support P operator parsing in md tag

bigdatagenomics · Oct 31, 2015 · bc38a1c · bc38a1c
1 parent 5175c2f
commit bc38a1c
Show file tree

Hide file tree

Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/util/MdTag.scala b/adam-core/src/main/scala/org/bdgenomics/adam/util/MdTag.scala
@@ -158,9 +158,8 @@ object MdTag {
             cigarIdx += 1
             cigarOperatorIndex = 0
 
-          case (CigarOperator.INSERTION | CigarOperator.H | CigarOperator.S, _) =>
+          case (CigarOperator.INSERTION | CigarOperator.H | CigarOperator.S | CigarOperator.P, _) =>
             cigarIdx += 1
-
         }
       }
       new MdTag(referenceStart, matches, mismatches, deletions)

diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/util/MdTagSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/util/MdTagSuite.scala
@@ -226,6 +226,13 @@ class MdTagSuite extends FunSuite {
     assert(tag.toString === "20")
   }
 
+  test("CIGAR with P operators") {
+    val tag = MdTag("8", 0L, TextCigarCodec.decode("4=1P4="))
+    assert(tag.toString === "8")
+    (0 until 8).foreach(locus => assert(tag.isMatch(locus)))
+
+  }
+
   test("Get correct matches for mdtag with insertion") {
     val tag = MdTag("10", 0L, TextCigarCodec.decode("5M3I5M"))
     assert(tag.end === 9)