From 83759ef9a1cf4a9a47e9d655199bccf7e416eff7 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Mon, 22 Oct 2012 16:47:24 +0100
Subject: [PATCH] add option for creating features from reads on opposite
strand - for single strand cDNA
---
.../artemis/components/alignment/BamView.java | 15 ++++++---
.../components/alignment/MappedReads.java | 32 +++++++++++--------
2 files changed, 28 insertions(+), 19 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index be26ccb51..ca938c72d 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -3916,17 +3916,17 @@ public class BamView extends JPanel
if(groupsFrame.getNumberOfGroups() == 1)
useGroup.setEnabled(false);
- ButtonGroup group = new ButtonGroup();
+ final ButtonGroup group = new ButtonGroup();
group.add(useAllBams);
group.add(useGroup);
- Box xBox = Box.createHorizontalBox();
+ final Box xBox = Box.createHorizontalBox();
xBox.add(useAllBams);
xBox.add(useGroup);
xBox.add(Box.createHorizontalGlue());
c.gridy++;
gridPanel.add(xBox, c);
-
+
c.gridy++;
gridPanel.add(new JSeparator(), c);
c.gridy++;
@@ -3934,6 +3934,11 @@ public class BamView extends JPanel
c.gridy++;
gridPanel.add(minSize, c);
+ final JCheckBox cbOpposite = new JCheckBox("Assume reads on opposite strand", false);
+ cbOpposite.setToolTipText("for cDNA experiments when the reads are on the opposite strand");
+ c.gridy++;
+ gridPanel.add(cbOpposite, c);
+
int status =
JOptionPane.showConfirmDialog(feature_display, gridPanel,
"Options", JOptionPane.OK_CANCEL_OPTION);
@@ -3968,8 +3973,8 @@ public class BamView extends JPanel
new MappedReads((String)combo.getSelectedItem(),BamView.this, samFileReaderHash,
seqNames, offsetLengths, concatSequences, seqLengths,
- (useGroup.isSelected() ? groupsFrame : null),
- threshold.getValue(), minSize.getValue(), minBams.getValue(), true);
+ (useGroup.isSelected() ? groupsFrame : null), threshold.getValue(),
+ minSize.getValue(), minBams.getValue(), cbOpposite.isSelected(), true);
}
}
diff --git a/uk/ac/sanger/artemis/components/alignment/MappedReads.java b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
index 83b75df54..145442b53 100644
--- a/uk/ac/sanger/artemis/components/alignment/MappedReads.java
+++ b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
@@ -201,6 +201,7 @@ public class MappedReads
* @param threshold
* @param minSize
* @param minBams
+ * @param readsOnOppositeStrand assume reads are on the opposite strand if true.
* @param contained
*/
public MappedReads(
@@ -215,6 +216,7 @@ public class MappedReads
final int threshold,
final int minSize,
final int minBams,
+ final boolean readsOnOppositeStrand,
final boolean contained)
{
this.refName = refName;
@@ -247,7 +249,7 @@ public class MappedReads
centerDialog();
final CalculateNewFeatures cmr = new CalculateNewFeatures(
- feature_display, refName, groupsFrame, threshold, minSize, minBams);
+ feature_display, refName, groupsFrame, threshold, minSize, minBams, readsOnOppositeStrand);
cmr.start();
dialog.setVisible(true);
}
@@ -502,6 +504,7 @@ public class MappedReads
private int threshold;
private int minSize;
private int minBams;
+ private boolean readsOnOppositeStrand;
private GroupBamFrame groupsFrame;
CalculateNewFeatures(final FeatureDisplay feature_display,
@@ -509,7 +512,8 @@ public class MappedReads
final GroupBamFrame groupsFrame,
final int threshold,
final int minSize,
- final int minBams)
+ final int minBams,
+ final boolean readsOnOppositeStrand)
{
entryGroup = feature_display.getEntryGroup();
bases = feature_display.getBases();
@@ -518,6 +522,7 @@ public class MappedReads
this.threshold = threshold;
this.minSize = minSize;
this.minBams = minBams;
+ this.readsOnOppositeStrand = readsOnOppositeStrand;
}
class MarkerObj
@@ -583,7 +588,7 @@ public class MappedReads
int concatShift = 0;
if(offset > start)
concatShift = offset-start;
-
+
cnt =
BamUtils.countOverRange(bamList.get(i), samFileReaderHash,
name, thisStart, thisEnd, concatShift, cnt,
@@ -592,26 +597,24 @@ public class MappedReads
}
}
else
- {
cnt =
BamUtils.countOverRange(bamList.get(i), samFileReaderHash,
refSeq, start, stop, 0, cnt,
samRecordFlagPredicate, samRecordMapQPredicate);
- }
-
+
for(int k=0; k<cnt.length; k++)
{
final Range r = new Range(start+k, start+k+1);
-
// find forward strand potential features
- fwdStart = findFeatures(cnt[k][0], true, fwdStart, j+k,
- r, excluseKeys, fwdMarkers, entryGroup, i);
-
+ fwdStart = findFeatures(
+ (!readsOnOppositeStrand ? cnt[k][0] : cnt[k][1]), true,
+ fwdStart, j+k, r, excluseKeys, fwdMarkers, entryGroup, i);
+
// find reverse strand potential features
- revStart = findFeatures(cnt[k][1], false, revStart, j+k,
- r, excluseKeys, revMarkers, entryGroup, i);
+ revStart = findFeatures(
+ (!readsOnOppositeStrand ? cnt[k][1] : cnt[k][0]), false,
+ revStart, j+k, r, excluseKeys, revMarkers, entryGroup, i);
}
-
}
catch (OutOfRangeException e1)
{
@@ -620,7 +623,8 @@ public class MappedReads
}
}
- final Entry newEntry = entryGroup.createEntry ("align_"+threshold+"_"+minBams+"_"+minSize);
+ final Entry newEntry = entryGroup.createEntry (
+ "align_"+threshold+"_"+minBams+"_"+minSize+(!readsOnOppositeStrand ? "":"_opp"));
createFeatures(fwdMarkers, true, newEntry);
createFeatures(revMarkers, false, newEntry);
return null;
--
GitLab