From 18e4532d10cfb05a2bcbe4edb1e0d7e3df368e47 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Sun, 22 Apr 2012 13:23:24 -0400
Subject: [PATCH] Turning down the amount of assembly graph pruning slightly in
 the case of low coverage.

---
 .../sting/gatk/walkers/annotator/FisherStrand.java          | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

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<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;