From 167712f025b2d6b41bcea1040a81cc47eef6f826 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 9 Feb 2010 18:43:38 +0000
Subject: [PATCH] filter out unmapped reads by default
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13254 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/components/alignment/BamView.java | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index ba2d7e5af..4b312caba 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -211,6 +211,10 @@ public class BamView extends JPanel
this.bamList = bamList;
this.nbasesInView = nbasesInView;
+ // filter out unmapped reads by default
+ setSamRecordFlagPredicate(
+ new SAMRecordFlagPredicate(SAMRecordFlagPredicate.READ_UNMAPPED_FLAG));
+
if(reference != null)
{
EntryGroup entryGroup = new SimpleEntryGroup();
--
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