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fix to respond to the change in IndelLikelihood constructor. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1119 348d0f76-0448-11de-a6fe-93d51630548a
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jmaguire 2009-06-29 19:05:33 +00:00
parent 7ecc43e9a7
commit a17bf145f6
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
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@ -229,7 +229,7 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
*/ */
private IndelLikelihood callIndel(LocusContext context, List<SAMRecord> reads, List<Integer> offsets) { private IndelLikelihood callIndel(LocusContext context, List<SAMRecord> reads, List<Integer> offsets) {
String[] indels = BasicPileup.indelPileup(reads, offsets); String[] indels = BasicPileup.indelPileup(reads, offsets);
IndelLikelihood indelCall = new IndelLikelihood(indels); IndelLikelihood indelCall = new IndelLikelihood(indels, 1e-4);
if (! indelCall.getType().equals("ref")) { if (! indelCall.getType().equals("ref")) {
System.out.printf("INDEL %s %s\n", context.getLocation(), indelCall); System.out.printf("INDEL %s %s\n", context.getLocation(), indelCall);