bamCoverage --MNase: three centre bases for odd fragment lengths - #1466
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bamCoverage --MNase: three centre bases for odd fragment lengths#1466cindykrafft wants to merge 1 commit into
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manipulate_record returned frag_start..frag_start + 4 for an odd template length, i.e. four bases -- one left and two right of the fragment centre -- where the --MNase help documents "only 3 nucleotides at the center of each fragment" (deeptools#1118; the Python implementation had the same defect through true division of read.tlen). Even lengths are unchanged. Tests: cargo tests on synthetic proper-pair records of insert size 150, 149 and 131; a pytest on the shipped test_paired2.bam (147-bp pairs give 3 bases, 166/154-bp pairs give 2). Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TaHntBDKuZJpMAAMenkC44
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CHANGES.txtbullet onlyAlignmentfilters::manipulate_record(src/filtering.rs) returnedfrag_start..frag_start + 4for an odd template length: four bases, one left and two right of the fragment centre, where the--MNasehelp documents "only 3 nucleotides at the center of each fragment" (#1118; the Python implementation had the same four bases through true division ofread.tlen).+ 3restores the documented three; even lengths are unchanged.Tests: two cargo tests in
src/tests/test_filtering.rson synthetic proper-pair records (insert sizes 150 →[174, 175]; 149 →[173, 174, 175]; 131 →[1064, 1065, 1066]), andtest_bam_coverage_MNase_odd_fragment_lengthon the shippedtest_paired2.bam(147-bp pairs give 3 bases, 166/154-bp pairs give 2). The cargo test fails onmaster(left: Some([173, 174, 175, 176])), the pytest fails on themasterbuild; with the patchcargo test50 passed,test_bamCoverage_and_bamCompare.pyand the full pytest suite pass.Found in Mytochondria, a volunteer project that checks the numerical core of research software and verifies every finding by execution (methods and harnesses: https://github.com/cindykrafft/mytochondria/tree/main/audits/deeptools)
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