diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 3a37de284b06847b0ecd9c38c1cb9d302780946f..0e2c3afd690dee4e672955aaf4bd24223fb6cea2 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -63,6 +63,7 @@ import java.lang.management.ManagementFactory;
import java.lang.management.MemoryMXBean;
import java.lang.reflect.Field;
import java.net.URL;
+import java.util.ArrayList;
import java.util.Collections;
import java.util.Enumeration;
import java.util.HashMap;
@@ -225,8 +226,8 @@ public class BamView extends JPanel
private static Color DEEP_PINK = new Color(139,10,80);
private Point lastMousePoint = null;
- private SAMRecord mouseOverSAMRecord = null;
- private SAMRecord highlightSAMRecord = null;
+ private BamViewRecord mouseOverSAMRecord = null;
+ private BamViewRecord highlightSAMRecord = null;
private String mouseOverInsertion;
// record of where a mouse drag starts
protected int dragStart = -1;
@@ -374,26 +375,26 @@ public class BamView extends JPanel
return null;
String msg =
- mouseOverSAMRecord.getReadName() + "\n" +
- mouseOverSAMRecord.getAlignmentStart() + ".." +
- mouseOverSAMRecord.getAlignmentEnd() + "\nisize=" +
- mouseOverSAMRecord.getInferredInsertSize() + "\nmapq=" +
- mouseOverSAMRecord.getMappingQuality()+"\nrname="+
- mouseOverSAMRecord.getReferenceName();
+ mouseOverSAMRecord.sam.getReadName() + "\n" +
+ mouseOverSAMRecord.sam.getAlignmentStart() + ".." +
+ mouseOverSAMRecord.sam.getAlignmentEnd() + "\nisize=" +
+ mouseOverSAMRecord.sam.getInferredInsertSize() + "\nmapq=" +
+ mouseOverSAMRecord.sam.getMappingQuality()+"\nrname="+
+ mouseOverSAMRecord.sam.getReferenceName();
- if( mouseOverSAMRecord.getReadPairedFlag() &&
- mouseOverSAMRecord.getProperPairFlag() &&
- !mouseOverSAMRecord.getMateUnmappedFlag())
+ if( mouseOverSAMRecord.sam.getReadPairedFlag() &&
+ mouseOverSAMRecord.sam.getProperPairFlag() &&
+ !mouseOverSAMRecord.sam.getMateUnmappedFlag())
{
msg = msg +
"\nstrand (read/mate): "+
- (mouseOverSAMRecord.getReadNegativeStrandFlag() ? "-" : "+")+" / "+
- (mouseOverSAMRecord.getMateNegativeStrandFlag() ? "-" : "+");
+ (mouseOverSAMRecord.sam.getReadNegativeStrandFlag() ? "-" : "+")+" / "+
+ (mouseOverSAMRecord.sam.getMateNegativeStrandFlag() ? "-" : "+");
}
else
msg = msg +
"\nstrand (read/mate): "+
- (mouseOverSAMRecord.getReadNegativeStrandFlag() ? "-" : "+");
+ (mouseOverSAMRecord.sam.getReadNegativeStrandFlag() ? "-" : "+");
if(msg != null && mouseOverInsertion != null)
msg = msg + "\nInsertion at:" +mouseOverInsertion;
@@ -662,7 +663,7 @@ public class BamView extends JPanel
int cnt = 0;
- int nbins = 600;
+ int nbins = 800;
int binSize = ((end-start)/nbins)+1;
if(binSize < 1)
{
@@ -1077,30 +1078,30 @@ public class BamView extends JPanel
{
ypos += 11;
- SAMRecord thisRead = readsInView.get(i).sam;
+ BamViewRecord thisRead = readsInView.get(i);
if (ypos < r.getMaxY() || ypos > r.getMinY())
drawSequence(g2, thisRead, ypos, refSeq, refSeqStart);
drawn[i] = true;
- int thisEnd = thisRead.getAlignmentEnd();
+ int thisEnd = thisRead.sam.getAlignmentEnd();
if (thisEnd == 0)
- thisEnd = thisRead.getAlignmentStart() + thisRead.getReadLength();
+ thisEnd = thisRead.sam.getAlignmentStart() + thisRead.sam.getReadLength();
for (int j = i + 1; j < nreads; j++)
{
if (!drawn[j])
{
- SAMRecord nextRead = readsInView.get(j).sam;
- int nextStart = nextRead.getAlignmentStart();
+ BamViewRecord nextRead = readsInView.get(j);
+ int nextStart = nextRead.sam.getAlignmentStart();
if (nextStart > thisEnd + 1)
{
if (ypos < r.getMaxY() || ypos > r.getMinY())
drawSequence(g2, nextRead, ypos, refSeq, refSeqStart);
drawn[j] = true;
