From 15183ed778a2cfc27aa275696a06c98bb4eb17a9 Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 27 Oct 2010 23:02:10 +0000
Subject: [PATCH] Reduced header to single sample when useSingleSample arg is
 given (to prevent lots of pointless no-calls)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4588 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../MergePhasedSegregatingAlternateAllelesVCFWriter.java    | 6 ++++++
 .../phasing/MergeSegregatingAlternateAllelesWalker.java     | 3 +++
 2 files changed, 9 insertions(+)

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 160d0c307..32b72c394 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java
@@ -88,6 +88,12 @@ public class MergePhasedSegregatingAlternateAllelesVCFWriter implements VCFWrite
     }
 
     public void writeHeader(VCFHeader header) {
+        if (useSingleSample != null) { // only want to output context for one sample
+            Set<String> singSampSet = new TreeSet<String>();
+            singSampSet.add(useSingleSample);
+            header = new VCFHeader(header.getMetaData(), singSampSet);
+        }
+
         innerWriter.writeHeader(header);
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
index 55fbaca97..ad168399b 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
@@ -144,6 +144,9 @@ public class MergeSegregatingAlternateAllelesWalker extends RodWalker<Integer, I
     public void onTraversalDone(Integer result) {
         vcMergerWriter.close();
 
+        if (useSingleSample != null)
+            System.out.println("Only considered single sample: " + useSingleSample);
+
         System.out.println("Number of successive pairs of records (any distance): " + vcMergerWriter.getNumRecordsAttemptToMerge());
         System.out.println("Number of potentially merged records (distance <= " + maxGenomicDistanceForMNP + "): " + vcMergerWriter.getNumRecordsWithinDistance());
         System.out.println("Number of records merged [all samples are mergeable, some sample has a MNP of ALT alleles]: " + vcMergerWriter.getNumMergedRecords());