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don't have a null-pointer hissy fit when the reference is N. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@997 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-06-12 13:59:16 +00:00
parent 1fb241a8b8
commit dbf2cc037c
1 changed files with 1 additions and 0 deletions
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1
java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
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@ -208,6 +208,7 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
public String reduce(AlleleFrequencyEstimate alleleFreq, String sum)
{
if (alleleFreq == null) { return ""; }
if ( alleleFreq.lodVsRef >= lodThreshold ) {
String line = GeliOutputFormat ? alleleFreq.asGeliString() : alleleFreq.asTabularString();
calls_file.println(line);