From 3d014d08ad92de78864fad1c44e37bc9677547f0 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 18 Apr 2013 10:49:38 +0100
Subject: [PATCH] fix for colour by strand option when XS tag is missing
---
uk/ac/sanger/artemis/components/alignment/BamView.java | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index e49f1af9e..7c04ed884 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -1490,7 +1490,9 @@ public class BamView extends JPanel
{
if(colourByStrandTag.isSelected())
{
- if( ((Character)samRecord.getAttribute("XS")).equals('+') )
+ if(samRecord.getAttribute("XS") == null)
+ g2.setColor(Color.BLACK);
+ else if( ((Character)samRecord.getAttribute("XS")).equals('+') )
g2.setColor(Color.BLUE);
else if( ((Character)samRecord.getAttribute("XS")).equals('-') )
g2.setColor(Color.RED);
@@ -1602,7 +1604,9 @@ public class BamView extends JPanel
{
if(colourByStrandTag.isSelected())
{
- if( ((Character)samRecord.getAttribute("XS")).equals('+') )
+ if(samRecord.getAttribute("XS") == null)
+ g2.setColor(Color.BLACK);
+ else if( ((Character)samRecord.getAttribute("XS")).equals('+') )
g2.setColor(Color.BLUE);
else if( ((Character)samRecord.getAttribute("XS")).equals('-') )
g2.setColor(Color.RED);
--
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