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skip N's in the reference (rather than crash. doh!) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1039 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-06-17 23:22:35 +00:00
parent f45d5a73a5
commit 5992d88409
1 changed files with 1 additions and 0 deletions
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java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java
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@ -80,6 +80,7 @@ public class MultiSampleCaller extends LocusWalker<String,String>
public String map(RefMetaDataTracker tracker, char ref, LocusContext context)
{
if (ref == 'N') { return null; }
this.ref = ref;
if (tracker.lookup("DBSNP", null) != null) { in_dbsnp = "known"; } else { in_dbsnp = "novel"; }
this.MultiSampleCall(context, sample_names);