From 60880b925ff894f3deb0c7068e210dc4fd4da40e Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 20 Dec 2010 16:33:14 +0000
Subject: [PATCH] VC utils prune method now will keep genotype attributes as
 well as info keys.  RBP now emits a far reduce (NO INFO, only GT:GQ:PG)
 records, further reducing size of phasing output

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4882 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/contexts/variantcontext/VariantContextUtils.java   | 6 +++++-
 .../sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java | 3 ++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
index 1f0d732e5..f901a8f4e 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -293,7 +293,8 @@ public class VariantContextUtils {
             Map<String, Object> d = mvc.getAttributes();
             mvc.clearAttributes();
             for ( String key : keysToPreserve )
-                mvc.putAttribute(key, d.get(key));
+                if ( d.containsKey(key) )
+                    mvc.putAttribute(key, d.get(key));
         }
 
         Collection<Genotype> gs = mvc.getGenotypes().values();
@@ -301,6 +302,9 @@ public class VariantContextUtils {
         for ( Genotype g : gs ) {
             MutableGenotype mg = new MutableGenotype(g);
             mg.clearAttributes();
+            for ( String key : keysToPreserve )
+                if ( g.hasAttribute(key) )
+                    mg.putAttribute(key, g.getAttribute(key));
             mvc.addGenotype(mg);
         }
 
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 c329e4bfc..edb6ec6e8 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -241,13 +241,14 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         return new PhasingStatsAndOutput(phaseStats, completedList);
     }
 
+    private static final Set<String> KEYS_TO_KEEP_IN_REDUCED_VCF = new HashSet<String>(Arrays.asList("PQ"));
     private VariantContext reduceVCToSamples(VariantContext vc, List<String> samplesToPhase) {
 //        for ( String sample : samplesToPhase )
 //            logger.debug(String.format("  Sample %s has genotype %s, het = %s", sample, vc.getGenotype(sample), vc.getGenotype(sample).isHet() ));
         VariantContext subvc = vc.subContextFromGenotypes(vc.getGenotypes(samplesToPhase).values());
 //        logger.debug("original VC = " + vc);
 //        logger.debug("sub      VC = " + subvc);
-        return subvc;
+        return VariantContextUtils.pruneVariantContext(subvc, KEYS_TO_KEEP_IN_REDUCED_VCF );
     }
 
     private List<VariantContext> processQueue(PhasingStats phaseStats, boolean processAll) {