From 09c8d323107302cff22027d0f12b32285422e4a9 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 15 Mar 2011 12:24:22 +0000
Subject: [PATCH] catch NullPointerException from TabixReader
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15721 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/variant/IOUtils.java | 25 ++++++++++++-------
1 file changed, 16 insertions(+), 9 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index 1de636c8f..601d55471 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -234,7 +234,7 @@ class IOUtils
{
e.printStackTrace();
}
-
+
if(!view)
new MessageDialog (null, "Saved Files", fastaFiles, false);
else
@@ -565,15 +565,22 @@ class IOUtils
}
else
{
- TabixReader.Iterator iter =
- (((TabixReader) reader).query(chr+":"+sbeg+"-"+send)); // get the iterator
- String s;
- while ((s = iter.next()) != null)
+ try
{
- VCFRecord record = VCFRecord.parse(s);
- int basePosition = record.getPos() + vcfView.getSequenceOffset(record.getChrom());
- if(vcfView.showVariant(record, features, basePosition, vcf_v4) )
- basesStr = getSeqsVariation(record, basesStr, sbeg, isFwd, vcf_v4);
+ TabixReader.Iterator iter =
+ (((TabixReader) reader).query(chr+":"+sbeg+"-"+send)); // get the iterator
+ String s;
+ while (iter != null && (s = iter.next()) != null)
+ {
+ VCFRecord record = VCFRecord.parse(s);
+ int basePosition = record.getPos() + vcfView.getSequenceOffset(record.getChrom());
+ if(vcfView.showVariant(record, features, basePosition, vcf_v4) )
+ basesStr = getSeqsVariation(record, basesStr, sbeg, isFwd, vcf_v4);
+ }
+ }
+ catch(NullPointerException e)
+ {
+ System.err.println(chr+":"+sbeg+"-"+send+"\n"+e.getMessage());
}
}
return basesStr;
--
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