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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
This commit is contained in:
chartl 2010-08-02 17:32:08 +00:00
parent c203e0fb02
commit 2bc69572cb
1 changed files with 6 additions and 1 deletions
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5
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java
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@ -916,6 +916,7 @@ public class TranscriptToInfo extends RodWalker<TreeMap<String, String>, TreeMap
final char lastChromChar = txChrom.charAt(txChrom.length() -1); final char lastChromChar = txChrom.charAt(txChrom.length() -1);
switch( Character.toLowerCase(lastChromChar) ) { switch( Character.toLowerCase(lastChromChar) ) {
case 'm': case 'm':
case 't': // for hg19 or b36
key = 0; key = 0;
break; break;
case 'x': case 'x':
@ -925,7 +926,11 @@ public class TranscriptToInfo extends RodWalker<TreeMap<String, String>, TreeMap
key = 24; key = 24;
break; break;
default: default:
if( txChrom.startsWith("chr") ) {
key = Integer.parseInt(txChrom.substring(3)); key = Integer.parseInt(txChrom.substring(3));
} else {
key = Integer.parseInt(txChrom);
}
break; break;
} }