From 5934b9cb82ecd905992ec0e765a177234c54100a Mon Sep 17 00:00:00 2001
From: scalvo <scalvo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 28 Jan 2011 22:45:45 +0000
Subject: [PATCH] Augment function isChrM by allowing "CRS" in addition to
 "chrM" or "MT", as a standard contig name indicating the mitochondrial
 chromosome.  CRS stands for Cambridge Reference Sequence and is the standard
 in the field.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5119 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../annotator/genomicannotator/TranscriptToGenomicInfo.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java
index fe6b2c012..c1b0440da 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java
@@ -294,7 +294,7 @@ public class TranscriptToGenomicInfo extends RodWalker<Integer, Integer> {
     }
 
     private static boolean isChrM(final TranscriptTableRecord record) {
-        return record.txChrom.equals("chrM") || record.txChrom.equals("MT");
+        return record.txChrom.equals("chrM") || record.txChrom.equals("MT")|| record.txChrom.equals("CRS");
     }
     
     private void generateOutputRecordsForROD(TranscriptTableRecord parsedTranscriptRod) throws IOException {