From 165b936fcd6160bfd82da79c36ef2e32765006fd Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 24 Jun 2013 14:06:21 -0400
Subject: [PATCH] Fixing the 'header is negative' problem in Reduce Reads...
 again.

Previous fixes and tests only covered trailing soft-clips.  Now that up front
hard-clipping is working properly though, we were failing on those in the tool.

Added a patch for this as well as a separate test independent of the soft-clips
to make sure that it's working properly.
---
 .../reducereads/SlidingWindowUnitTest.java      | 17 +++++++++++++++--
 .../sting/utils/sam/ReadUtils.java              |  6 +++---
 2 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
index c9bb2f084..bf45fc298 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
@@ -94,7 +94,7 @@ public class SlidingWindowUnitTest extends BaseTest {
     //////////////////////////////////////////////////////////////////////////////////////
 
     @Test(enabled = true)
-    public void testLeadingClipThenInsertion() {
+    public void testLeadingSoftClipThenInsertion() {
 
         final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 1, 10);
         read.setReadBases(Utils.dupBytes((byte) 'A', 10));
@@ -104,8 +104,21 @@ public class SlidingWindowUnitTest extends BaseTest {
 
         final SlidingWindow slidingWindow = new SlidingWindow("1", 0, 1);
         slidingWindow.addRead(read);
-        Pair<ObjectSet<GATKSAMRecord>, CompressionStash> result = slidingWindow.close(null);
+        slidingWindow.close(null);
+    }
 
+    @Test(enabled = true)
+    public void testLeadingHardClipThenInsertion() {
+
+        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 1, 8);
+        read.setReadBases(Utils.dupBytes((byte) 'A', 8));
+        read.setBaseQualities(Utils.dupBytes((byte)30, 8));
+        read.setMappingQuality(30);
+        read.setCigarString("2H2I6M");
+
+        final SlidingWindow slidingWindow = new SlidingWindow("1", 0, 10, header, new GATKSAMReadGroupRecord("test"), 0, 0.05, 0.05, 0.05, 20, 20, 100, ReduceReads.DownsampleStrategy.Normal, false);
+        slidingWindow.addRead(read);
+        slidingWindow.close(null);
     }
 
     //////////////////////////////////////////////////////////////////////////////////////
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index cf1c9cb8e..f9393cc4b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -613,15 +613,15 @@ public class ReadUtils {
      * Checks if a read starts with an insertion.
      *
      * @param cigarForRead    the CIGAR to evaluate
-     * @param ignoreClipOps   should we ignore S and H operators when evaluating whether an I operator is at the beginning?
+     * @param ignoreSoftClipOps   should we ignore S operators when evaluating whether an I operator is at the beginning?  Note that H operators are always ignored.
      * @return the element if it's a leading insertion or null otherwise
      */
-    public static CigarElement readStartsWithInsertion(final Cigar cigarForRead, final boolean ignoreClipOps) {
+    public static CigarElement readStartsWithInsertion(final Cigar cigarForRead, final boolean ignoreSoftClipOps) {
         for ( final CigarElement cigarElement : cigarForRead.getCigarElements() ) {
             if ( cigarElement.getOperator() == CigarOperator.INSERTION )
                 return cigarElement;
 
-            else if ( !ignoreClipOps || (cigarElement.getOperator() != CigarOperator.HARD_CLIP && cigarElement.getOperator() != CigarOperator.SOFT_CLIP) )
+            else if ( cigarElement.getOperator() != CigarOperator.HARD_CLIP && ( !ignoreSoftClipOps || cigarElement.getOperator() != CigarOperator.SOFT_CLIP) )
                 break;
         }
         return null;