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Update to latest htscodecs #1717

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merged 1 commit into from
Dec 6, 2023
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  • 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

 * Name tokeniser fixes.
 * Fix tok3 decode bounds checking.
 * Fix rans_set_cpu to work a second time.
 * Bug fix the -c <DEC><ENC> 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
@jkbonfield jkbonfield merged commit 4020780 into samtools:develop Dec 6, 2023
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@daviesrob daviesrob deleted the htscodecs_latest branch December 6, 2023 13:47
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2 participants