From 8c583ea405e7a66bb23b70ff09a76b70f67bc3d6 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 23 Dec 2010 13:11:22 +0000
Subject: [PATCH] RBP now operates correctly at non-variant sites so we can
 phase hom-ref genotypes with -sampleToPhase

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4903 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/phasing/ReadBackedPhasingWalker.java  | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index 0d8fdb69f..6c4a1ba69 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -201,7 +201,6 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         if (tracker == null)
             return null;
 
-        // todo -- potential performance problem here with unconditional, frequent writes to debug
         mostDownstreamLocusReached = ref.getLocus();
         if ( DEBUG ) logger.debug("map() at: " + mostDownstreamLocusReached);
 
@@ -217,7 +216,6 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
                 VariantAndReads vr = new VariantAndReads(vc, context);
                 unphasedSiteQueue.add(vr);
 
-                // todo -- potential performance problem here with unconditional, frequent writes to debug
                 if ( DEBUG ) logger.debug("Added variant to queue = " + VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(),vr.variant));
             }
             else {
@@ -1008,12 +1006,14 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
     }
 
     private void writeVCF(VariantContext vc) {
-        if ( samplesToPhase == null || (vc.isVariant() && vc.isNotFiltered())) // if we are only operating on specific samples, don't write out all sites, just those where the VC is variant
+        if ( vc.isNotFiltered() )
+	    //if ( samplesToPhase == null || (vc.isVariant() && vc.isNotFiltered())) // if we are only operating on specific samples, don't write out all sites, just those where the VC is variant
             WriteVCF.writeVCF(vc, writer, logger);
     }
 
     public static boolean processVariantInPhasing(VariantContext vc) {
-        return isUnfilteredBiallelicSNP(vc);
+        return vc.isNotFiltered() && ((vc.isSNP() && vc.isBiallelic()) || ! vc.isVariant()); // we can handle the non-variant case as well
+        //return isUnfilteredBiallelicSNP(vc);
     }
 
 
@@ -1887,4 +1887,4 @@ class MultipleBaseCounts {
 
         return sb.toString();
     }
-}
\ No newline at end of file
+}