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print indels in the format required for 1KG submissions 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1275 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-17 15:59:18 +00:00
parent d45c90b166
commit da4af3b620
1 changed files with 3 additions and 1 deletions
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4
java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
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@ -37,7 +37,9 @@ public class SimpleIndelROD extends TabularROD implements Genotype {
public String toString() {
StringBuffer sb = new StringBuffer();
sb.append(getLocation() + "\t" + getFWDAlleles().get(0));
sb.append(getLocation().getContig() + "\t" + getLocation().getStart() + "\t");
String indel = getFWDAlleles().get(0);
sb.append((indel.length()-1) + "\t" + (isInsertion() ? "I" : "D") + "\t" + indel.substring(1));
return sb.toString();
}
}