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gatk MarkDuplicates crashes if the BAM file has no reads #715

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terrycojones opened this issue Feb 25, 2020 · 0 comments
Open

gatk MarkDuplicates crashes if the BAM file has no reads #715

terrycojones opened this issue Feb 25, 2020 · 0 comments

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@terrycojones
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You get 400 million lines of Java spewed on stderr, and if you dig through it you find the obscure single line saying "empty collection". Blerg.

markDuplicatesGATK in dark/bowtie2.py should catch this and just copy its input file to its output.
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@terrycojones