From 64599d107435cdb439fd21bb83dbf9340181e7e0 Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 1 Nov 2010 19:51:42 +0000
Subject: [PATCH] Added debugging message

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4605 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java | 1 +
 1 file changed, 1 insertion(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java
index c01051b8f..3ae4d47a0 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java
@@ -357,6 +357,7 @@ public class MergePhasedSegregatingAlternateAllelesVCFWriter implements VCFWrite
                             logger.debug("Unknown segregation of alleles [not phased] for " + samp + " at " + VariantContextUtils.getLocation(vc1) + ", " + VariantContextUtils.getLocation(vc2));
                         }
                         else if (gt1.isHomRef() || gt2.isHomRef()) {
+                            logger.debug("gt1.isHomRef() || gt2.isHomRef() for " + samp + " at " + VariantContextUtils.getLocation(vc1) + ", " + VariantContextUtils.getLocation(vc2));
                             aas.eitherNotVariant++;
                         }
                         else { // BOTH gt1 and gt2 have at least one variant allele (so either hets, or homozygous variant):