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

Fixes: #951

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

@@ -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)
+      supp("ms")  = primary[Int]("AS")
     }
     for (primary <- r2; supp <- r1Supplementals) {
       SamPairUtil.setMateInformationOnSupplementalAlignment(supp.asSam, primary.asSam, true)
+      supp("ms")  = primary[Int]("AS")
     }
     for (first <- r1; second <- r2) {
       SamPairUtil.setMateInfo(first.asSam, second.asSam, true)
+      first("ms")  = second[Int]("AS")
+      second("ms") = first[Int]("AS")
     }
   }