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Will now work with simplest tabular format - genotype string ("+ACTT") does not have to be followed by ':' 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2755 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-02-01 15:40:01 +00:00
parent e0808e6c37
commit 990af3f76e
1 changed files with 5 additions and 1 deletions
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6
java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
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@ -33,7 +33,11 @@ public class SimpleIndelROD extends TabularROD implements VariationRod {
return Arrays.asList(this.get("4")); return Arrays.asList(this.get("4"));
String str = this.get("3"); String str = this.get("3");
return Arrays.asList(str.substring(1, str.indexOf(":"))); int pos = str.indexOf(":");
if ( pos == -1 ) {
return Arrays.asList(str.substring(1));
}
return Arrays.asList(str.substring(1, pos));
} }
public String getFWDRefBases() { return ""; } public String getFWDRefBases() { return ""; }