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tools.bwa.filter_sam_on_alignment_score is a memory hog #21

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dpark01 opened this issue May 7, 2020 · 0 comments
Open

tools.bwa.filter_sam_on_alignment_score is a memory hog #21

dpark01 opened this issue May 7, 2020 · 0 comments

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@dpark01
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dpark01 commented May 7, 2020

tools.bwa.filter_sam_on_alignment_score populates a python dict for every read ID it sees on input. This means that simple tasks like spike-in counting on a >10-100M read bam file will fail on a 7GB RAM machine. Ideally convert to an O(1) implementation if possible, or, failing that, convert to a sqlite disk-backed solution.

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