From de89f0e084bd534592c6b5100ced510d77342b86 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 5 Apr 2012 11:45:37 +0100
Subject: [PATCH] fix in getMate()
---
uk/ac/sanger/artemis/components/alignment/BamView.java | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index d25eef573..79ca4b63c 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -124,7 +124,6 @@ import uk.ac.sanger.artemis.components.MessageDialog;
import uk.ac.sanger.artemis.components.NonModalDialog;
import uk.ac.sanger.artemis.components.SwingWorker;
import uk.ac.sanger.artemis.components.genebuilder.AutoCompleteComboDocument;
-import uk.ac.sanger.artemis.components.variant.FeatureContigPredicate;
import uk.ac.sanger.artemis.editor.MultiLineToolTipUI;
import uk.ac.sanger.artemis.io.EntryInformation;
import uk.ac.sanger.artemis.io.Range;
@@ -3341,7 +3340,7 @@ public class BamView extends JPanel
viewDetail.appendString("Strand "+
(thisSAMRecord.getReadNegativeStrandFlag() ? "-\n\n" : "+\n\n"), Level.DEBUG);
- if(!thisSAMRecord.getMateUnmappedFlag())
+ if(thisSAMRecord.getReadPairedFlag() && !thisSAMRecord.getMateUnmappedFlag())
{
if(thisSAMRecordMate != null)
{
@@ -3411,6 +3410,10 @@ public class BamView extends JPanel
*/
protected SAMRecord getMate(SAMRecord thisSAMRecord)
{
+ if(!thisSAMRecord.getReadPairedFlag() || // read is not paired in sequencing
+ thisSAMRecord.getMateUnmappedFlag())
+ return null;
+
SAMRecord mate = null;
try
{
--
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