From bceb2a94604312b0b984f70a3b27b9638945d3c4 Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 7 Feb 2011 20:26:57 +0000
Subject: [PATCH] Now that Mauricio has updated the PacBio BAM to properly have
 RG, can use sample name in the walker

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5212 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/phasing/ReadBasedPhasingValidationWalker.java   | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java
index e263a7217..ad2972d9d 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java
@@ -144,10 +144,6 @@ public class ReadBasedPhasingValidationWalker extends RodWalker<Integer, Integer
         ReadBackedPileup pileup = context.getBasePileup();
         String nextName = null;
 
-        //
-        // TODO: ASSUMES THAT ALL READS COME FROM A SINGLE SAMPLE:
-        // TODO: CODE SHOULD BE AS FOLLOWS:
-        /*
         Collection<String> sampNames = pileup.getSampleNames();
         if (sampNames.size() != 1)
             throw new UserException("Reads must be for exactly one sample [not multi-sample]");
@@ -161,8 +157,6 @@ public class ReadBasedPhasingValidationWalker extends RodWalker<Integer, Integer
             throw new UserException("Reads must have a single consistent sample name");
 
         pileup = pileup.getPileupForSampleName(sampleName);
-        */
-        //
 
         ReadBasesAtPosition readBases = new ReadBasesAtPosition();
         for (PileupElement p : pileup)