Always filter out secondary alignments, always remove soft clipped bases #30
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…ases removed with --ubam
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Okay, I think you are right :) |
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If secondary alignments are filtered out without
--ubamthey 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