- thisEnd = nextRead.getAlignmentEnd();
+ thisEnd = nextRead.sam.getAlignmentEnd();
if (thisEnd == 0)
- thisEnd = nextStart + nextRead.getReadLength();
+ thisEnd = nextStart + nextRead.sam.getReadLength();
}
else if (ypos > r.getMaxY() || ypos < r.getMinY())
break;
@@ -1132,9 +1133,10 @@ public class BamView extends JPanel
* @param pixPerBase
* @param ypos
*/
- private void drawSequence(Graphics2D g2, SAMRecord samRecord,
+ private void drawSequence(Graphics2D g2, BamViewRecord bamViewRecord,
int ypos, String refSeq, int refSeqStart)
{
+ SAMRecord samRecord = bamViewRecord.sam;
if (!samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped ) // mate is unmapped
g2.setColor(Color.black);
@@ -1211,7 +1213,7 @@ public class BamView extends JPanel
// highlight
if(highlightSAMRecord != null &&
- highlightSAMRecord.getReadName().equals(samRecord.getReadName()))
+ highlightSAMRecord.sam.getReadName().equals(samRecord.getReadName()))
{
refPos = block.getReferenceStart() + offset - refSeqStart;
int xstart = refPos*ALIGNMENT_PIX_PER_BASE;
@@ -1252,7 +1254,7 @@ public class BamView extends JPanel
if(lastMousePoint.getX() > xstart &&
lastMousePoint.getX() < xend)
{
- mouseOverSAMRecord = samRecord;
+ mouseOverSAMRecord = bamViewRecord;
if(insertions != null)
mouseOverInsertion = insertions.get((int)lastMousePoint.getX());
@@ -1308,8 +1310,11 @@ public class BamView extends JPanel
{
BamViewRecord bamViewRecord = readsInView.get(i);
SAMRecord samRecord = bamViewRecord.sam;
+ BamViewRecord bamViewNextRecord = null;
SAMRecord samNextRecord = null;
+ ArrayList<Integer> snps = getSNPs(samRecord);
+
if( !samRecord.getReadPairedFlag() || // read is not paired in sequencing
samRecord.getMateUnmappedFlag() ) // mate is unmapped
{
@@ -1320,7 +1325,7 @@ public class BamView extends JPanel
continue;
g2.setColor(Color.black);
- drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
+ drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps);
}
continue;
}
@@ -1331,7 +1336,8 @@ public class BamView extends JPanel
if(i < readsInView.size()-1)
{
- samNextRecord = readsInView.get(++i).sam;
+ bamViewNextRecord = readsInView.get(++i);
+ samNextRecord = bamViewNextRecord.sam;
if(samRecord.getReadName().equals(samNextRecord.getReadName()))
{
@@ -1361,18 +1367,18 @@ public class BamView extends JPanel
else
g2.setColor(Color.blue);
- drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
- drawRead(g2, samNextRecord, pixPerBase, ypos, baseAtStartOfView);
+ drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps);
+ drawRead(g2, bamViewNextRecord, pixPerBase, ypos, baseAtStartOfView, getSNPs(samNextRecord));
}
else
{
- drawLoneRead(g2, bamViewRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight);
+ drawLoneRead(g2, bamViewRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight, snps);
i--;
}
}
else
{
- drawLoneRead(g2, bamViewRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight);
+ drawLoneRead(g2, bamViewRecord, ypos, pixPerBase, baseAtStartOfView, scaleHeight, snps);
}
}
@@ -1445,8 +1451,10 @@ public class BamView extends JPanel
int recordStart = samRecord.getAlignmentStart()+offset;
int recordEnd = samRecord.getAlignmentEnd()+offset;
+ ArrayList<Integer> snps = getSNPs(samRecord);
+
if(colourByCoverageColour.isSelected() ||
- lstStart != recordStart || lstEnd != recordEnd)
+ lstStart != recordStart || lstEnd != recordEnd || snps != null)
{
if(colourByCoverageColour.isSelected())
g2.setColor(getColourByCoverageColour(bamViewRecord));
@@ -1467,12 +1475,17 @@ public class BamView extends JPanel
else
g2.setColor(DARK_GREEN);
- lstStart = recordStart;
- lstEnd = recordEnd;
+ if(snps != null)
