[Debian-med-packaging] Bug#1074739: hisat2: FTBFS: make[1]: *** [debian/rules:39: override_dh_auto_build] Error 1
Lucas Nussbaum
lucas at debian.org
Tue Jul 2 14:30:30 BST 2024
Source: hisat2
Version: 2.2.1-4
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20240702 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \
> -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"14 October 2022\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -Wl,-z,now
> /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \
> -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"14 October 2022\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -Wl,-z,now
> /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \
> -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"14 October 2022\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -Wl,-z,now
> /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \
> -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"14 October 2022\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
> -I. -I third_party \
> -o hisat2-align-l hisat2.cpp \
> ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \
> -lpthread -Wl,-z,relro -Wl,-z,now
> /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \
> -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \
> -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"14 October 2022\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \
> -I. -I third_party -I . \
> -o hisat2-inspect-s hisat2_inspect.cpp \
> ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
> -lpthread -Wl,-z,relro -Wl,-z,now
> /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \
> -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \
> -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"14 October 2022\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \
> -I. -I third_party -I . \
> -o hisat2-inspect-l hisat2_inspect.cpp \
> ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
> -lpthread -Wl,-z,relro -Wl,-z,now
> /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \
> -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"14 October 2022\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
> -I. -I third_party \
> -o hisat2-repeat hisat2_repeat.cpp \
> ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp mask.cpp qual.cpp aligner_bt.cpp scoring.cpp simple_func.cpp dp_framer.cpp aligner_result.cpp aligner_sw_driver.cpp aligner_sw.cpp aligner_swsse_ee_i16.cpp aligner_swsse_ee_u8.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse.cpp bit_packed_array.cpp repeat_builder.cpp diff_sample.cpp hisat2_repeat_main.cpp \
> -lpthread -Wl,-z,relro -Wl,-z,now
> make[2]: Nothing to be done for 'doc'.
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 hisat2_repeat.cpp:36:
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from hisat2_inspect.cpp:25:
> alt.h: In member function ‘bool ALT<index_t>::repOk() const’:
> assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
> 227 | if(!((a) <= (b))) { \
> | ~~~~^~~~~~
> alt.h:180:13: note: in expansion of macro ‘assert_leq’
> 180 | assert_leq(fw, 1);
> | ^~~~~~~~~~
> In file included from hisat2_inspect.cpp:25:
> alt.h: In member function ‘bool ALT<index_t>::repOk() const’:
> assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
> 227 | if(!((a) <= (b))) { \
> | ~~~~^~~~~~
> alt.h:180:13: note: in expansion of macro ‘assert_leq’
> 180 | assert_leq(fw, 1);
> | ^~~~~~~~~~
> gfm.h: In 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;
> | ^~~~~~~~~~~~
> 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());
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> 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));
> | ^~~~~~~~
> /usr/include/c++/13/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());
> | ^~~~~~~~
> /usr/include/c++/13/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));
> | ^~~~~~~~
> /usr/include/c++/13/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(
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> 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 = long unsigned int; local_index_t = short unsigned int]’:
> hisat2.cpp:3537:48: required from here
> hi_aligner.h:4385:84: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare]
> 4385 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits)
> | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
> hi_aligner.h:4404:55: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefId’ {aka ‘long int’} [-Wsign-compare]
> 4404 | if(positions[p].first.tid != res.refid()) continue;
> | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> hi_aligner.h:4405:63: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare]
> 4405 | if(positions[p].first.toff + 1000 < res.refoff() ||
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> hi_aligner.h:4406:52: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare]
> 4406 | res.refoff() + 1000 < positions[p].first.toff) continue;
> | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
> hi_aligner.h:4407:88: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare]
> 4407 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits)
> | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
> hi_aligner.h:4489:92: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare]
> 4489 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits)
> | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
> hi_aligner.h:4578:69: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare]
> 4578 | align2repeat = (numBestPair == 0 || numBestPair > rp.khits);
> | ~~~~~~~~~~~~^~~~~~~~~~
> hi_aligner.h:4584:83: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare]
> 4584 | align2repeat = (rs->size() == 0 || sink.numBestUnp(rdi).first > rp.khits);
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
> hi_aligner.h:4614:55: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare]
> 4614 | if(sink.numBestUnp(rdi).first > rp.khits) {
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
> In file included from hgfm.h:24,
> from hisat2_inspect.cpp:27:
