Replace sambamba with samtools for merge, view, flagstat in contamination analysis - #15
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nikostr wants to merge 1 commit into
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Replace sambamba with samtools for merge, view, flagstat in contamination analysis#15nikostr wants to merge 1 commit into
nikostr wants to merge 1 commit into
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This PR resolves #6. It replaces sambamba with samtools in the contamination analysis.
The only other place I see sambamba used is in the coverage calculation in the Hi-C analysis. Samtools implements coverage/depth calculations, but I'm not sure if they are one-to-one replacements for sambamba. Either way, the crashes I have experienced with sambamba do not seem to happen for the coverage calculation.