From 7bc6ee93e62b4df394ef1c0281cd3d3daf84285c Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 14 Feb 2013 16:07:15 +0000
Subject: [PATCH] set log level
---
uk/ac/sanger/artemis/components/alignment/BamView.java | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index ea63c0085..f92967d23 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -444,7 +444,12 @@ public class BamView extends JPanel
{
final File cramIndexFile = new File(bam + ".crai");
if(cramIndexFile.exists())
+ {
+ logger4j.debug(
+ "ERROR: CRAM INDEX FILE ("+cramIndexFile.getName()+
+ ") EXPECTING A BAM INDEX FILE (USE THIS OPTION --bam-style-index) ");
return cramIndexFile;
+ }
}
}
@@ -494,6 +499,9 @@ public class BamView extends JPanel
if(feature_display != null && bam.endsWith("cram"))
{
+ // set log level
+ net.sf.picard.util.Log.setGlobalLogLevel(
+ net.sf.picard.util.Log.LogLevel.ERROR);
final CRAMReferenceSequenceFile ref = new CRAMReferenceSequenceFile(
feature_display.getEntryGroup().getSequenceEntry(), this);
--
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