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ZipperBams to produce mate score ("ms") for samtools markdup #952

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merged 4 commits into from
Feb 9, 2024
Merged

ZipperBams to produce mate score ("ms") for samtools markdup #952

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6aa20ab
ZipperBams to produce mate score ("ms") for samtools markdup
nh13 Dec 18, 2023
7e33b82
Update src/main/scala/com/fulcrumgenomics/bam/Bams.scala
nh13 Dec 27, 2023
2affbac
Update src/main/scala/com/fulcrumgenomics/bam/Bams.scala
nh13 Dec 27, 2023
87e8288
add to the unit test a read with ms
nh13 Feb 9, 2024
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7 changes: 6 additions & 1 deletion src/main/scala/com/fulcrumgenomics/bam/Bams.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -105,16 +105,21 @@ case class Template(r1: Option[SamRecord],
Template(x1, x2)
}

/** Fixes mate information and sets mate cigar on all primary and supplementary (but not secondary) records. */
/** Fixes mate information and sets mate cigar and mate score on all primary and supplementary (but not secondary) records. */
def fixMateInfo(): Unit = {
// Developer note: the mate score ("ms") tag is used by samtools markdup
for (primary <- r1; supp <- r2Supplementals) {
SamPairUtil.setMateInformationOnSupplementalAlignment(supp.asSam, primary.asSam, true)
primary.get[Int]("AS").foreach(supp("ms") = _)
}
for (primary <- r2; supp <- r1Supplementals) {
SamPairUtil.setMateInformationOnSupplementalAlignment(supp.asSam, primary.asSam, true)
primary.get[Int]("AS").foreach(supp("ms") = _)
}
for (first <- r1; second <- r2) {
SamPairUtil.setMateInfo(first.asSam, second.asSam, true)
first.get[Int]("AS").foreach(second("ms") = _)
second.get[Int]("AS").foreach(first("ms") = _)
}
}

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