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Turning down the amount of assembly graph pruning slightly in the case of low coverage.

This commit is contained in:
Ryan Poplin 2012-04-22 13:23:24 -04:00
parent a1596791af
commit 18e4532d10
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;