Should FASTQ output use reads' "original qualities"? #436

ryan-williams opened this Issue Oct 26, 2014 · 1 comment


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ryan-williams commented Oct 26, 2014

AlignmentRecordConverter.convertToFastq currently outputs getQual as the FASTQ qualities; should it instead output getOrigQual? I'm not super familiar with the difference between read qualities and "original qualities" but I am having a hard time imagining that "original qualities" would not be the thing that was originally found in the FASTQ data the reads originated from.

I have this change ready, lmk if it seems reasonable.


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fnothaft Mar 25, 2016


I think this was resolved by 322c32f.


fnothaft commented Mar 25, 2016

I think this was resolved by 322c32f.

@fnothaft fnothaft closed this Mar 25, 2016

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