From 4543ece0889cc07acc9d2a9cbefda7882ae340ef Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 27 Nov 2012 11:00:33 -0500
Subject: [PATCH] Fixing parsing of genomelocs that contain colons in the
 contig names (which is allowed by the spec) as reported on the forum.  Added
 unit test for this case.

---
 .../sting/utils/GenomeLocParser.java          |  2 +-
 .../sting/utils/GenomeLocParserUnitTest.java  | 21 ++++++++++++++++++-
 2 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index a3ffe708c..bf60b4a80 100644
--- a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -374,7 +374,7 @@ public final class GenomeLocParser {
         int start = 1;
         int stop = -1;
 
-        final int colonIndex = str.indexOf(":");
+        final int colonIndex = str.lastIndexOf(":");
         if(colonIndex == -1) {
             contig = str.substring(0, str.length());  // chr1
             stop = Integer.MAX_VALUE;
diff --git a/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java
index e9f138a0e..e4313b30a 100644
--- a/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java
@@ -2,6 +2,8 @@ package org.broadinstitute.sting.utils;
 
 
 import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMSequenceDictionary;
+import net.sf.samtools.SAMSequenceRecord;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -74,6 +76,23 @@ public class GenomeLocParserUnitTest extends BaseTest {
         genomeLocParser.parseGenomeLoc("Bad:0-1");
     }
 
+    @Test
+    public void testContigHasColon() {
+        SAMFileHeader header = new SAMFileHeader();
+        header.setSortOrder(net.sf.samtools.SAMFileHeader.SortOrder.coordinate);
+        SAMSequenceDictionary dict = new SAMSequenceDictionary();
+        SAMSequenceRecord rec = new SAMSequenceRecord("c:h:r1", 10);
+        rec.setSequenceLength(10);
+        dict.addSequence(rec);
+        header.setSequenceDictionary(dict);
+
+        final GenomeLocParser myGenomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
+        GenomeLoc loc = myGenomeLocParser.parseGenomeLoc("c:h:r1:4-5");
+        assertEquals(0, loc.getContigIndex());
+        assertEquals(loc.getStart(), 4);
+        assertEquals(loc.getStop(), 5);
+    }
+
     @Test
     public void testParseGoodString() {
         GenomeLoc loc = genomeLocParser.parseGenomeLoc("chr1:1-10");
@@ -81,7 +100,7 @@ public class GenomeLocParserUnitTest extends BaseTest {
         assertEquals(loc.getStop(), 10);
         assertEquals(loc.getStart(), 1);
     }
-    
+
     @Test
     public void testCreateGenomeLoc1() {
         GenomeLoc loc = genomeLocParser.createGenomeLoc("chr1", 1, 100);