From fa3ff5350800f1449b6e4e5f365cf2b745906932 Mon Sep 17 00:00:00 2001
From: Menachem Fromer <fromer@broadinstitute.org>
Date: Wed, 13 Jul 2011 11:58:16 -0400
Subject: [PATCH] Filters should only be applied to the new VC if the old VC
 had filters applied

---
 .../sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java  | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index e59b29502..af24035c8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -220,6 +220,9 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
             }
             else {
                 unprocessedList.add(vc); // Finished with the unprocessed variant, and writer can enforce sorting on-the-fly
+
+                if (DEBUG)
+                    logger.debug("Unprocessed variant = " + VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc));
             }
 
             int numReads = 0;
@@ -1105,7 +1108,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
             this.alleles = vc.getAlleles();
             this.genotypes = new HashMap<String, Genotype>(vc.getGenotypes()); // since vc.getGenotypes() is unmodifiable
             this.negLog10PError = vc.getNegLog10PError();
-            this.filters = vc.getFilters();
+            this.filters = vc.filtersWereApplied() ? vc.getFilters() : null;
             this.attributes = new HashMap<String, Object>(vc.getAttributes());
         }