+ 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