From dce13c3ab9b11a76f23e1db964feeb4f272db996 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 18 May 2010 17:57:19 +0000
Subject: [PATCH] fix SAMRecordPositionComparator by looking up offset
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13861 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/alignment/BamView.java | 2 +-
.../alignment/SAMRecordPositionComparator.java | 13 +++++++++++--
2 files changed, 12 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 4631271e9..03d3c4271 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -624,7 +624,7 @@ public class BamView extends JPanel
bamList.size() > 1)
{
// merge multiple BAM files
- Collections.sort(readsInView, new SAMRecordPositionComparator());
+ Collections.sort(readsInView, new SAMRecordPositionComparator(BamView.this));
}
}
catch (OutOfMemoryError ome)
diff --git a/uk/ac/sanger/artemis/components/alignment/SAMRecordPositionComparator.java b/uk/ac/sanger/artemis/components/alignment/SAMRecordPositionComparator.java
index d1ff725a2..7b42f7950 100644
--- a/uk/ac/sanger/artemis/components/alignment/SAMRecordPositionComparator.java
+++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordPositionComparator.java
@@ -30,14 +30,23 @@ import net.sf.samtools.SAMRecord;
class SAMRecordPositionComparator implements Comparator<Object>
{
+ public BamView bamView;
+ public SAMRecordPositionComparator(BamView bamView)
+ {
+ this.bamView = bamView;
+ }
+
public int compare(Object o1, Object o2)
{
SAMRecord pr1 = (SAMRecord) o1;
SAMRecord pr2 = (SAMRecord) o2;
- if(pr1.getAlignmentStart() < pr2.getAlignmentStart())
+ int offset1 = bamView.getSequenceOffset(pr1.getReferenceName());
+ int offset2 = bamView.getSequenceOffset(pr2.getReferenceName());
+
+ if(pr1.getAlignmentStart()+offset1 < pr2.getAlignmentStart()+offset2)
return -1;
- else if(pr1.getAlignmentStart() > pr2.getAlignmentStart())
+ else if(pr1.getAlignmentStart()+offset1 > pr2.getAlignmentStart()+offset2)
return 1;
return 0;
}
--
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