From 05fd869413d7adf4c7fc93d002924a5e92d86118 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 2 Aug 2011 16:44:54 +0100
Subject: [PATCH] add mate attributes to read details display
---
.../artemis/components/alignment/BamView.java | 76 +++++++++++++++----
1 file changed, 61 insertions(+), 15 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 94ad3da0f..96aafd715 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -3139,7 +3139,7 @@ public class BamView extends JPanel
public void actionPerformed(ActionEvent e)
{
FileViewer viewDetail = new FileViewer(thisSAMRecord.getReadName(), true, false, false);
- appendToDetailView(thisSAMRecord, viewDetail);
+ appendToDetailView(thisSAMRecord, getMate(thisSAMRecord), viewDetail);
}
});
popup.add(showDetails);
@@ -3150,7 +3150,7 @@ public class BamView extends JPanel
}
}
- private void appendToDetailView(SAMRecord thisSAMRecord, FileViewer viewDetail)
+ private void appendToDetailView(SAMRecord thisSAMRecord, SAMRecord thisSAMRecordMate, FileViewer viewDetail)
{
viewDetail.appendString("Read Name "+thisSAMRecord.getReadName()+"\n", Level.INFO);
viewDetail.appendString("Coordinates "+thisSAMRecord.getAlignmentStart()+".."+
@@ -3159,23 +3159,35 @@ public class BamView extends JPanel
viewDetail.appendString("Reference Name "+thisSAMRecord.getReferenceName()+"\n", Level.DEBUG);
viewDetail.appendString("Inferred Size "+thisSAMRecord.getInferredInsertSize()+"\n", Level.DEBUG);
viewDetail.appendString("Mapping Quality "+thisSAMRecord.getMappingQuality()+"\n", Level.DEBUG);
-
- if(thisSAMRecord.getReadPairedFlag() && thisSAMRecord.getProperPairFlag() && !thisSAMRecord.getMateUnmappedFlag())
- {
- viewDetail.appendString("Mate Reference Name "+thisSAMRecord.getMateReferenceName()+"\n", Level.DEBUG);
- viewDetail.appendString("Mate Start Coordinate "+thisSAMRecord.getMateAlignmentStart()+"\n", Level.DEBUG);
- viewDetail.appendString("Strand (read/mate) "+
- (thisSAMRecord.getReadNegativeStrandFlag() ? "-" : "+")+" / "+
- (thisSAMRecord.getMateNegativeStrandFlag() ? "-" : "+"), Level.DEBUG);
+ viewDetail.appendString("Cigar String "+thisSAMRecord.getCigarString()+"\n", Level.DEBUG);
+ viewDetail.appendString("Strand "+
+ (thisSAMRecord.getReadNegativeStrandFlag() ? "-\n\n" : "+\n\n"), Level.DEBUG);
+
+ if(!thisSAMRecord.getMateUnmappedFlag())
+ {
+ if(thisSAMRecordMate != null)
+ {
+ viewDetail.appendString("Mate Coordinates "+thisSAMRecordMate.getAlignmentStart()+".."+
+ thisSAMRecordMate.getAlignmentEnd()+"\n", Level.DEBUG);
+ viewDetail.appendString("Mate Length "+thisSAMRecordMate.getReadLength()+"\n", Level.DEBUG);
+ viewDetail.appendString("Mate Reference Name "+thisSAMRecordMate.getReferenceName()+"\n", Level.DEBUG);
+ viewDetail.appendString("Mate Inferred Size "+thisSAMRecordMate.getInferredInsertSize()+"\n", Level.DEBUG);
+ viewDetail.appendString("Mate Mapping Quality "+thisSAMRecordMate.getMappingQuality()+"\n", Level.DEBUG);
+ viewDetail.appendString("Mate Cigar String "+thisSAMRecordMate.getCigarString()+"\n", Level.DEBUG);
+ }
+ else
+ {
+ viewDetail.appendString("Mate Start Coordinate "+thisSAMRecord.getMateAlignmentStart()+"\n", Level.DEBUG);
+ viewDetail.appendString("Mate Reference Name "+thisSAMRecord.getMateReferenceName()+"\n", Level.DEBUG);
+ }
+ viewDetail.appendString("Mate Strand "+
+ (thisSAMRecord.getMateNegativeStrandFlag() ? "-" : "+"), Level.DEBUG);
}
else
{
- viewDetail.appendString("Strand (read) "+
- (thisSAMRecord.getReadNegativeStrandFlag() ? "-" : "+"), Level.DEBUG);
+ viewDetail.appendString("Mate Unmapped ", Level.DEBUG);
}
- viewDetail.appendString("\n\nCigar String "+thisSAMRecord.getCigarString(), Level.DEBUG);
-
viewDetail.appendString("\n\nFlags:", Level.INFO);
viewDetail.appendString("\nDuplicate Read "+
(thisSAMRecord.getDuplicateReadFlag() ? "yes" : "no"), Level.DEBUG);
@@ -3201,9 +3213,43 @@ public class BamView extends JPanel
(thisSAMRecord.getSecondOfPairFlag() ? "yes" : "no"), Level.DEBUG);
viewDetail.appendString("\n\nRead Bases:\n", Level.INFO);
- viewDetail.appendString(new String(thisSAMRecord.getReadBases()), Level.DEBUG);
+
+ // wrap the read bases
+ String seq = new String(thisSAMRecord.getReadBases());
+ int MAX_SEQ_LINE_LENGTH = 100;
+ for(int i=0; i<=seq.length(); i+=MAX_SEQ_LINE_LENGTH)
+ {
+ int iend = i+MAX_SEQ_LINE_LENGTH;
+ if(iend > seq.length())
+ iend = seq.length();
+ viewDetail.appendString(seq.substring(i, iend)+"\n", Level.DEBUG);
+ }
}
+ /**
+ * Query for the mate of a read
+ * @param mate
+ * @return
+ */
+ private SAMRecord getMate(SAMRecord thisSAMRecord)
+ {
+ SAMRecord mate = null;
+ try
+ {
+ int fileIndex = 0;
+ if(bamList.size()>1)
+ fileIndex = (Integer) thisSAMRecord.getAttribute("FL");
+ String bam = bamList.get(fileIndex);
+ final SAMFileReader inputSam = getSAMFileReader(bam);
+ mate = inputSam.queryMate(thisSAMRecord);
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ return mate;
+ }
+
protected SAMRecordPredicate getSamRecordFlagPredicate()
{
return samRecordFlagPredicate;
--
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