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-5 option bitwise flag #20

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wbrandler opened this issue Dec 6, 2018 · 0 comments

wbrandler commented Dec 6, 2018 •

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What is the bitwise flag for -5 option for bwamem? Also is there any documentation on this new flag?

I can't find it here:

https://github.com/broadinstitute/gatk-bwamem-jni/blob/master/src/main/java/org/broadinstitute/hellbender/utils/bwa/BwaMemAligner.java#L75-L86

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