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1. Commits on Oct 27, 2026

   • Merge pull request #1163 from kimmanbo/fix/avx512-hmax-gcc12-uninit

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   • fix: Avoid GCC 12 uninitialized warning in AVX512 hmax

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   • Merge pull request #1162 from kimmanbo/fix/mac-clt-sdk-link-dir

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   • build: Drop Command Line Tools link dir on macOS

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2. Commits on Oct 25, 2026

   • Merge pull request #1157 from soedinglab/ungapped-signed-sweep

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   • Merge pull request #1158 from soedinglab/hugepage-page-cache

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3. Commits on Oct 24, 2026

   • Advise huge pages for memory mapped databases

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   • Signed multi-column kernel for the CPU ungapped prefilter

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4. Commits on Oct 20, 2026

   • fix: Convert uppercase RNA U to T before ORF search

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     kimmanbo

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     milot-mirdita

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5. Commits on Oct 15, 2026

   • Use SIMD exp in 512-bit FwBw first column

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   • Parenthesise macro arguments used in expressions

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   • Give flag-dependent SIMD helpers internal linkage

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   • Allocate gapless aligner only when prefilter needs it

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   • Keep FwBwAligner API usable from outside this repository

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   • Fix AVX512 paths in CSProfile and zero context library padding

     milot-mirdita

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   • Require AVX512DQ and AVX512VL for AVX512 SIMD path

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   • Skip precompiled headers for AVX512 translation units

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   • Add runtime AVX512 dispatch for gapless alignment and FwBw

     

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     milot-mirdita

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   • Fix compile error on old gcc in Fwbw

     milot-mirdita

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   • Run FwBw at 256-bit with AVX512VL masks

     

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   • Fix AVX2 and SSE fallbacks and add mask-based comparisons

     

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   • Add AVX512 path to CSProfile

     

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   • Speed up simd_abs on AVX512 and add SIMD macros for foldseek

     

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     milot-mirdita

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   • Tune FwBw kernel

     

     Eulium

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     milot-mirdita

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   • Add AVX512 variants of simd_exp and simd_log

     

     Eulium

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     milot-mirdita

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   • Add AVX512 SIMD macros

     

     Eulium

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     milot-mirdita

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6. Commits on Sep 30, 2026

   • Fix platform-specific compilation issues

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     kimmanbo

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     milot-mirdita

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   • Fix full-byte substitution matrix indexing

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     kimmanbo

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     milot-mirdita

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   • Remove long-target ungapped alignment regression test

     

     kimmanbo

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     milot-mirdita

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   • Fix hit identity during long-target ungapped rescoring

     

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     milot-mirdita

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   • [fix] fastSeqIdToBuffer function edge case error fixed.

     

     kimmanbo

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     milot-mirdita

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   • Fix E-value truncation in iterative profile search

     

     kimmanbo

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     milot-mirdita

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7. Commits on Sep 29, 2026

   • Merge pull request #1134 from Gyuuul2/SW

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   • Revert aligner allocation size to par.maxSeqLen

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   • Resize the Smith-Waterman buffers when needed and allocate the block trace only when used

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