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> 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 = long unsigned 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 = long unsigned int; local_index_t = short unsigned int]’
> hisat2.cpp:3537:48: required from here
> hi_aligner.h:5990:51: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare]
> 5990 | if(_repeatConcordant[r].first == left.off() &&
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
> hi_aligner.h:5991:52: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare]
> 5991 | _repeatConcordant[r].second == left2.off()) {
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> In file included from hgfm.h:24,
> from hisat2_inspect.cpp:27:
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> 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 = long unsigned 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 = long unsigned int; local_index_t = short unsigned int]’
> hisat2.cpp:3537:48: required from here
> hi_aligner.h:5661:33: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare]
> 5661 | if(nelt > 0 && nelt <= rp.kseeds && hitlen > max_hitlen) {
> | ~~~~~^~~~~~~~~~~~
> hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare]
> 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off())
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
> gfm.h: In instantiation of ‘void GFM<index_t>::checkOrigs(const EList<SString<char> >&, bool) const [with index_t = long unsigned 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:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable]
> 6935 | int lastorig = -1;
> | ^~~~~~~~
> 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());
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> 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 = long unsigned 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 = long unsigned 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 = long unsigned int; local_index_t = short unsigned int]’
> hisat2.cpp:3537:48: required from here
> hi_aligner.h:5150:32: warning: comparison of integer expressions of different signedness: ‘TRefId’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare]
> 5150 | if(coord.ref() == numeric_limits<index_t>::max())
> | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 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 = long unsigned 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 = long unsigned 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 = long unsigned int; local_index_t = short unsigned int]’
> hisat2.cpp:3537:48: required from here
> hi_aligner.h:2267:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare]
> 2267 | findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs);
> | ~~~~~~~~~~~~~~~~~~^~~~~~~~
> 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));
> | ^~~~~~~~
> /usr/include/c++/13/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());
> | ^~~~~~~~
> /usr/include/c++/13/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));
> | ^~~~~~~~
> /usr/include/c++/13/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(
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> 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 = long unsigned 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 = long unsigned 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 = long unsigned 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 = long unsigned 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 = long unsigned 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 = long unsigned 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 = long unsigned 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 = long unsigned int; local_index_t = short unsigned int]’
> hisat2.cpp:3537:48: required from here
> 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: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:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
> 3044 | for(int i = 0; i < alt.len; i++) {
> | ~~^~~~~~~~~
> hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
> 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) {
> | ~~~~~^~~~~~~~
> hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
> 3161 | if(alignedLen == next_rdlen) return rdlen;
> | ~~~~~~~~~~~^~~~~~~~~~~~~
> hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
> 3197 | if(mm_max_rd_i + rdoff > best_rdoff) {
> | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
> hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
> 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) {
> | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
> hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
> 3454 | if(best_rdoff < rdoff + rd_i) {
> | ~~~~~~~~~~~^~~~~~~~~~~~~~
> 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 = long unsigned 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 = long unsigned 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 = long unsigned 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 = long unsigned 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 = long unsigned 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 = long unsigned 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 = long unsigned 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 = long unsigned 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 = long unsigned 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:2675:37: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
> 2675 | if(ht_list[h].first == ht_range.first) {
> | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
> hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
> 2713 | if(ht_list[h].first == ht_range.first) {
> | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
> 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:2744:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
> 2744 | if(ht_list[h].first == ht_range.second) {
> | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
> In file included from spliced_aligner.h:23,
> from hisat2.cpp:46:
> 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 = unsigned 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 = unsigned int; local_index_t = short unsigned int]’
