Add samtools-compatible outputs, TIN analysis, and gene body coverage#17

Merged

ewels merged 21 commits into

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samtools-tin-genebody

Feb 16, 2026

Commits on Feb 16, 2026

Fix preseq PE fragment key bug and remove compat mode
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Fix review bugs: TIN u8 overflow, genebody exonic counting, Qualimap secondary
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Add documentation for preseq, TIN, gene body coverage, and samtools tools
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perf: optimize hot-path allocations for 27% overall speedup
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perf: avoid per-read allocations in sequence hashing and chrom prefix lookup
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docs: move TIN and gene body coverage benchmarks to RSeQC page
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Update benchmark script and SVG charts to include all tools
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fix: address code review findings across TIN, genebody, stats, and shared utilities
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refactor: move upstream reference outputs from benchmark/expected/ to benchmark/input/large/
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refactor: organize RSeQC benchmark images into tool subdirectories
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refactor: organize upstream RSeQC reference outputs into tool subdirectories
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fix: populate TIN reference summary with actual upstream tin.py values
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refactor: update benchmark script and docs to use per-tool RSeQC subdirectories
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Add upstream samtools, preseq, and Qualimap reference outputs
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Add TODO for generating large Qualimap reference output
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Revert "Add TODO for generating large Qualimap reference output"
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