Addressing review comments.

bigdatagenomics · Mar 30, 2017 · 106da85 · 106da85
1 parent 2c868e1
commit 106da85
Showing 1 changed file with 20 additions and 19 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndels.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndels.scala
@@ -410,31 +410,32 @@ private[read] class RealignIndels(
                       finalRemapping,
                       bestConsensus)
 
-                    builder.setStart(newStart)
-                      .setEnd(newEnd)
-                      .setCigar(newCigar.toString)
-
-                    // update mdtag and cigar
-                    val newMdTag = MdTag.moveAlignment(r,
-                      newCigar,
-                      reference.drop((newStart - refStart).toInt),
-                      newStart).toString()
-                    builder.setMismatchingPositions(newMdTag)
-                    builder.setOldPosition(r.getStart())
-                    builder.setOldCigar(r.getCigar())
-                    val rec = builder.build()
-                    if (r.getReadName == "H06JUADXX130110:1:1108:12070:36897") {
-                      log.warn("for H06JUADXX130110:1:1108:12070:36897, ended with: %s".format(rec))
+                    if (newEnd <= newStart) {
+                      log.warn("Realigning read %s failed because realignment issued an illegal alignment: start %d, end %d, CIGAR %s.".format(r, newStart, newEnd, newCigar))
+                      r
+                    } else {
+                      builder.setStart(newStart)
+                        .setEnd(newEnd)
+                        .setCigar(newCigar.toString)
+
+                      // update mdtag and cigar
+                      val newMdTag = MdTag.moveAlignment(r,
+                        newCigar,
+                        reference.drop((newStart - refStart).toInt),
+                        newStart).toString()
+                      builder.setMismatchingPositions(newMdTag)
+                      builder.setOldPosition(r.getStart())
+                      builder.setOldCigar(r.getCigar())
+                      val rec = builder.build()
+
+                      new RichAlignmentRecord(rec)
                     }
-                    new RichAlignmentRecord(rec)
                   } else {
                     r
                   }
                 } catch {
                   case t: Throwable => {
                     log.warn("Realigning read %s failed with %s. At:".format(r, t))
-                    val stack = t.getStackTrace()
-                    stack.foreach(s => log.warn(s.toString))
                     r
                   }
                 }
@@ -492,7 +493,7 @@ private[read] class RealignIndels(
    * @param remappingIdx The location in the consensus sequence where this
    *   read has been realigned.
    * @param consensus The consensus variant to realign against.
-   * @peturn Returns a tuple with the (read start, read end, cigar).
+   * @return Returns a tuple with the (read start, read end, cigar).
    */
   def cigarAndCoordinates(readLength: Int,
                           basesSoftClippedAtStart: Int,