Stores original position and original cigar during realignment.

adam-core/src/main/scala/org/bdgenomics/adam/converters/AlignmentRecordConverter.scala

@@ -115,7 +115,8 @@ class AlignmentRecordConverter extends Serializable {
 
           // set the cigar, if provided
           Option(adamRecord.getCigar).map(_.toString).foreach(builder.setCigarString)
-
+          // set the old cigar, if provided
+          Option(adamRecord.getOldCigar).map(_.toString).foreach(v => builder.setAttribute("OC", v))
           // set mapping flags
           Option(adamRecord.getReadNegativeStrand)
             .foreach(v => builder.setReadNegativeStrandFlag(v.booleanValue))
@@ -125,6 +126,8 @@ class AlignmentRecordConverter extends Serializable {
             .foreach(v => builder.setSupplementaryAlignmentFlag(v.booleanValue))
           Option(adamRecord.getStart)
             .foreach(s => builder.setAlignmentStart(s.toInt + 1))
+          Option(adamRecord.getOldPosition)
+            .foreach(s => builder.setAttribute("OP", s.toInt + 1))
           Option(adamRecord.getMapq).foreach(v => builder.setMappingQuality(v))
         } else {
           // mapping quality must be 0 if read is unmapped

adam-core/src/main/scala/org/bdgenomics/adam/converters/SAMRecordConverter.scala

@@ -66,6 +66,12 @@ class SAMRecordConverter extends Serializable {
       assert(start != 0, "Start cannot equal 0 if contig is set.")
       builder.setStart((start - 1).asInstanceOf[Long])
 
+      // set OP and OC flags, if applicable
+      if (samRecord.getAttribute("OP") != null) {
+        builder.setOldPosition(samRecord.getIntegerAttribute("OP").toLong - 1)
+        builder.setOldCigar(samRecord.getStringAttribute("OC"))
+      }
+
       val end = samRecord.getCigar.getCigarElements
         .asScala
         .filter((p: CigarElement) => p.getOperator.consumesReferenceBases())

adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndels.scala

@@ -357,6 +357,8 @@ private[rdd] class RealignIndels(val consensusModel: ConsensusGenerator = new Co
 
               // update mdtag and cigar
               builder.setMismatchingPositions(MdTag.moveAlignment(r, newCigar, reference.drop(remapping), refStart + remapping).toString())
+              builder.setOldPosition(r.getStart())
+              builder.setOldCigar(r.getCigar())
               builder.setCigar(newCigar.toString)
               new RichAlignmentRecord(builder.build())
             } else

adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala

@@ -43,6 +43,8 @@ class AlignmentRecordConverterSuite extends FunSuite {
       .setMapq(60)
       .setQual(sequence) // no typo, we just don't care
       .setMismatchingPositions(mdtag)
+      .setOldPosition(12)
+      .setOldCigar("2^AAA3")
       .build()
   }
 
@@ -82,6 +84,8 @@ class AlignmentRecordConverterSuite extends FunSuite {
     assert(toSAM.getMappingQuality === 60)
     assert(toSAM.getBaseQualityString === sequence)
     assert(toSAM.getAttribute("MD") === "2^AAA2")
+    assert(toSAM.getIntegerAttribute("OP") === 13)
+    assert(toSAM.getStringAttribute("OC") === "2^AAA3")
   }
 
   test("convert a read to fastq") {

adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndelsSuite.scala

@@ -254,4 +254,18 @@ class RealignIndelsSuite extends SparkFunSuite {
     // this should be a NOP
     assert(RealignIndels(reads).count === 4)
   }
+
+  sparkTest("test OP and OC tags") {
+    artificial_realigned_reads.collect().foreach(realn => {
+      val readName = realn.getReadName()
+      val op = realn.getOldPosition()
+      val oc = realn.getOldCigar()
+
+      Option(op).filter(_ >= 0).foreach(oPos => {
+        val s = artificial_reads.collect().filter(x => (x.getReadName() == readName))
+        assert(s.filter(x => (x.getStart() == oPos)).length > 0)
+        assert(s.filter(x => (x.getCigar() == oc)).length > 0)
+      })
+    })
+  }
 }

pom.xml

@@ -305,7 +305,7 @@
       <dependency>
         <groupId>org.bdgenomics.bdg-formats</groupId>
         <artifactId>bdg-formats</artifactId>
-        <version>0.3.1</version>
+        <version>0.3.2</version>
       </dependency>
       <dependency>
         <groupId>commons-io</groupId>