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src/main/scala/com/fulcrumgenomics/bam
1 file changed +4
-4
lines changed Original file line number Diff line number Diff line change @@ -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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