+ lstStart = -1;
+ else
+ {
+ lstStart = recordStart;
+ lstEnd = recordEnd;
+ }
if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
- drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
+ drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps);
}
}
@@ -1541,9 +1554,10 @@ public class BamView extends JPanel
final int offset = getSequenceOffset(samRecord.getReferenceName());
final int recordStart = samRecord.getAlignmentStart()+offset;
final int recordEnd = samRecord.getAlignmentEnd()+offset;
-
+ ArrayList<Integer> snps = getSNPs(samRecord);
+
if(colourByCoverageColour.isSelected() ||
- lstStart != recordStart || lstEnd != recordEnd)
+ lstStart != recordStart || lstEnd != recordEnd || snps != null)
{
if(colourByCoverageColour.isSelected())
g2.setColor(getColourByCoverageColour(bamViewRecord));
@@ -1564,12 +1578,18 @@ public class BamView extends JPanel
else
g2.setColor(DARK_GREEN);
- lstStart = recordStart;
- lstEnd = recordEnd;
+ if(snps != null)
+ lstStart = -1;
+ else
+ {
+ lstStart = recordStart;
+ lstEnd = recordEnd;
+ }
if(ypos > r.getMaxY() || ypos < r.getMinY())
continue;
- drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
+
+ drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps);
}
}
}
@@ -1672,7 +1692,7 @@ public class BamView extends JPanel
g2.setStroke(originalStroke);
if(highlightSAMRecord != null &&
- highlightSAMRecord.getReadName().equals(pr.sam1.sam.getReadName()))
+ highlightSAMRecord.sam.getReadName().equals(pr.sam1.sam.getReadName()))
g2.setColor(Color.black);
else
g2.setColor(Color.gray);
@@ -1717,11 +1737,10 @@ public class BamView extends JPanel
g2.setColor(Color.red);
else
g2.setColor(Color.blue);
-
- drawRead(g2, pr.sam1.sam, pixPerBase, ypos, baseAtStartOfView);
-
+
+ drawRead(g2, pr.sam1, pixPerBase, ypos, baseAtStartOfView, getSNPs(pr.sam1.sam));
if(pr.sam2 != null)
- drawRead(g2, pr.sam2.sam, pixPerBase, ypos, baseAtStartOfView);
+ drawRead(g2, pr.sam2, pixPerBase, ypos, baseAtStartOfView, getSNPs(pr.sam2.sam));
}
}
@@ -1791,10 +1810,10 @@ public class BamView extends JPanel
int hgt = jspView.getVisibleRect().height-scaleHeight;
if(!cbCoverageStrandView.isSelected())
{
- int y = getHeight()-10-( (hgt* MAX_COVERAGE)/(coverageView.max/coverageView.windowSize) );
+ int y = getHeight()-6-( (hgt* MAX_COVERAGE)/(coverageView.max/coverageView.windowSize) );
g2.setColor(Color.YELLOW);
// draw the threshold for the coverage max read cut-off
- g2.fillRect(0, y, getWidth(), 10);
+ g2.fillRect(0, y, getWidth(), 8);
}
g2.translate(0, getHeight()-hgt-scaleHeight);
@@ -1813,7 +1832,7 @@ public class BamView extends JPanel
* @param stroke
*/
private void drawLoneRead(Graphics2D g2, BamViewRecord bamViewRecord, int ypos,
- float pixPerBase, int baseAtStartOfView, int scaleHeight)
+ float pixPerBase, int baseAtStartOfView, int scaleHeight, ArrayList<Integer> snps)
{
SAMRecord samRecord = bamViewRecord.sam;
boolean offTheTop = false;
@@ -1864,10 +1883,10 @@ public class BamView extends JPanel
else
g2.setColor(Color.blue);
- drawRead(g2, samRecord, pixPerBase, ypos, baseAtStartOfView);
+ drawRead(g2, bamViewRecord, pixPerBase, ypos, baseAtStartOfView, snps);
- if (isSNPs)
- showSNPsOnReads(g2, samRecord, pixPerBase, ypos, offset);
+ /*if (isSNPs)
+ showSNPsOnReads(g2, samRecord, pixPerBase, ypos, offset);*/
}
@@ -1968,20 +1987,23 @@ public class BamView extends JPanel
* @param pixPerBase
* @param ypos
* @param baseAtStartOfView
+ * @param snps
*/
private void drawRead(Graphics2D g2,
- final SAMRecord thisRead,
+ final BamViewRecord bamViewRecord,
final float pixPerBase,
final int ypos,
- final int baseAtStartOfView)
