Commit 7bc6ee93 authored by tcarver's avatar tcarver
Browse files

set log level

parent 7002fc19
......@@ -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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