> hisat2.cpp:3537:48: required from here
> 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())
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
> gfm.h: In instantiation of ‘void GFM<index_t>::checkOrigs(const EList<SString<char> >&, bool) const [with index_t = unsigned 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:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable]
> 6935 | int lastorig = -1;
> | ^~~~~~~~
> 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 = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’:
> spliced_aligner.h:331:9: required from here
> spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable]
> 408 | bool another_spliced = false;
> | ^~~~~~~~~~~~~~~
> spliced_aligner.h:782:65: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare]
> 782 | tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) {
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> spliced_aligner.h:1465:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare]
> 1465 | combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) {
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> 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 = long unsigned 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 = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’
> spliced_aligner.h:331:9: required from here
> 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: 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 = long unsigned 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 = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’
> spliced_aligner.h:331:9: required from here
> hi_aligner.h:6719:85: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare]
> 6719 | if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) {
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
> 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 = unsigned 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 = unsigned 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 = unsigned 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 = unsigned 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 = unsigned 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 = unsigned 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 = unsigned 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 = unsigned int; local_index_t = short unsigned int]’
> hisat2.cpp:3537:48: required from here
> 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: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:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
> 3044 | for(int i = 0; i < alt.len; i++) {
> | ~~^~~~~~~~~
> hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
> 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) {
> | ~~~~~^~~~~~~~
> hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
> 3161 | if(alignedLen == next_rdlen) return rdlen;
> | ~~~~~~~~~~~^~~~~~~~~~~~~
> hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
> 3197 | if(mm_max_rd_i + rdoff > best_rdoff) {
> | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
> hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
> 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) {
> | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
> hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
> 3454 | if(best_rdoff < rdoff + rd_i) {
> | ~~~~~~~~~~~^~~~~~~~~~~~~~
> 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 = unsigned 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 = unsigned 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 = unsigned 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 = unsigned 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 = unsigned 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 = unsigned 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 = unsigned 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 = unsigned 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 = unsigned 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:2675:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
> 2675 | if(ht_list[h].first == ht_range.first) {
> | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
> hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
> 2713 | if(ht_list[h].first == ht_range.first) {
> | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
> 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:2744:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
> 2744 | if(ht_list[h].first == ht_range.second) {
> | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
> 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 = unsigned int; local_index_t = short unsigned int; int64_t = long int]’:
> spliced_aligner.h:331:9: required from here
> spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable]
> 408 | bool another_spliced = false;
> | ^~~~~~~~~~~~~~~
> 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 = unsigned 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 = unsigned int; local_index_t = short unsigned int; int64_t = long int]’
> spliced_aligner.h:331:9: required from here
> 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) {
> | ~~~~~~~~^~~~~~
> 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 ‘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 ‘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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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*, size_t, size_t, 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;
> | ^~~~~~~~~~~~~~
> 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 ‘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 ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
> 440 | if(i + 1 >= recs.size() || recs[i+1].first) {
> | ~~~~~~^~~~~~~~~~~~~~
> ref_read.cpp: In function ‘std::pair<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 ‘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 ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
> 440 | if(i + 1 >= recs.size() || recs[i+1].first) {
> | ~~~~~~^~~~~~~~~~~~~~
