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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
This commit is contained in:
scalvo 2011-01-28 22:45:45 +00:00
parent 7af0532292
commit 5934b9cb82
1 changed files with 1 additions and 1 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java
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@ -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 {