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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2012-04-23 09:34:08 -04:00
parent 4edb005411 35bb55f562
commit 7b5fbf9567
1 changed files with 3 additions and 3 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
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@ -84,13 +84,13 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
if ( !vc.isVariant() )
return null;
int[][] table = getContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount());
final int[][] table = getContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount());
Double pvalue = Math.max(pValueForContingencyTable(table), MIN_PVALUE);
final Double pvalue = Math.max(pValueForContingencyTable(table), MIN_PVALUE);
if ( pvalue == null )
return null;
Map<String, Object> map = new HashMap<String, Object>();
final Map<String, Object> map = new HashMap<String, Object>();
map.put(FS, String.format("%.3f", QualityUtils.phredScaleErrorRate(pvalue)));
return map;