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allow RefSeq files to optionally contain the header line, which is the default output from the UCSC table browser 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4065 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-08-19 20:25:37 +00:00
parent effeedf1a3
commit 63ada20da5
1 changed files with 2 additions and 0 deletions
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2
java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java
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@ -19,6 +19,7 @@ public class RefSeqCodec implements FeatureCodec {
@Override
public Feature decodeLoc(String line) {
if (line.startsWith("#")) return null;
String fields[] = line.split("\t");
if (fields.length < 3) throw new TribbleException("RefSeq (decodeLoc) : Unable to parse line -> " + line + ", we expected at least 3 columns, we saw " + fields.length);
String contig_name = fields[2];
@ -28,6 +29,7 @@ public class RefSeqCodec implements FeatureCodec {
/** Fills this object from a text line in RefSeq (UCSC) text dump file */
@Override
public Feature decode(String line) {
if (line.startsWith("#")) return null;
String fields[] = line.split("\t");
// we reference postion 15 in the split array below, make sure we have at least that many columns