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Update htscodecs to v1.5.2 (2aca18b3) #1685

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merged 1 commit into from
Oct 6, 2023

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  • Fix illegal shift complaint from UBSAN
  • Fix ARM compilation with certain Conda compilers
  • Remove asserts from encode_freq1 and encode_freq_d
  • Fix a 1 byte heap buffer overflow read.
  • Add bounds checking to range coder.
  • Make use of range-coder bounds checks in fqzcomp.
  • Fix the output size estimation in compress_block_fqz2f.
  • Fix buffer overflow in name tokeniser encoder.
  • Add extra checking on 7-bit ASCII for name tokeniser inputs
  • Correct a buffer read-overflow (max 8 bytes) in AVX2 rans decode
  • Fix an overflow with freq=4096 in the SSE4 decoder.
  • Remove divide by zero in rANS 4x8.
  • r4x16pr: protect against input being NULL and in_size of zero.

 * Fix illegal shift complaint from UBSAN
 * Fix ARM compilation with certain Conda compilers
 * Remove asserts from encode_freq1 and encode_freq_d
 * Fix a 1 byte heap buffer overflow read.
 * Add bounds checking to range coder.
 * Make use of range-coder bounds checks in fqzcomp.
 * Fix the output size estimation in compress_block_fqz2f.
 * Fix buffer overflow in name tokeniser encoder.
 * Add extra checking on 7-bit ASCII for name tokeniser inputs
 * Correct a buffer read-overflow (max 8 bytes) in AVX2 rans decode
 * Fix an overflow with freq=4096 in the SSE4 decoder.
 * Remove divide by zero in rANS 4x8.
 * r4x16pr: protect against input being NULL and in_size of zero.
@jkbonfield jkbonfield merged commit 28a980b into samtools:develop Oct 6, 2023
@daviesrob daviesrob deleted the htscodecs_v1.5.2 branch October 12, 2023 10:09
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2 participants