From 5f34054cc1c4368c0b11cb7eee34169b7b30b903 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 1 Jul 2013 14:55:15 -0400
Subject: [PATCH] Remove filtering of MAPQ 0 reads from
 CalledHaplotypeBAMWriter

---
 .../utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java  | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java b/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java
index fd90cf6e9..c298485f6 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java
@@ -98,10 +98,8 @@ class CalledHaplotypeBAMWriter extends HaplotypeBAMWriter {
         // next, output the interesting reads for each sample aligned against one of the called haplotypes
         for ( final PerReadAlleleLikelihoodMap readAlleleLikelihoodMap : stratifiedReadMap.values() ) {
             for ( final Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : readAlleleLikelihoodMap.getLikelihoodReadMap().entrySet() ) {
-                if ( entry.getKey().getMappingQuality() > 0 ) {
-                    final MostLikelyAllele bestAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(entry.getValue(), allelesOfCalledHaplotypes);
-                    writeReadAgainstHaplotype(entry.getKey(), alleleToHaplotypeMap.get(bestAllele.getMostLikelyAllele()), paddedReferenceLoc.getStart(), bestAllele.isInformative());
-                }
+                final MostLikelyAllele bestAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(entry.getValue(), allelesOfCalledHaplotypes);
+                writeReadAgainstHaplotype(entry.getKey(), alleleToHaplotypeMap.get(bestAllele.getMostLikelyAllele()), paddedReferenceLoc.getStart(), bestAllele.isInformative());
             }
         }
     }