From a7d739a3b8edce3a28b7c868cf549a79a82b7336 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 15 Aug 2012 11:38:42 +0100
Subject: [PATCH] parsing of the header happens during SAMFileReader
construction, so need to set the default stringency
---
uk/ac/sanger/artemis/components/alignment/BamView.java | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 53e6152e6..1378391ca 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -430,7 +430,11 @@ public class BamView extends JPanel
* @throws IOException
*/
private SAMFileReader getSAMFileReader(final String bam) throws IOException
- {
+ {
+ // parsing of the header happens during SAMFileReader construction,
+ // so need to set the default stringency
+ SAMFileReader.setDefaultValidationStringency(ValidationStringency.LENIENT);
+
if(samFileReaderHash.containsKey(bam))
return samFileReaderHash.get(bam);
--
GitLab