From 78b7fb25c7ea40c889e4b37d73ce110ffae3a0f9 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 16 Jun 2009 22:23:12 +0000
Subject: [PATCH] allow contig names to have spaces in the fai.  This is not
 yet supported by samtools fai generator (which truncates at the first space),
 but we might as well fix it on our side.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1022 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/utils/fasta/FastaSequenceIndex.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java b/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
index 490826c86..7d44c3786 100755
--- a/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
+++ b/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
@@ -48,7 +48,7 @@ public class FastaSequenceIndex implements Iterable {
 
         while( scanner.hasNext() ) {
             // Tokenize and validate the index line.
-            String result = scanner.findInLine("([\\w\\.]+)\\s+(\\d+)\\s+(\\d+)\\s+(\\d+)\\s+(\\d+)");
+            String result = scanner.findInLine("([\\w\\s\\.]+)\\t+(\\d+)\\s+(\\d+)\\s+(\\d+)\\s+(\\d+)");
             if( result == null )
                 throw new PicardException("Found invalid line in index file:" + scanner.nextLine());
             MatchResult tokens = scanner.match();