSinkWrap<index_t>&, index_t, const GenomeHit<index_t>&) [with index_t = short int; local_index_t = short unsigned int]':
spliced_aligner.h:407:28:   required from 'int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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
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<index_t>::combineWith(const GenomeHit<index_t>&, const Read&, const GFM<index_t>&, const BitPairReference&, const ALTDB<index_t>&, const RepeatDB<index_t>&, 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<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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
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<index_t>::getLeftAnchor(index_t&, index_t&) const [with index_t = short int]':
spliced_aligner.h:518:46:   required from 'int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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
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<index_t>::adjustWithALT(const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = short int]':
spliced_aligner.h:946:46:   required from 'int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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
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<index_t, local_index_t>::globalGFMSearch(const GFM<index_t>&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList<std::pair<_FIter, _FIter> >&, 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<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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
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<index_t>::printAlignedOptFlags(BTString&, bool, const Read&, AlnRes&, StackedAln&, const AlnFlags&, const AlnSetSumm&, const SeedAlSumm&, const PerReadMetrics&, const Scoring&, const char*, const ALTDB<index_t>*) const [with index_t = short int; BTString = SStringExpandable<char, 1024, 2>]':
aln_sink.h:3225:29:   required from 'void AlnSinkSam<index_t>::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<char, 1024, 2>; TReadId = long unsigned int]'
aln_sink.h:1569:4:   required from 'void AlnSinkSam<index_t>::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<char, 1024, 2>; size_t = long unsigned int; TReadId = long unsigned int]'
aln_sink.h:1547:15:   required from here
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<bool, bool> GenomeHit<index_t>::spliced() const [with index_t = short int]':
hi_aligner.h:6100:43:   required from 'bool HI_Aligner<index_t, local_index_t>::reportHit(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, const SpliceSiteDB&, AlnSinkWrap<index_t>&, index_t, const GenomeHit<index_t>&, bool, const GenomeHit<index_t>*) [with index_t = short int; local_index_t = short unsigned int]'
spliced_aligner.h:672:40:   required from 'int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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
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<index_t>::splicing_dir() const [with index_t = short int]':
hi_aligner.h:6102:28:   required from 'bool HI_Aligner<index_t, local_index_t>::reportHit(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, const SpliceSiteDB&, AlnSinkWrap<index_t>&, index_t, const GenomeHit<index_t>&, bool, const GenomeHit<index_t>*) [with index_t = short int; local_index_t = short unsigned int]'
spliced_aligner.h:672:40:   required from 'int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, 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
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<long unsigned int, long unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, 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<long unsigned int, long unsigned int> fastaRefReadFragsNames(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList<std::__cxx11::basic_string<char> >&)':
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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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_seed.h:30,
                 from aligner_seed.cpp:21:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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_i16.cpp:56:
gfm.h: In static member function 'static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> 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<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, 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> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /opt/tools/gcc13/include/c++/13.1.0/memory:78,
                 from gfm.h:28:
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/opt/tools/gcc13/include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
splice_site.cpp: In member function 'void SpliceSiteDB::read(const GFM<unsigned int>&, const EList<ALT<unsigned int> >&)':
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<T, S>::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
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 {
      |       ^~~~
gmake: *** [Makefile:362: hisat2-align-s] Error 1
*** Error code 2

Stop.
bmake[1]: stopped in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/hisat2
*** Error code 1

Stop.
bmake: stopped in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/hisat2