From 4657921fdf6f17a4733a9cb94f807c03dfa6c36c Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Mon, 13 Feb 2012 17:32:36 +0000
Subject: [PATCH] set VALIDATION_STRINGENCY=LENIENT
---
uk/ac/sanger/artemis/components/alignment/BamView.java | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index c47c2504c..c89252165 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -420,7 +420,7 @@ public class BamView extends JPanel
// Use Picard to index the file
// requires reads to be sorted by coordinate
new BuildBamIndex().instanceMain(
- new String[]{ "I="+bam, "O="+bamIndexFile.getAbsolutePath(), "MAX_RECORDS_IN_RAM=50000" });
+ new String[]{ "I="+bam, "O="+bamIndexFile.getAbsolutePath(), "MAX_RECORDS_IN_RAM=50000", "VALIDATION_STRINGENCY=LENIENT" });
}
catch(SAMException e)
{
--
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