From 76b09a879b37b2c3e1a233ebbcf1bfd800765e9d Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 14 Jul 2009 18:36:09 +0000
Subject: [PATCH] Display a more intelligent error message if the user runs a
 locus traversal across an unmapped reads file.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1238 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/datasources/simpleDataSources/SAMDataSource.java | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
index f4ce5071c..5122b691c 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
@@ -161,6 +161,8 @@ public class SAMDataSource implements SimpleDataSource {
      * @return an iterator for that region
      */
     private StingSAMIterator seekLocus( GenomeLoc location ) throws SimpleDataSourceLoadException {
+        if( getHeader().getSequenceDictionary().getSequences().size() == 0 )
+            throw new StingException("Unable to seek to the given locus; reads data source has no alignment information.");
         return createIterator( new MappedStreamSegment(location) );
     }