+ final int baseAtStartOfView,
+ final ArrayList<Integer> snps)
{
+ SAMRecord thisRead = bamViewRecord.sam;
int offset = getSequenceOffset(thisRead.getReferenceName());
int thisStart = thisRead.getAlignmentStart()+offset-baseAtStartOfView;
int thisEnd = thisRead.getAlignmentEnd()+offset-baseAtStartOfView;
if(highlightSAMRecord != null &&
- highlightSAMRecord.getReadName().equals(thisRead.getReadName()))
+ highlightSAMRecord.sam.getReadName().equals(thisRead.getReadName()))
{
Stroke originalStroke = g2.getStroke();
Stroke stroke =
@@ -2032,12 +2054,12 @@ public class BamView extends JPanel
if(lastMousePoint.getX() > thisStart * pixPerBase &&
lastMousePoint.getX() < thisEnd * pixPerBase)
{
- mouseOverSAMRecord = thisRead;
+ mouseOverSAMRecord = bamViewRecord;
}
}
- if (isSNPs)
- showSNPsOnReads(g2, thisRead, pixPerBase, ypos, offset);
+ if (isSNPs && snps != null)
+ showSNPsOnReads(snps, g2, pixPerBase, ypos);
}
/**
@@ -2136,52 +2158,71 @@ public class BamView extends JPanel
/**
* Display the SNPs for the given read.
+ * @param snps
* @param g2
- * @param thisRead
* @param pixPerBase
* @param ypos
*/
- private void showSNPsOnReads(Graphics2D g2, SAMRecord thisRead,
- float pixPerBase, int ypos, int offset)
+ private void showSNPsOnReads(final ArrayList<Integer> snps,
+ final Graphics2D g2,
+ float pixPerBase, int ypos)
{
- int thisStart = thisRead.getAlignmentStart();
- int thisEnd = thisRead.getAlignmentEnd();
+ g2.setColor(Color.red);
+ for(int pos: snps)
+ g2.drawLine((int) (pos * pixPerBase), ypos + 2,
+ (int) (pos * pixPerBase), ypos - 2);
+ }
+
+
+ /**
+ * Get the SNP positions
+ * @param samRecord
+ */
+ private ArrayList<Integer> getSNPs(final SAMRecord samRecord)
+ {
+ if(!isSNPs) // return null if not displaying SNPs
+ return null;
+ int rbeg = samRecord.getAlignmentStart();
+ int rend = samRecord.getAlignmentEnd();
+ int offset = getSequenceOffset(samRecord.getReferenceName());
+ ArrayList<Integer> snps = null;
// use alignment blocks of the contiguous alignment of
// subsets of read bases to a reference sequence
try
{
- char[] refSeq = bases.getSubSequenceC(
- new Range(thisStart+offset, thisEnd+offset), Bases.FORWARD);
- byte[] readSeq = thisRead.getReadBases();
-
- Color col = g2.getColor();
- g2.setColor(Color.red);
+ final char[] refSeq = bases.getSubSequenceC(
+ new Range(rbeg+offset, rend+offset), Bases.FORWARD);
+ final byte[] readSeq = samRecord.getReadBases();
offset = offset - getBaseAtStartOfView();
- final List<AlignmentBlock> blocks = thisRead.getAlignmentBlocks();
+ final List<AlignmentBlock> blocks = samRecord.getAlignmentBlocks();
for(AlignmentBlock block: blocks)
{
- for(int j=0; j<block.getLength(); j++)
+ int readStart = block.getReadStart();
+ int refStart = block.getReferenceStart();
+ int len = block.getLength();
+ for(int j=0; j<len; j++)
{
- int readPos = block.getReadStart()-1+j;
- int refPos = block.getReferenceStart()+j;
-
- if (Character.toUpperCase(refSeq[refPos-thisStart]) != readSeq[readPos])
+ int readPos = readStart-1+j;
+ int refPos = refStart+j;
+ if (Character.toUpperCase(refSeq[refPos-rbeg]) != readSeq[readPos])
{
- g2.drawLine((int) ((refPos+offset) * pixPerBase), ypos + 2,
- (int) ((refPos+offset) * pixPerBase), ypos - 2);
+ if(snps == null)
+ snps = new ArrayList<Integer>();
+ snps.add(refPos+offset);
}
}
}
- g2.setColor(col);
}
catch (OutOfRangeException e)
{
- System.err.println(thisRead.getReadName()+" "+e.getMessage());
+ System.err.println(samRecord.getReadName()+" "+e.getMessage());
}
+ return snps;
}
+
/**
* Add the alignment view to the supplied <code>JPanel</code> in
* a <code>JScrollPane</code>.
