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wdecoster / cramino

A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
MIT License
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Always filter out secondary alignments, always remove soft clipped bases #30

Closed fellen31 closed 4 months ago

fellen31 commented 4 months ago

If secondary alignments are filtered out without --ubam they should also be filtered out with --ubam.

Unaligned reads should never have any soft clipped bases, and since softclipped_bases(&read) should always be 0 for these, it can always be removed.

Potentially closes #29

wdecoster commented 4 months ago

Okay, I think you are right :)