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Update src/main/scala/com/fulcrumgenomics/bam/Bams.scala
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src/main/scala/com/fulcrumgenomics/bam/Bams.scala

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@@ -110,16 +110,16 @@ case class Template(r1: Option[SamRecord],
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// Developer note: the mate score ("ms") tag is used by samtools markdup
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for (primary <- r1; supp <- r2Supplementals) {
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SamPairUtil.setMateInformationOnSupplementalAlignment(supp.asSam, primary.asSam, true)
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primary.get[Int]("AS").foreach(supp("ms") = _))
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primary.get[Int]("AS").foreach(supp("ms") = _)
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}
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for (primary <- r2; supp <- r1Supplementals) {
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SamPairUtil.setMateInformationOnSupplementalAlignment(supp.asSam, primary.asSam, true)
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primary.get[Int]("AS").foreach(supp("ms") = _))
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primary.get[Int]("AS").foreach(supp("ms") = _)
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}
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for (first <- r1; second <- r2) {
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SamPairUtil.setMateInfo(first.asSam, second.asSam, true)
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first.get[Int]("AS").foreach(second("ms") = _))
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second.get[Int]("AS").foreach(first("ms") = _))
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first.get[Int]("AS").foreach(second("ms") = _)
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second.get[Int]("AS").foreach(first("ms") = _)
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}
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}
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