From f82fe6589306b007dc3c829d2c38a22556ba4755 Mon Sep 17 00:00:00 2001
From: Frank Austin Nothaft <fnothaft@alumni.stanford.edu>
Date: Tue, 28 Mar 2017 23:23:43 -0700
Subject: [PATCH] End clip passes.

---
 .../rdd/read/realignment/RealignIndels.scala  |  8 +++--
 .../read/realignment/RealignIndelsSuite.scala | 29 +++++++++++++++++--
 2 files changed, 33 insertions(+), 4 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
index c773cf549d..a65af507d1 100644
--- 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
@@ -481,19 +481,23 @@ private[read] class RealignIndels(
 
                       val cigarElements = if (bestConsensus.consensus.length > 0) {
                         List[CigarElement](
+                          new CigarElement(r.getBasesTrimmedFromStart, CigarOperator.H),
                           new CigarElement(startClipped, CigarOperator.S),
                           new CigarElement((bestConsensus.index.start - (refStart + finalRemapping) + 1 - startClipped).toInt, CigarOperator.M),
                           adjustedIdElement,
                           new CigarElement(endLength.toInt - endClipped, CigarOperator.M),
-                          new CigarElement(endClipped, CigarOperator.S)
+                          new CigarElement(endClipped, CigarOperator.S),
+                          new CigarElement(r.getBasesTrimmedFromEnd, CigarOperator.H)
                         ).filter(_.getLength > 0)
                       } else {
                         List[CigarElement](
+                          new CigarElement(r.getBasesTrimmedFromStart, CigarOperator.H),
                           new CigarElement(startClipped, CigarOperator.S),
                           new CigarElement((bestConsensus.index.start - (refStart + finalRemapping)).toInt - startClipped, CigarOperator.M),
                           adjustedIdElement,
                           new CigarElement(endLength.toInt - endClipped, CigarOperator.M),
-                          new CigarElement(endClipped, CigarOperator.S)
+                          new CigarElement(endClipped, CigarOperator.S),
+                          new CigarElement(r.getBasesTrimmedFromEnd, CigarOperator.H)
                         ).filter(_.getLength > 0)
                       }
 
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndelsSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndelsSuite.scala
index 0e1d0074c8..30376f952d 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndelsSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndelsSuite.scala
@@ -459,6 +459,7 @@ class RealignIndelsSuite extends ADAMFunSuite {
     // ovs:   AGTT   CCAC
     // st:      TT   CCACA
     // sc:     agA   GGTC
+    // ec:       A   GGTCt
     val insRead = AlignmentRecord.newBuilder
       .setContigName("1")
       .setStart(10L)
@@ -525,14 +526,32 @@ class RealignIndelsSuite extends ADAMFunSuite {
       .setReadMapped(true)
       .setMapq(44)
       .build
+    val ecRead = AlignmentRecord.newBuilder
+      .setContigName("1")
+      .setStart(13L)
+      .setEnd(18L)
+      .setSequence("AGGTCA")
+      .setQual("......")
+      .setCigar("5M1S1H")
+      .setMismatchingPositions("1C0C0A1")
+      .setBasesTrimmedFromEnd(1)
+      .setReadMapped(true)
+      .setMapq(45)
+      .build
 
-    val rdd = AlignmentRecordRDD(sc.parallelize(Seq(insRead, extRead, ovlRead, ovsRead, stRead, scRead)),
+    val rdd = AlignmentRecordRDD(sc.parallelize(Seq(insRead,
+      extRead,
+      ovlRead,
+      ovsRead,
+      stRead,
+      scRead,
+      ecRead)),
       new SequenceDictionary(Vector(SequenceRecord("1", 20L))),
       RecordGroupDictionary.empty)
     val realignedReads = rdd.realignIndels(lodThreshold = 0.0)
       .rdd
       .collect
-    assert(realignedReads.count(_.getMapq >= 50) === 5)
+    assert(realignedReads.count(_.getMapq >= 50) === 6)
     val realignedExtRead = realignedReads.filter(_.getMapq == 50).head
     assert(realignedExtRead.getStart === 8L)
     assert(realignedExtRead.getEnd === 14L)
@@ -558,6 +577,12 @@ class RealignIndelsSuite extends ADAMFunSuite {
     assert(realignedScRead.getEnd === 15L)
     assert(realignedScRead.getCigar === "2S1M3I1M")
     assert(realignedScRead.getMismatchingPositions === "2")
+    val realignedEcRead = realignedReads.filter(_.getMapq == 55).head
+    assert(realignedEcRead.getStart === 13L)
+    assert(realignedEcRead.getEnd === 15L)
+    assert(realignedEcRead.getCigar === "1M3I1M1S1H")
+    assert(realignedEcRead.getMismatchingPositions === "2")
+    assert(realignedEcRead.getBasesTrimmedFromEnd === 1)
   }
 
   sparkTest("if realigning a target doesn't improve the LOD, don't drop reads") {