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htslib
C library for high-throughput sequencing data formats
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Update to latest htscodecs
#1717
Closed
daviesrob
closed
7 months ago
daviesrob
commented
7 months ago
Name tokeniser fixes.
Fix tok3 decode bounds checking.
Fix rans_set_cpu to work a second time.
Bug fix the -c
option for testing codecs.
Bug fix the tests/entropy PACK+RLE+SIMD.
Add round-trip fuzzer for entropy codecs (rANS, arithmetic)
Add fuzzers to .gitignore
Add a tok3 and fqzcomp round-trip fuzzer
Replace SIMD gather with simulated gathers.
Speed up rans_F_to_s3 function.
AVX2 rans32x16 O1 speed up.
AVX512 rans32x16 O1 speed up.
Speed up AVX2 O1 encoder.
Fix mem bounds checking in rans_uncompress_O0_32x16_avx2.
Replace _mm512_i32gather_epi32(mm512, array, 1) with simulated gather.
Fix the previous rans_set_cpu code to work with AVX2/AVX512 checks.
Fix O1 AVX512 encoder.
Minor improvement to -DENC_DEBUG diagnostics in name tokeniser.
Fix tok3 encoding bug with duplicated streams.
Remove undefined behaviour in transpose_and_copy.
Add explicit -mpopcnt to avx2 and avx512 builds.
Allow builds on old gcc's that don't like declarations in for loops