> In file included from splice_site.h:34,
> from edit.h:30,
> from aligner_result.h:30,
> from aligner_sw_common.h:23,
> from aligner_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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from edit.h:26,
> from edit.cpp:21:
> alt.h: In member function ‘bool ALT<index_t>::repOk() const’:
> assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
> 227 | if(!((a) <= (b))) { \
> | ~~~~^~~~~~
> alt.h:180:13: note: in expansion of macro ‘assert_leq’
> 180 | assert_leq(fw, 1);
> | ^~~~~~~~~~
> In file included from splice_site.h:34,
> from edit.h:30:
> gfm.h: In static member function ‘static std::pair<GFM<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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from edit.h:26,
> from edit.cpp:21:
> alt.h: In member function ‘bool ALT<index_t>::repOk() const’:
> assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
> 227 | if(!((a) <= (b))) { \
> | ~~~~^~~~~~
> alt.h:180:13: note: in expansion of macro ‘assert_leq’
> 180 | assert_leq(fw, 1);
> | ^~~~~~~~~~
> In file included from splice_site.h:34,
> from edit.h:30:
> gfm.h: In static member function ‘static std::pair<GFM<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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from alphabet.h:27,
> from gfm.h:40,
> from gfm.cpp:21:
> alt.h: In member function ‘bool ALT<index_t>::repOk() const’:
> assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
> 227 | if(!((a) <= (b))) { \
> | ~~~~^~~~~~
> alt.h:180:13: note: in expansion of macro ‘assert_leq’
> 180 | assert_leq(fw, 1);
> | ^~~~~~~~~~
> In file included from splice_site.h:34,
> from edit.h:30,
> from aligner_result.h:30,
> from aligner_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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from alphabet.h:27,
> from gfm.h:40,
> from gfm.cpp:21:
> alt.h: In member function ‘bool ALT<index_t>::repOk() const’:
> assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
> 227 | if(!((a) <= (b))) { \
> | ~~~~^~~~~~
> alt.h:180:13: note: in expansion of macro ‘assert_leq’
> 180 | assert_leq(fw, 1);
> | ^~~~~~~~~~
> gfm.h: In static member function ‘static std::pair<GFM<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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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:75,
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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:75,
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from sequence_io.h:30,
> from hisat2_build.cpp:28:
> In member function ‘void SString<T>::resize(size_t) [with T = char]’,
> inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:687:9,
> inlined from ‘void SString<T>::install(const T*, 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(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(size_t) [with T = char]’,
> inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:687:9,
> inlined from ‘void SString<T>::install(const T*, 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(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(size_t) [with T = char]’,
> inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:687:9,
> inlined from ‘void SString<T>::install(const T*, 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(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(size_t) [with T = char]’,
> inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:687:9,
> inlined from ‘void SString<T>::install(const T*, 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(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 file included from sequence_io.h:30,
> from hisat2_build.cpp:28:
> In member function ‘void SString<T>::resize(size_t) [with T = char]’,
> inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:687:9,
> inlined from ‘void SString<T>::install(const T*, 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(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(size_t) [with T = char]’,
> inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:687:9,
> inlined from ‘void SString<T>::install(const T*, 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(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 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:75,
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> 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 ‘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 ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
> 440 | if(i + 1 >= recs.size() || recs[i+1].first) {
> | ~~~~~~^~~~~~~~~~~~~~
> In member function ‘void SString<T>::resize(size_t) [with T = char]’,
> inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:687:9,
> inlined from ‘void SString<T>::install(const T*, 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(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(size_t) [with T = char]’,
> inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:687:9,
> inlined from ‘void SString<T>::install(const T*, 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(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 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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:75,
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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*, size_t, size_t, 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;
> | ^~~~~~~~~~~~~~
> 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 ‘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 ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
> 440 | if(i + 1 >= recs.size() || recs[i+1].first) {
> | ~~~~~~^~~~~~~~~~~~~~
> In file included from splice_site.h:34,
> from edit.h:30,
> from aligner_result.h:30,
> from aligner_sw_common.h:23,
> from aligner_sw.h:75,
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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*, size_t, size_t, size_t) const’:
> reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
> 522 | uint64_t origBufOff = bufOff;
> | ^~~~~~~~~~
> reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
