From ff91ab8ba21992799eb6a6b3f8b333f570d7afe8 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 1 Sep 2014 12:53:37 -0400
Subject: [PATCH] Make sure that the OverhangFixingManager (used for splitting
 RNA reads) handles unmapped reads.

---
 .../walkers/rnaseq/OverhangFixingManager.java  |  5 +++--
 .../tools/walkers/rnaseq/SplitNCigarReads.java |  2 --
 .../rnaseq/OverhangFixingManagerUnitTest.java  | 18 ++++++++++++++++++
 3 files changed, 21 insertions(+), 4 deletions(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java
index a340a62b8..4f325684e 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java
@@ -232,7 +232,7 @@ public class OverhangFixingManager {
      */
     private void fixSplit(final SplitRead read, final Splice splice) {
         // if the read doesn't even overlap the split position then we can just exit
-        if ( !splice.loc.overlapsP(read.loc) )
+        if ( read.loc == null || !splice.loc.overlapsP(read.loc) )
             return;
 
         if ( isLeftOverhang(read.loc, splice.loc) ) {
@@ -326,7 +326,8 @@ public class OverhangFixingManager {
         public void setRead(final GATKSAMRecord read) {
             if ( !read.isEmpty() ) {
                 this.read = read;
-                loc = genomeLocParser.createGenomeLoc(read.getReferenceName(), read.getSoftStart(), read.getSoftEnd());
+                if ( ! read.getReadUnmappedFlag() )
+                    loc = genomeLocParser.createGenomeLoc(read.getReferenceName(), read.getSoftStart(), read.getSoftEnd());
             }
         }
     }
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java
index 9e77340e2..ea00a93a9 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java
@@ -161,8 +161,6 @@ public class SplitNCigarReads extends ReadWalker<GATKSAMRecord, OverhangFixingMa
         catch (FileNotFoundException ex) {
             throw new UserException.CouldNotReadInputFile(toolkit.getArguments().referenceFile, ex);
         }
-
-
     }
 
     @Override
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java
index c1a6a190c..bb20d61dd 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java
@@ -50,6 +50,8 @@ import org.broadinstitute.gatk.utils.BaseTest;
 import org.broadinstitute.gatk.utils.GenomeLoc;
 import org.broadinstitute.gatk.utils.GenomeLocParser;
 import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
@@ -169,4 +171,20 @@ public class OverhangFixingManagerUnitTest extends BaseTest {
         final OverhangFixingManager manager = new OverhangFixingManager(null, genomeLocParser, referenceReader, 10000, 1, 40, false);
         Assert.assertEquals(manager.overhangingBasesMismatch(read, readStart, ref, refStart, overhang), expected, new String(read) + " vs. " + new String(ref) + " @" + overhang);
     }
+
+    @Test
+    public void testUnmappedReadsDoNotFail() {
+        // create an unmapped read
+        final GATKSAMRecord read = new GATKSAMRecord(ArtificialSAMUtils.createArtificialSamHeader());
+        read.setReadName("foo");
+        read.setReferenceName("*");
+        read.setAlignmentStart(100);
+        read.setCigarString("*");
+        read.setReadUnmappedFlag(true);
+
+        // try to add it to the manager
+        final OverhangFixingManager manager = new OverhangFixingManager(null, null, null, 100, 1, 30, false);
+        manager.addRead(read); // we just want to make sure that the following call does not fail
+        Assert.assertTrue(true);
+    }
 }