diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java index 0d3bd11a7..8af69d862 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java @@ -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 map = new HashMap(); + final Map map = new HashMap(); map.put(FS, String.format("%.3f", QualityUtils.phredScaleErrorRate(pvalue))); return map;