From 2bc69572cbea8e52646bac637612eefdbced4340 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 2 Aug 2010 17:32:08 +0000
Subject: [PATCH] Make transcript2info capable of handling b37/hg19 contigs

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3915 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/annotator/TranscriptToInfo.java           | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java
index 4dddcb240..4518b33d0 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java
@@ -916,6 +916,7 @@ public class TranscriptToInfo extends RodWalker<TreeMap<String, String>, TreeMap
         final char lastChromChar = txChrom.charAt(txChrom.length() -1);
         switch( Character.toLowerCase(lastChromChar) ) {
         case 'm':
+        case 't': // for hg19 or b36
             key = 0;
             break;
         case 'x':
@@ -925,7 +926,11 @@ public class TranscriptToInfo extends RodWalker<TreeMap<String, String>, TreeMap
             key = 24;
             break;
         default:
-            key = Integer.parseInt(txChrom.substring(3));
+	    if( txChrom.startsWith("chr") ) {
+		key = Integer.parseInt(txChrom.substring(3));
+	    } else {
+		key = Integer.parseInt(txChrom);
+	    }
             break;
         }