Improve handling of "*" sequences during BQSR #484

fnothaft opened this Issue Nov 17, 2014 · 1 comment


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fnothaft commented Nov 17, 2014

In SAM/BAM, the sequence and quality of a read can be set to "*" if the sequence/quality isn't stored. These reads aren't special cased during processing and cause an array out-of-bounds exception during BQSR. This issue was reported on the mailing list.

@fnothaft fnothaft added the bug label Nov 17, 2014

@fnothaft fnothaft referenced this issue in bigdatagenomics/bdg-formats Mar 1, 2015


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fnothaft commented Mar 25, 2016

I believe this was resolved by 4e30187#diff-82ce2bf869f57c75dbc357935c5d46fd.

@fnothaft fnothaft closed this Mar 25, 2016

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