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validate correctGCBias produced BAM files #248

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dpryan79 opened this issue Jan 27, 2016 · 2 comments
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validate correctGCBias produced BAM files #248

dpryan79 opened this issue Jan 27, 2016 · 2 comments
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@dpryan79
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This is basically a note to remind me to look sometime at the BAM files produced by correctGCBias. Since it's not playing around with the flags, they should pass htsjdk's rather absurd validator as long as the input file does as well. However, this may not always be the case and it's actually quite simple to just munge the flags such that they're valid (or at least produce a little warning that the BAM file is valid, but IGV/Picard/GATK/etc. will possibly bork). Cf. https://groups.google.com/forum/#!topic/deeptools/2gufhgs2YBQ

@dpryan79 dpryan79 self-assigned this Jan 27, 2016
@dpryan79
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It looks like correctGCBias is also adding invalid auxiliary tags (CO:f, GC:i) and misusing some legit ones (CP:i). This should be corrected at the same time.

@dpryan79
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This should be fixed by #253

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