From b94fa2916e784f0118fdfafb067a3387c41be43c Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 3 Aug 2012 12:32:16 +0100
Subject: [PATCH] add option to create new features where the read count is
seen in a minimum number of BAM files
---
.../artemis/components/alignment/BamView.java | 11 +-
.../components/alignment/MappedReads.java | 109 +++++++++++-------
2 files changed, 76 insertions(+), 44 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 5fb944a03..e610135d0 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -2356,10 +2356,16 @@ public class BamView extends JPanel
final Box yBox = Box.createVerticalBox();
final TextFieldInt threshold = new TextFieldInt();
final TextFieldInt minSize = new TextFieldInt();
+ final TextFieldInt minBams = new TextFieldInt();
+
threshold.setValue(6);
minSize.setValue(6);
+ minBams.setValue(bamList.size());
+
yBox.add(new JLabel("Minimum number of reads:"));
yBox.add(threshold);
+ yBox.add(new JLabel("Minimum number of BAMs for reads to be present in:"));
+ yBox.add(minBams);
yBox.add(new JLabel("Minimum feature size:"));
yBox.add(minSize);
@@ -2368,11 +2374,14 @@ public class BamView extends JPanel
"Options", JOptionPane.OK_CANCEL_OPTION);
if(status == JOptionPane.CANCEL_OPTION)
return;
+
+ if(minBams.getValue() > bamList.size())
+ minBams.setValue(bamList.size());
new MappedReads(feature_display, (String)combo.getSelectedItem(),
samFileReaderHash, bamList, seqNames, offsetLengths,
concatSequences, seqLengths, samRecordFlagPredicate, samRecordMapQPredicate,
- threshold.getValue(), minSize.getValue(), true);
+ threshold.getValue(), minSize.getValue(), minBams.getValue(), true);
}
});
diff --git a/uk/ac/sanger/artemis/components/alignment/MappedReads.java b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
index 230f26e0b..a6ca6f05e 100644
--- a/uk/ac/sanger/artemis/components/alignment/MappedReads.java
+++ b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
@@ -7,8 +7,10 @@ import java.awt.Toolkit;
import java.text.DecimalFormat;
import java.util.Arrays;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.Hashtable;
import java.util.List;
+import java.util.Set;
import java.util.Vector;
import javax.swing.JDialog;
@@ -195,6 +197,9 @@ public class MappedReads
* @param seqLengths
* @param samRecordFlagPredicate
* @param samRecordMapQPredicate
+ * @param threshold
+ * @param minSize
+ * @param minBams
* @param contained
*/
public MappedReads(
@@ -210,6 +215,7 @@ public class MappedReads
final SAMRecordMapQPredicate samRecordMapQPredicate,
final int threshold,
final int minSize,
+ final int minBams,
final boolean contained)
{
this.refName = refName;
@@ -238,7 +244,8 @@ public class MappedReads
dialog.pack();
centerDialog();
- CalculateNewFeatures cmr = new CalculateNewFeatures(feature_display, refName, threshold, minSize);
+ final CalculateNewFeatures cmr = new CalculateNewFeatures(
+ feature_display, refName, threshold, minSize, minBams);
cmr.start();
dialog.setVisible(true);
}
@@ -435,16 +442,30 @@ public class MappedReads
private String refSeq;
private int threshold;
private int minSize;
+ private int minBams;
CalculateNewFeatures(final FeatureDisplay feature_display,
final String refSeq, final int threshold,
- final int minSize)
+ final int minSize,
+ final int minBams)
{
entryGroup = feature_display.getEntryGroup();
bases = feature_display.getBases();
this.refSeq = refSeq;
this.threshold = threshold;
this.minSize = minSize;
+ this.minBams = minBams;
+ }
+
+ class MarkerObj
+ {
+ MarkerRange r;
+ int bamIdx;
+ MarkerObj(MarkerRange r, int bamIdx)
+ {
+ this.r = r;
+ this.bamIdx = bamIdx;
+ }
}
public Object construct()
@@ -458,8 +479,8 @@ public class MappedReads
int fwdStart = -1;
int revStart = -1;
- final List<MarkerRange> fwdMarkers = new Vector<MarkerRange>();
- final List<MarkerRange> revMarkers = new Vector<MarkerRange>();
