bamCompare: keep bin coordinates after a --skipZeroOverZero gap - #1449
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bamCompare: keep bin coordinates after a --skipZeroOverZero gap#1449cindykrafft wants to merge 1 commit into
cindykrafft wants to merge 1 commit into
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writeBedGraph_worker derives the coordinates of every written interval from the end of the previous one, so a bin skipped by --skipZeroOverZero shifted all following intervals of the chunk one bin to the left (issues deeptools#1108, deeptools#1130). Flush the current run and restart from the next bin's own coordinate, as the bigWig-input implementation (writeBedGraph_bam_and_bw) already does. Found in a source-level correctness audit of research software (methods and harnesses: https://github.com/cindykrafft/research-software-audit/tree/main/audits/deeptools)
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bamCompare --skipZeroOverZerohas incorrect coordinates #1108 andbamCompare --skipZeroOverZerobugged #1130CHANGES.txtbullet onlywriteBedGraph_workerderives the coordinates of every written interval from the end of the previous one, so a bin skipped by--skipZeroOverZeroshifted all following intervals of the chunk one bin to the left, and a skipped bin between two equal values was merged into the run (#1108, #1130). The bigWig-input loop inwriteBedGraph_bam_and_bw.pyalready resets on the skip; this makes the BAM loop do the same (flush the current run, restart from the next bin's own coordinate).writeStart/writeEndare initialised before the loop.Test:
test_bam_compare_ZoverZ_interior_binsruns--operation first --skipZeroOverZeroontest_filtering.bam(a gap between positions 57 and 78, 10-bp bins) and compares with the bamCoverage track of the same file with its zero bins removed; fails onmaster(1 failed), passes with the patch.test_bamCoverage_and_bamCompare.py+ the multiBigwigSummary and countReadsPerBin modules: 54 passed; full suite 100 passed, 1 pre-existing failure (test_plotCoverage_default, also on unmodifiedmaster);flake8with the project's options clean.Found in a source-level correctness audit of research software (methods and harnesses: https://github.com/cindykrafft/research-software-audit/tree/main/audits/deeptools)
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