Open nh13 opened 7 months ago
Attention: 2 lines
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Comparison is base (
371db03
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) 95.64%.
Files | Patch % | Lines |
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src/main/scala/com/fulcrumgenomics/bam/Bams.scala | 90.00% | 2 Missing :warning: |
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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: https://github.com/samtools/hts-specs/issues/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
ZipperBams
will now add these, thatSortBam
will correctly sort in template-coordinate, and finally thatGroupReadsByUmi
passes. I added tests forGroupReadsByUmi
andSamOrder
.Also, in my hands, secondary and supplementary records will never be output by
GroupReadsByUmi
as currently only primary alignments are output.