From abd2f1a7d5268d8448c03235f2b812c803e4fa44 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 10 Nov 2010 12:27:55 +0000
Subject: [PATCH] fix
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14993 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/io/IndexFastaStream.java | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/uk/ac/sanger/artemis/io/IndexFastaStream.java b/uk/ac/sanger/artemis/io/IndexFastaStream.java
index 6595ab79b..b8128b275 100644
--- a/uk/ac/sanger/artemis/io/IndexFastaStream.java
+++ b/uk/ac/sanger/artemis/io/IndexFastaStream.java
@@ -59,7 +59,13 @@ public class IndexFastaStream extends StreamSequence
else
{
File fasta = ((FileDocument)doc.getDocument()).getFile();
- File fastaIndexFile = new File(fasta.getParentFile().getAbsolutePath(), fasta.getName()+".fai");
+ File parentDir = fasta.getParentFile();
+ File fastaIndexFile;
+ if(parentDir != null)
+ fastaIndexFile = new File(parentDir.getAbsolutePath(), fasta.getName() + ".fai");
+ else
+ fastaIndexFile = new File(fasta.getName() + ".fai");
+
fastaIndex = new FastaSequenceIndex(fastaIndexFile);
try
--
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