From 967ff647b886e2421dd7f1960e519ca4bded029b Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 2 Nov 2011 13:07:20 -0400
Subject: [PATCH] Reduced reads shouldn't contribute to Fisher Strand
 calculations

---
 .../sting/gatk/walkers/annotator/FisherStrand.java            | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

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 393eb549c..2d1d1978c 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
@@ -205,7 +205,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
 
         for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
             for (PileupElement p : sample.getValue().getBasePileup()) {
-                if ( p.isDeletion() ) // ignore deletions
+                if ( p.isDeletion() || p.isReducedRead() ) // ignore deletions and reduced reads
                     continue;
 
                 if ( p.getRead().getMappingQuality() < 20 || p.getQual() < 20 )
@@ -258,6 +258,8 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
                  continue;
 
             for (final PileupElement p: pileup) {
+                if ( p.isReducedRead() ) // ignore reduced reads
+                    continue;
                 if ( p.getRead().getMappingQuality() < 20)
                     continue;
                 if (indelLikelihoodMap.containsKey(p)) {