> 516 | bool binarySearched = false;
> | ^~~~~~~~~~~~~~
> In file included from splice_site.h:34,
> from edit.h:30,
> from aligner_result.h:30,
> from aligner_sw_common.h:23,
> from aligner_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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> 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 ‘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 ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
> 440 | if(i + 1 >= recs.size() || recs[i+1].first) {
> | ~~~~~~^~~~~~~~~~~~~~
> In file included from splice_site.h:34,
> from edit.h:30,
> from aligner_result.h:30,
> from aligner_sw_common.h:23,
> from aligner_sw.h:75,
> from bit_packed_array.cpp:24:
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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:75,
> from repeat_builder.cpp:26:
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> 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 ‘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 ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
> 440 | if(i + 1 >= recs.size() || recs[i+1].first) {
> | ~~~~~~^~~~~~~~~~~~~~
> repeat_builder.cpp: In function ‘std::string reverse_complement(const std::string&)’:
> repeat_builder.cpp:88:30: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 88 | rev[i] = asc2dnacomp[nt];
> | ^~
> repeat_builder.cpp: In function ‘std::string reverseComplement(const std::string&)’:
> repeat_builder.cpp:200:53: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 200 | rc.push_back(asc2dnacomp[str[si - 1]]);
> | ^
> repeat_builder.cpp: In member function ‘int CoordHelper::mapJoinedOffToSeq(TIndexOffU)’:
> repeat_builder.cpp:403:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
> 403 | for(size_t i = 0; i < num_cached_; i++) {
> | ~~^~~~~~~~~~~~~
> repeat_builder.cpp: In function ‘size_t extract_kmer(const std::string&, size_t, size_t)’:
> repeat_builder.cpp:1217:53: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 1217 | kmer = (kmer << 2) | asc2dna[seq[offset + i]];
> | ^
> repeat_builder.cpp: In function ‘size_t next_kmer(size_t, char, size_t)’:
> repeat_builder.cpp:1225:34: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 1225 | kmer = (kmer << 2) | asc2dna[base];
> | ^~~~
> repeat_builder.cpp: In function ‘void find_gap_pos(const std::string&, const std::string&, EList<long unsigned int>&, EList<long unsigned int>&, bool, size_t, size_t, size_t&, size_t&, bool)’:
> repeat_builder.cpp:1275:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
> 1275 | for(int i = seq_len - 1; i >= gap_len; i--) {
> | ~~^~~~~~~~~~
> repeat_builder.cpp:1277:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
> 1277 | if(i == seq_len - 1) ed2[i] = add;
> | ~~^~~~~~~~~~~~~~
> repeat_builder.cpp: In member function ‘void RB_SWAligner::makePadString(const std::string&, const std::string&, std::string&, size_t)’:
> repeat_builder.cpp:2915:39: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 2915 | pad[i] = "CGTA"[asc2dna[ref[i]]];
> | ^
> repeat_builder.cpp:2919:43: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 2919 | pad[i] = "CGTA"[asc2dna[pad[i]]];
> | ^
> repeat_builder.cpp:2926:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
> 2926 | for(size_t i = 0; i < head_len; i++) {
> | ~~^~~~~~~~~~
> repeat_builder.cpp:2929:67: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 2929 | pad[pad_start + i] = "CGTA"[asc2dna[pad[pad_start + i]]];
> | ^
> repeat_builder.cpp: In member function ‘int RB_SWAligner::alignStrings(const std::string&, const std::string&, EList<Edit>&, Coord&)’:
> repeat_builder.cpp:3065:13: warning: variable ‘max_match_len’ set but not used [-Wunused-but-set-variable]
> 3065 | int max_match_len = 0;
> | ^~~~~~~~~~~~~
> In file included from repeat_builder.cpp:31:
> repeat_builder.cpp: In instantiation of ‘RepeatBuilder<TStr>::RepeatBuilder(TStr&, const EList<RefRecord>&, const EList<std::__cxx11::basic_string<char> >&, bool, const std::string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’:
> repeat_builder.cpp:4753:16: required from here
> repeat_builder.h:947:17: warning: ‘RepeatBuilder<SString<char> >::coordHelper_’ will be initialized after [-Wreorder]
> 947 | CoordHelper coordHelper_;
> | ^~~~~~~~~~~~
> repeat_builder.h:940:10: warning: ‘bool RepeatBuilder<SString<char> >::forward_only_’ [-Wreorder]
> 940 | bool forward_only_;
> | ^~~~~~~~~~~~~
> repeat_builder.cpp:3167:1: warning: when initialized here [-Wreorder]
> 3167 | RepeatBuilder<TStr>::RepeatBuilder(TStr& s,
> | ^~~~~~~~~~~~~~~~~~~
> repeat_builder.cpp: In instantiation of ‘void RepeatBuilder<TStr>::build(const RepeatParameter&) [with TStr = SString<char>]’:
> repeat_builder.cpp:4753:16: required from here
> repeat_builder.cpp:3396:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
> 3396 | if(spos != string::npos) {
> | ~~~~~^~~~~~~~~~~~~~~
> repeat_builder.cpp:3426:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
> 3426 | if(spos != string::npos) {
> | ~~~~~^~~~~~~~~~~~~~~
> repeat_builder.cpp:3553:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
> 3553 | if(pos != string::npos) {
> | ~~~~^~~~~~~~~~~~~~~
> repeat_builder.cpp:3563:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
> 3563 | if(pos != string::npos) {
> | ~~~~^~~~~~~~~~~~~~~
> repeat_builder.cpp: In instantiation of ‘void RepeatBuilder<TStr>::saveConsensus(const RepeatParameter&, const std::string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’:
> repeat_builder.cpp:4753:16: required from here
> repeat_builder.cpp:4114:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
> 4114 | if((oskip + out_len) == output_width) {
> | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
> repeat_builder.cpp: In instantiation of ‘void dump_tstr(const TStr&) [with TStr = SString<char>]’:
> repeat_builder.cpp:4754:46: required from here
> repeat_builder.cpp:309:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
> 309 | for(size_t j = 0; (j < print_width) && (i + j < s_len); j++) {
> | ~~~^~~~~~~~~~~~~~
> repeat_builder.cpp:310:46: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 310 | buf.push_back("ACGTN"[s[i + j]]);
