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

fulcrumgenomics · Dec 27, 2023 · 7e33b82 · 7e33b82
1 parent 6aa20ab
commit 7e33b82
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/src/main/scala/com/fulcrumgenomics/bam/Bams.scala b/src/main/scala/com/fulcrumgenomics/bam/Bams.scala
@@ -110,16 +110,16 @@ case class Template(r1: Option[SamRecord],
     // Developer note: the mate score ("ms") tag is used by samtools markdup
     for (primary <- r1; supp <- r2Supplementals) {
       SamPairUtil.setMateInformationOnSupplementalAlignment(supp.asSam, primary.asSam, true)
-      supp("ms")  = primary[Int]("AS")
+      primary.get[Int]("AS").foreach(supp("ms") = _))
     }
     for (primary <- r2; supp <- r1Supplementals) {
       SamPairUtil.setMateInformationOnSupplementalAlignment(supp.asSam, primary.asSam, true)
-      supp("ms")  = primary[Int]("AS")
+      primary.get[Int]("AS").foreach(supp("ms") = _))
     }
     for (first <- r1; second <- r2) {
       SamPairUtil.setMateInfo(first.asSam, second.asSam, true)
-      first("ms")  = second[Int]("AS")
-      second("ms") = first[Int]("AS")
+      first.get[Int]("AS").foreach(second("ms") = _))
+      second.get[Int]("AS").foreach(first("ms") = _))
     }
   }