Open gancho-ivanov opened 2 years ago
Hm!
https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/commit/e2c7ccca74633ac61150d55e7c03270ab049b439#diff-ccfb8f3b7607fe494fe5c37a7db56e59cbcef2e76182dc9f8e3e4522e3984c4e added support for SSE2/NEON, but git submodule update
checks out commit 8c9933a1685e0ab50c7d8b7926c9068bc0c9d7d2
from https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library which is 7 years old ...
I don't see/understand why it checks out this particular version. https://github.com/zeeev/wham/blob/4e8c9bee568211596cdc634d15600114e75d2619/.gitmodules#L7-L9 does not specify any revision.
I've updated manually the submodule (cd src/Complete-Striped-Smith-Waterman-Library; git pull --rebase origin master
) and now the new problem is:
src/Complete-Striped-Smith-Waterman-Library/src/ssw_cpp.h:156:8: note: candidate expects 6 arguments, 5 provided
src/bin/wham.cpp:2201:89: error: no matching function for call to ‘StripedSmithWaterman::Aligner::Align(const char*, const char*, std::__cxx11::basic_string<char>::size_type, StripedSmithWaterman::Filter&, StripedSmithWaterman::Alignment*)’
aligner.Align(altSeq.c_str(), endChunk.c_str(), endChunk.size(), filter, &alignmentEnd);
^
In file included from src/bin/wham.cpp:11:0:
src/Complete-Striped-Smith-Waterman-Library/src/ssw_cpp.h:139:8: note: candidate: bool StripedSmithWaterman::Aligner::Align(const char*, const StripedSmithWaterman::Filter&, StripedSmithWaterman::Alignment*, int32_t) const
bool Align(const char* query, const Filter& filter, Alignment* alignment, const int32_t maskLen) const;
^~~~~
src/Complete-Striped-Smith-Waterman-Library/src/ssw_cpp.h:139:8: note: candidate expects 4 arguments, 5 provided
src/Complete-Striped-Smith-Waterman-Library/src/ssw_cpp.h:156:8: note: candidate: bool StripedSmithWaterman::Aligner::Align(const char*, const char*, const int&, const StripedSmithWaterman::Filter&, StripedSmithWaterman::Alignment*, int32_t) const
bool Align(const char* query, const char* ref, const int& ref_len,
^~~~~
src/Complete-Striped-Smith-Waterman-Library/src/ssw_cpp.h:156:8: note: candidate expects 6 arguments, 5 provided
Any help is welcome!
I could try to add support for Neon (ARM64) if there is interest in the community! But the project seems abandoned since 2017 and I am not sure whether such contribution would ever be merged and released.
Hi @julien-faye not completely abandoned; just busy doing other things. AFAIK Whamg is still being used in best-in-class ensemble pipelines.
Hi,
Is ARM64 architecture supported ? Linux and/or MacOS ?
I am trying to build the project on Ubuntu 20.04 ARM64 but it fails with:
emmintrin.h
could be used only on x86_64 when SSE is available.