Propagate read negative flag to SAM records for unmapped reads

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

@@ -290,6 +290,10 @@ class AlignmentRecordConverter extends Serializable {
  .foreach(m => {
  builder.setReadUnmappedFlag(!m.booleanValue)
 
+ // Sometimes aligners like BWA-MEM mark a read as negative even if it's not mapped
+ Option(adamRecord.getReadNegativeStrand)
+ .foreach(v => builder.setReadNegativeStrandFlag(v.booleanValue))
+
  // only set alignment flags if read is aligned
  if (m) {
  // if we are aligned, we must have a reference
@@ -301,8 +305,6 @@ class AlignmentRecordConverter extends Serializable {
  // set the old cigar, if provided
  Option(adamRecord.getOldCigar).foreach(v => builder.setAttribute("OC", v))
  // set mapping flags
- Option(adamRecord.getReadNegativeStrand)
- .foreach(v => builder.setReadNegativeStrandFlag(v.booleanValue))
  Option(adamRecord.getPrimaryAlignment)
  .foreach(v => builder.setNotPrimaryAlignmentFlag(!v.booleanValue))
  Option(adamRecord.getSupplementaryAlignment)

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

@@ -326,5 +326,15 @@ class AlignmentRecordConverterSuite extends FunSuite {
  assert(read.getQual === "?????*****")
  assert(read.getContigName === "1")
  }
+
+ test("read negative strand is propagated even when not mapped") {
+ val record = AlignmentRecord.newBuilder()
+ .setReadMapped(false)
+ .setReadNegativeStrand(true)
+ .build()
+ val fragment = Fragment.newBuilder().setAlignments(List(record)).build()
+ val converted = adamRecordConverter.convertFragment(fragment)
+ assert(converted.head.getReadNegativeStrand)
+ }
 }