From 0f6bfaaf73cb0a87b155d5ed082d70207b8d9e35 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 14 Jul 2009 02:03:36 +0000
Subject: [PATCH] Skip validation in case of no reads aligning.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1230 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/executive/MicroScheduler.java  | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
index 029ad0c4e..89720b8cc 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
@@ -308,6 +308,11 @@ public abstract class MicroScheduler {
         for( SAMSequenceRecord dictionaryEntry: referenceDictionary.getSequences() )
             referenceSequenceNames.add(dictionaryEntry.getSequenceName());
 
+        if( readsSequenceNames.size() == 0 ) {
+            logger.info("Reads file is unmapped.  Skipping validation against reference.");
+            return;
+        }
+
         // If there's no overlap between reads and reference, data will be bogus.  Throw an exception.
         Set<String> intersectingSequenceNames = new HashSet<String>(readsSequenceNames);
         intersectingSequenceNames.retainAll(referenceSequenceNames);