From d58073a6929899d4dd4dc48dcb7a557bb095afbb Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 1 Mar 2010 15:08:32 +0000
Subject: [PATCH] fix colours in paired read display and add FL attribute to
reads when using multiple bam files
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13366 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/alignment/BamView.java | 15 ++++++++-------
1 file changed, 8 insertions(+), 7 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 2a822aeab..88902417f 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -132,7 +132,7 @@ public class BamView extends JPanel
private Hashtable<String, Integer> seqLengths = new Hashtable<String, Integer>();
private Hashtable<String, Integer> offsetLengths;
private Vector<String> seqNames = new Vector<String>();
- private List<String> bamList;
+ protected List<String> bamList;
private List<Integer> hideBamList = new Vector<Integer>();
private SAMRecordFlagPredicate samRecordFlagPredicate;
@@ -447,9 +447,9 @@ public class BamView extends JPanel
String refName, int start, int end,
int bamIndex)
{
- //boolean multipleBAM = false;
- //if(bamList.size() > 1)
- // multipleBAM = true;
+ boolean multipleBAM = false;
+ if(bamList.size() > 1)
+ multipleBAM = true;
CloseableIterator<SAMRecord> it = inputSam.queryOverlapping(refName, start, end);
MemoryMXBean memory = ManagementFactory.getMemoryMXBean();
@@ -469,8 +469,8 @@ public class BamView extends JPanel
if(samRecordMapQPredicate == null ||
samRecordMapQPredicate.testPredicate(samRecord))
{
- //if(multipleBAM)
- // samRecord.setAttribute("FL", bamIndex);
+ if(multipleBAM)
+ samRecord.setAttribute("FL", bamIndex);
readsInView.add(samRecord);
}
}
@@ -1408,7 +1408,8 @@ public class BamView extends JPanel
if(offTheTop)
g2.setColor(darkOrange);
- else if(samRecord.getReadNegativeStrandFlag()) // strand of the query (1 for reverse)
+ else if(samRecord.getReadNegativeStrandFlag() &&
+ samRecord.getMateNegativeStrandFlag()) // strand of the query (1 for reverse)
g2.setColor(Color.red);
else
g2.setColor(Color.blue);
--
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