> | ~~~~~~~^
> repeat_builder.cpp: In instantiation of ‘std::string getString(const TStr&, TIndexOffU, size_t) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long unsigned int; size_t = long unsigned int]’:
> repeat_builder.cpp:3312:30: required from ‘void RepeatBuilder<TStr>::build(const RepeatParameter&) [with TStr = SString<char>]’
> repeat_builder.cpp:4753:16: required from here
> repeat_builder.cpp:272:33: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 272 | char nt = "ACGT"[ref[start + i]];
> | ~~~~~~^
> repeat_builder.cpp: In instantiation of ‘void getString(const TStr&, TIndexOffU, size_t, std::string&) [with TStr = SString<char>; TIndexOffU = long unsigned int; size_t = long unsigned int; std::string = std::__cxx11::basic_string<char>]’:
> repeat_builder.cpp:3545:22: required from ‘void RepeatBuilder<TStr>::build(const RepeatParameter&) [with TStr = SString<char>]’
> repeat_builder.cpp:4753:16: required from here
> repeat_builder.cpp:286:25: warning: array subscript has type ‘char’ [-Wchar-subscripts]
> 286 | char nt = "ACGT"[ref[start + i]];
> | ~~~~~~^
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
> 65 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from /usr/include/c++/13/iostream:41,
> from repeat_builder.cpp:21:
> In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char; _Traits = std::char_traits<char>]’,
> inlined from ‘void RepeatBuilder<TStr>::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList<SeedExt>&, std::ostream&) [with TStr = SString<char>]’ at repeat_builder.cpp:3678:31:
> /usr/include/c++/13/ostream:173:25: warning: ‘pos_in_chr’ may be used uninitialized [-Wmaybe-uninitialized]
> 173 | { return _M_insert(__n); }
> | ~~~~~~~~~^~~~~
> repeat_builder.cpp: In member function ‘void RepeatBuilder<TStr>::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList<SeedExt>&, std::ostream&) [with TStr = SString<char>]’:
> repeat_builder.cpp:3664:20: note: ‘pos_in_chr’ was declared here
> 3664 | TIndexOffU pos_in_chr;
> | ^~~~~~~~~~
> reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, 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 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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*, size_t, size_t, 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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_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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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:75,
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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:75,
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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:75,
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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:75,
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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:75,
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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:75,
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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:75,
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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:75,
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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:75,
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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:75,
> 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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’:
> splice_site.cpp:722:31: required from here
> ds.h:663:28: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
> 663 | std::memcpy(list_ + cur_, l, bytes);
> | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
> splice_site.h:377:7: note: ‘class Exon’ declared here
> 377 | class Exon {
> | ^~~~
> In file included from splice_site.h:34,
> from edit.h:30,
> from splice_site.cpp:20:
> gfm.h: In static member function ‘static std::pair<GFM<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 /usr/include/c++/13/memory:78,
> from gfm.h:28:
> /usr/include/c++/13/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()));
> | ^~~~~~~~
> /usr/include/c++/13/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<long unsigned int>&, const EList<ALT<long 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*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’:
> splice_site.cpp:722:31: required from here
> ds.h:663:28: warning: ‘void* 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 {
> | ^~~~
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> help2man ./hisat2 --no-info --name \
> 'graph-based alignment of short nucleotide reads to many genomes, wrapper script' \
> > debian/hisat2.1
> help2man ./hisat2-align-l --name 'HISAT2 graph-based alignment of short nucleotide reads to many genomes, large index binary' \
> --no-info > debian/hisat2-align-l.1
> help2man ./hisat2-align-s --name 'HISAT2 graph-based alignment of short nucleotide reads to many genomes, small index binary' \
> --no-info > debian/hisat2-align-s.1
> help2man ./hisat2-build --name 'HISAT2 indexer, wrapper script' \
> --no-info > debian/hisat2-build.1
> #rm hisat2-buildc
> help2man ./hisat2-build-l --name 'HISAT2 indexer, large index binary' \
> --no-info > debian/hisat2-build-l.1
> help2man ./hisat2-build-s --name 'HISAT2 indexer, small index binary' \
> --no-info > debian/hisat2-build-s.1
> help2man ./hisat2-inspect --name 'HISAT2 index inspector, wrapper script' \
> --no-info > debian/hisat2-inspect.1
> help2man: can't get `--help' info from ./hisat2-inspect
> Try `--no-discard-stderr' if option outputs to stderr
> make[1]: *** [debian/rules:39: override_dh_auto_build] Error 1
The full build log is available from:
http://qa-logs.debian.net/2024/07/02/hisat2_2.2.1-4_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240702;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240702&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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