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Single-version (1.6) build; drop Haskell-parity machinery Build Rust #58: Commit f46e034 pushed by luispedro
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NEW Parallel module: port progress output and lock-hash fixes Build Rust #57: Commit 203d7fd pushed by luispedro
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NEW External module parity: sequenceset returns and filetype conversion Build Rust #56: Commit ec4c935 pushed by luispedro
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NEW Transparent xz/lzma (.xz) support for input and output Build Rust #55: Commit e903826 pushed by luispedro
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NEW Syntax-highlight the NGLess script in the HTML run report Build Rust #54: Commit e222898 pushed by luispedro
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NEW Support count() annotation against a packaged reference Build Rust #53: Commit faa3846 pushed by luispedro
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NEW Collect per-position quality percentiles in FASTQ QC Build Rust #52: Commit bac3326 pushed by luispedro
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Recompress paired write() outputs in parallel under --jobs Build Rust #51: Commit de9269f pushed by luispedro
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Make file output writes atomic (temp + rename) Build Rust #50: Commit a6c21e5 pushed by luispedro
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Fix function_casts_as_integer warning in signal handler setup Build Rust #49: Commit b1383ed pushed by luispedro
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NEW Port collect() --subsample .subsample ofile suffix Build Rust #48: Commit 8cc1399 pushed by luispedro
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NEW Port remaining Transform.hs passes: addCountsCheck, qcInPreproces… Build Rust #47: Commit 9936905 pushed by luispedro
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NEW Port addRSChecks: verify preprocess input readset files early Build Rust #46: Commit c0610f3 pushed by luispedro
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NEW Support auto_comments=[{date}] in write() and collect() Build Rust #45: Commit b9ac4e6 pushed by luispedro
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Support attached-value and clustered short options Build Rust #44: Commit 89a3b4b pushed by luispedro
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NEW Port addIndexChecks: constant out-of-bounds index fails early Build Rust #43: Commit 85cd8ca pushed by luispedro
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NEW samtools_sort emits BAM directly when result feeds only a BAM write Build Rust #42: Commit aae2c03 pushed by luispedro
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NEW Defer collect() partial-result guidance to end of run Build Rust #41: Commit ce80f29 pushed by luispedro
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DOC Fix stale migration/parity notes Build Rust #40: Commit 706746d pushed by luispedro
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NEW count() errors early on ambiguous annotation sources Build Rust #39: Commit ca24003 pushed by luispedro
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NEW Mock motus/soap modules abort with guidance errors Build Rust #38: Commit 7a3715a pushed by luispedro
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DOC Fix stale references in CLAUDE.md Build Rust #37: Commit 1dc6c3e pushed by luispedro
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NEW Recover terminal progress bars for downloads and bwa mapping Build Rust #36: Commit 508706f pushed by luispedro
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NEW Recover terminal progress bars for downloads and bwa mapping Build Rust #35: Commit e28a7c9 pushed by luispedro
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TST Test on all branches Build Rust #34: Commit 39c1d0d pushed by luispedro
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