+ final List<MarkerObj> fwdMarkers = new Vector<MarkerObj>();
+ final List<MarkerObj> revMarkers = new Vector<MarkerObj>();
for (int i = 0; i < bamList.size(); i++)
{
for(int j=beg; j<end; j+=MAX_BASE_CHUNK)
@@ -519,11 +540,11 @@ public class MappedReads
// find forward strand potential features
fwdStart = findFeatures(cnt[k][0], true, fwdStart, j+k,
- r, excluseKeys, fwdMarkers, entryGroup);
+ r, excluseKeys, fwdMarkers, entryGroup, i);
// find reverse strand potential features
revStart = findFeatures(cnt[k][1], false, revStart, j+k,
- r, excluseKeys, revMarkers, entryGroup);
+ r, excluseKeys, revMarkers, entryGroup, i);
}
}
@@ -534,62 +555,63 @@ public class MappedReads
}
}
- final Entry newEntry = entryGroup.createEntry ("align_"+threshold+"_"+minSize);
+ final Entry newEntry = entryGroup.createEntry ("align_"+threshold+"_"+minBams+"_"+minSize);
createFeatures(fwdMarkers, true, newEntry);
createFeatures(revMarkers, false, newEntry);
return null;
}
- private void createFeatures(final List<MarkerRange> markers, final boolean isFwd, final Entry newEntry)
+ private void createFeatures(final List<MarkerObj> markers, final boolean isFwd, final Entry newEntry)
{
final Key key = Key.CDS;
-/* if(entryGroup.getDefaultEntry() != null &&
- entryGroup.getDefaultEntry().getEMBLEntry() instanceof GFFDocumentEntry)
- key = new Key("region");
- else
- key = new Key("misc_feature");*/
// merge overlapping markers
- List<MarkerRange> featureMarkers = new Vector<MarkerRange>();
- List<Integer> ignoreMarkers = new Vector<Integer>();
+ final Set<Integer> ignoreMarkers = new HashSet<Integer>();
for(int i=0; i<markers.size(); i++)
{
if(ignoreMarkers.contains(i))
continue;
- MarkerRange mi = markers.get(i);
+
+ Set<Integer> bamIdxList = new HashSet<Integer>();
+ MarkerObj mi = markers.get(i);
+ MarkerRange mri = mi.r;
+ bamIdxList.add(mi.bamIdx);
for(int j=i+1; j<markers.size(); j++)
{
if(ignoreMarkers.contains(j))
continue;
- MarkerRange mj = markers.get(j);
- if(mi.overlaps(mj))
+ MarkerObj mj = markers.get(j);
+ MarkerRange mrj = mj.r;
+
+ if(mri.overlaps(mrj))
{
- mi = mi.combineRanges(mj, false);
+ bamIdxList.add(mj.bamIdx);
+ mri = mri.combineRanges(mrj, false);
ignoreMarkers.add(j);
}
}
- featureMarkers.add(mi);
- }
-
- for(MarkerRange r: featureMarkers)
- {
- try
- {
- newEntry.createFeature(key,
- ( isFwd ? r.createLocation() : r.createLocation().getComplement()), null);
- }
- catch (ReadOnlyException e1)
- {
- e1.printStackTrace();
- }
- catch (EntryInformationException e1)
- {
- e1.printStackTrace();
- }
- catch (OutOfRangeException e1)
+
+ if(bamIdxList.size() >= minBams)
{
- e1.printStackTrace();
+ // create a new feature
+ try
+ {
+ newEntry.createFeature(key,
+ ( isFwd ? mri.createLocation() : mri.createLocation().getComplement()), null);
+ }
+ catch (ReadOnlyException e)
+ {
+ e.printStackTrace();
+ }
+ catch (EntryInformationException e)
+ {
+ e.printStackTrace();
+ }
+ catch (OutOfRangeException e)
+ {
+ e.printStackTrace();
+ }
}
}
}
@@ -612,8 +634,9 @@ public class MappedReads
final int pos,
final Range range,
final Key excluseKeys[],
- final List<MarkerRange> markers,
- final EntryGroup entryGroup)
+ final List<MarkerObj> markers,
+ final EntryGroup entryGroup,
+ final int bamIdx)
{
if(cnt > threshold && fStart == -1) // START FEATURE
{
@@ -657,7 +680,7 @@ public class MappedReads
{
final MarkerRange marker = new MarkerRange(
bases.getForwardStrand(), fStart, range.getStart());
- markers.add( marker );
+ markers.add( new MarkerObj(marker, bamIdx) );
}
}
catch (OutOfRangeException e1){}
@@ -684,7 +707,7 @@ public class MappedReads
{
final MarkerRange marker = new MarkerRange(
bases.getForwardStrand(), fStart, f.getRawFirstBase() );
- markers.add( marker );
+ markers.add( new MarkerObj(marker, bamIdx) );
}
return -1;
}
--
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