@@ -3364,12 +3405,12 @@ public class BamView extends JPanel
return nbasesInView;
}
- protected void setHighlightSAMRecord(SAMRecord highlightSAMRecord)
+ protected void setHighlightSAMRecord(BamViewRecord highlightSAMRecord)
{
this.highlightSAMRecord = highlightSAMRecord;
}
- protected SAMRecord getHighlightSAMRecord()
+ protected BamViewRecord getHighlightSAMRecord()
{
return highlightSAMRecord;
}
@@ -3584,26 +3625,26 @@ public class BamView extends JPanel
popup.remove(showDetails);
if( mouseOverSAMRecord != null &&
- mouseOverSAMRecord.getReadPairedFlag() &&
- !mouseOverSAMRecord.getMateUnmappedFlag() )
+ mouseOverSAMRecord.sam.getReadPairedFlag() &&
+ !mouseOverSAMRecord.sam.getMateUnmappedFlag() )
{
- final SAMRecord thisSAMRecord = mouseOverSAMRecord;
+ final BamViewRecord thisSAMRecord = mouseOverSAMRecord;
gotoMateMenuItem = new JMenuItem("Go to mate of : "+
- thisSAMRecord.getReadName());
+ thisSAMRecord.sam.getReadName());
gotoMateMenuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- String name = thisSAMRecord.getMateReferenceName();
+ String name = thisSAMRecord.sam.getMateReferenceName();
if(name.equals("="))
- name = thisSAMRecord.getReferenceName();
+ name = thisSAMRecord.sam.getReferenceName();
int offset = getSequenceOffset(name);
if(feature_display != null)
feature_display.makeBaseVisible(
- thisSAMRecord.getMateAlignmentStart()+offset);
+ thisSAMRecord.sam.getMateAlignmentStart()+offset);
else
scrollBar.setValue(
- thisSAMRecord.getMateAlignmentStart()+offset-
+ thisSAMRecord.sam.getMateAlignmentStart()+offset-
(nbasesInView/2));
highlightSAMRecord = thisSAMRecord;
@@ -3614,14 +3655,14 @@ public class BamView extends JPanel
if( mouseOverSAMRecord != null)
{
- final SAMRecord thisSAMRecord = mouseOverSAMRecord;
+ final BamViewRecord thisSAMRecord = mouseOverSAMRecord;
showDetails = new JMenuItem("Show details of : "+
- thisSAMRecord.getReadName());
+ thisSAMRecord.sam.getReadName());
showDetails.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- openFileViewer(thisSAMRecord, getMate(thisSAMRecord), bamList);
+ openFileViewer(thisSAMRecord.sam, getMate(thisSAMRecord), bamList);
}
});
popup.add(showDetails);
@@ -3729,21 +3770,21 @@ public class BamView extends JPanel
* @param mate
* @return
*/
- protected SAMRecord getMate(SAMRecord thisSAMRecord)
+ protected SAMRecord getMate(BamViewRecord thisSAMRecord)
{
- if(!thisSAMRecord.getReadPairedFlag() || // read is not paired in sequencing
- thisSAMRecord.getMateUnmappedFlag())
+ if(!thisSAMRecord.sam.getReadPairedFlag() || // read is not paired in sequencing
+ thisSAMRecord.sam.getMateUnmappedFlag())
return null;
SAMRecord mate = null;
try
{
- int fileIndex = 0;
- if(bamList.size()>1)
- fileIndex = (Integer) thisSAMRecord.getAttribute("FL");
+ short fileIndex = 0;
+ if(bamList.size()>1 && thisSAMRecord.bamIndex > 0)
+ fileIndex = thisSAMRecord.bamIndex;
String bam = bamList.get(fileIndex);
final SAMFileReader inputSam = getSAMFileReader(bam);
- mate = inputSam.queryMate(thisSAMRecord);
+ mate = inputSam.queryMate(thisSAMRecord.sam);
}
catch (Exception e)
{