GroupReadsByUmi may fail when marking duplicates including secondary/supplementary reads #964
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## main #964 +/- ##
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nh13
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msto
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nh13
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| @@ -208,21 +208,31 @@ case class Cigar(elems: IndexedSeq[CigarElem]) extends Iterable[CigarElem] { | |||
| def trailingSoftClippedBases: Int = stats.trailingSoftClippedBases | |||
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| /** Returns the number of bases that are hard-clipped at the start of the sequence. */ | |||
| def leadingHardClippedBases = this.headOption.map { elem => | |||
| def leadingHardClippedBases: Int = this.headOption.map { elem => | |||
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public defs should have return types here and below
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…nd supplementary reads Secondary and supplementary reads must use the coordinates of the primary alignments within the template, otherwise they will not guaranteed to be next the primary alignments in the file. Therefore, we've added the "rp" and "mp" tags to store the SA-tag equivalent information for the primary alignment. This keeps information about the primary alignments with the secondary and supplementary alignments.
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There's an open issue in hts-specs about how we want to handle getting the primary alignment information when looking at a secondary or supplementary read: samtools/hts-specs#755
This PR adds the read primary "rp" tag to store the primary alignment for end of the current secondary/supplementary alignment, in the same format as the "SA" tag. The mate's primary alignment is stored in the "mp" tag. Both are currently lowercase as they are not reserved tags.
I have tested that
ZipperBamswill now add these, thatSortBamwill correctly sort in template-coordinate, and finally thatGroupReadsByUmipasses. I added tests forGroupReadsByUmiandSamOrder.Also, in my hands, secondary and supplementary records will never be output by
GroupReadsByUmias currently only primary alignments are output.