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View Code? Open in Web Editor NEWCode for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)
License: GNU General Public License v2.0
Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)
License: GNU General Public License v2.0
Deserializing following variants from disk doesn't work:
mef-matrix: Segmentation fault
mef-split: terminate called after throwing an instance of 'std::bad_alloc'
The build may fail due to missing support for the instruction _pext_u64:
In file included from /usr/lib/gcc/x86_64-linux-gnu/9/include/immintrin.h:105,
from /home/analanko/code/SBWT/include/MEF.hpp:29,
from /home/analanko/code/SBWT/include/variants.hh:15,
from /home/analanko/code/SBWT/src/sbwt_build.cpp:9:
/usr/lib/gcc/x86_64-linux-gnu/9/include/bmi2intrin.h: In member function ‘uint64_t mod_ef_vector<t_rank_1>::shrink(long long unsigned int) [with t_rank_1 = sdsl::rank_support_v<1, 1>]’:
/usr/lib/gcc/x86_64-linux-gnu/9/include/bmi2intrin.h:76:1: error: inlining failed in call to always_inline ‘long long unsigned int _pext_u64(long long unsigned int, long long unsigned int)’: target specific option mismatch
76 | _pext_u64 (unsigned long long __X, unsigned long long __Y)
| ^~~~~~~~~
In file included from /home/analanko/code/SBWT/include/variants.hh:15,
from /home/analanko/code/SBWT/src/sbwt_build.cpp:9:
/home/analanko/code/SBWT/include/MEF.hpp:314:36: note: called from here
314 | return((uint64_t) _pext_u64( ((x & 0xAAAAAAAAAAAAAAAAULL) >> 1 | x), 0x5555555555555555ULL));
Hi !
The CMake minimal version should be at least 3.13 to accept target_link_options
See https://cmake.org/cmake/help/git-stage/command/target_link_options.html
Best,
Pierre
Hi,
great software, congrats!
Is it possible to list all k-mers in SBWT instead of querying a specific k-mer?
If so, how to do this, is this somehow exposed in the C++ API?
Best
Marek
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