From 2dfde6a8d6a27af12c722bed685a0f88f6e32ff3 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 2 Jun 2011 08:02:53 +0000
Subject: [PATCH] catch ArrayIndexOutOfBoundsException thrown by tabix when
reference is not found
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16203 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/AbstractVCFReader.java | 11 ++++++++++-
1 file changed, 10 insertions(+), 1 deletion(-)
diff --git a/uk/ac/sanger/artemis/components/variant/AbstractVCFReader.java b/uk/ac/sanger/artemis/components/variant/AbstractVCFReader.java
index 08257af37..afa4a430c 100644
--- a/uk/ac/sanger/artemis/components/variant/AbstractVCFReader.java
+++ b/uk/ac/sanger/artemis/components/variant/AbstractVCFReader.java
@@ -64,7 +64,16 @@ public abstract class AbstractVCFReader
else
{
if(tabixIterator == null)
- tabixIterator = ((TabixReader)this).query(chr+":"+sbeg+"-"+send);
+ {
+ try
+ {
+ tabixIterator = ((TabixReader)this).query(chr+":"+sbeg+"-"+send);
+ }
+ catch(ArrayIndexOutOfBoundsException aob)
+ {
+ System.err.println(chr+":"+sbeg+"-"+send+" not found in "+((TabixReader)this).getFileName());
+ }
+ }
if(tabixIterator == null)
return null;
--
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