From c1595a383ab18269994a19afbcd3dcf7e2f23a10 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 17 Jun 2010 16:46:02 +0000
Subject: [PATCH] More bugfixes for cases where no sample name is present.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3578 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/iterators/DownsamplingLocusIteratorByState.java     | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/DownsamplingLocusIteratorByState.java b/java/src/org/broadinstitute/sting/gatk/iterators/DownsamplingLocusIteratorByState.java
index 0245e824b..675c3296e 100755
--- a/java/src/org/broadinstitute/sting/gatk/iterators/DownsamplingLocusIteratorByState.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/DownsamplingLocusIteratorByState.java
@@ -276,8 +276,11 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
     public DownsamplingLocusIteratorByState(final Iterator<SAMRecord> samIterator, Reads readInformation, List<LocusIteratorFilter> filters ) {
         // Aggregate all sample names.
         // TODO: Push in header via constructor
-        if(GenomeAnalysisEngine.instance != null && GenomeAnalysisEngine.instance.getDataSource() != null)
+        if(GenomeAnalysisEngine.instance != null && GenomeAnalysisEngine.instance.getDataSource() != null) {
             sampleNames.addAll(SampleUtils.getSAMFileSamples(GenomeAnalysisEngine.instance.getSAMFileHeader()));
+        }
+        // Add a null sample name as a catch-all for reads without samples
+        if(!sampleNames.contains(null)) sampleNames.add(null);        
         readStates = new ReadStateManager(samIterator,readInformation.getDownsamplingMethod(),readInformation.getMaxReadsAtLocus(),sampleNames);
         this.readInfo = readInformation;
         this.filters = filters;