From 15355f51489aab4ed813e6a18ba83b8fb3634a86 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 7 Mar 2013 11:07:14 +0000
Subject: [PATCH] show read mate sequence if available
---
.../artemis/components/alignment/BamView.java | 129 +++++++++---------
1 file changed, 67 insertions(+), 62 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index a933d301e..82bfd0daf 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -3812,89 +3812,95 @@ public class BamView extends JPanel
appendToDetailView(readRecord, mateRecord, viewDetail, bamList);
}
- private static void appendToDetailView(final SAMRecord thisSAMRecord,
- final SAMRecord thisSAMRecordMate,
- final FileViewer viewDetail,
+ private static void appendToDetailView(final SAMRecord sam,
+ final SAMRecord mate,
+ final FileViewer viewer,
final List<String> bamList)
{
- if(bamList.size() > 1 && thisSAMRecord.getAttribute("FL") != null)
+ if(bamList.size() > 1 && sam.getAttribute("FL") != null)
{
- int bamIndex = (Integer)thisSAMRecord.getAttribute("FL");
- if(bamIndex < bamList.size())
- viewDetail.appendString("File "+bamList.get(bamIndex)+"\n\n", Level.INFO);
+ int bamIdx = (Integer)sam.getAttribute("FL");
+ if(bamIdx < bamList.size())
+ viewer.appendString("File "+bamList.get(bamIdx)+"\n\n", Level.INFO);
}
- viewDetail.appendString("Read Name "+thisSAMRecord.getReadName()+"\n", Level.INFO);
- viewDetail.appendString("Coordinates "+thisSAMRecord.getAlignmentStart()+".."+
- thisSAMRecord.getAlignmentEnd()+"\n", Level.DEBUG);
- viewDetail.appendString("Length "+thisSAMRecord.getReadLength()+"\n", Level.DEBUG);
- 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);
- viewDetail.appendString("Cigar String "+thisSAMRecord.getCigarString()+"\n", Level.DEBUG);
- viewDetail.appendString("Strand "+
- (thisSAMRecord.getReadNegativeStrandFlag() ? "-\n\n" : "+\n\n"), Level.DEBUG);
+ viewer.appendString("Read Name "+sam.getReadName()+"\n", Level.INFO);
+ viewer.appendString("Coordinates "+sam.getAlignmentStart()+".."+
+ sam.getAlignmentEnd()+"\n", Level.DEBUG);
+ viewer.appendString("Length "+sam.getReadLength()+"\n", Level.DEBUG);
+ viewer.appendString("Reference Name "+sam.getReferenceName()+"\n", Level.DEBUG);
+ viewer.appendString("Inferred Size "+sam.getInferredInsertSize()+"\n", Level.DEBUG);
+ viewer.appendString("Mapping Quality "+sam.getMappingQuality()+"\n", Level.DEBUG);
+ viewer.appendString("Cigar String "+sam.getCigarString()+"\n", Level.DEBUG);
+ viewer.appendString("Strand "+
+ (sam.getReadNegativeStrandFlag() ? "-\n\n" : "+\n\n"), Level.DEBUG);
- if(thisSAMRecord.getReadPairedFlag() && !thisSAMRecord.getMateUnmappedFlag())
+ if(sam.getReadPairedFlag())
{
- if(thisSAMRecordMate != null)
+ if(mate != 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);
+ viewer.appendString("Mate Coordinates "+mate.getAlignmentStart()+".."+
+ mate.getAlignmentEnd()+"\n", Level.DEBUG);
+ viewer.appendString("Mate Length "+mate.getReadLength()+"\n", Level.DEBUG);
+ viewer.appendString("Mate Reference Name "+mate.getReferenceName()+"\n", Level.DEBUG);
+ viewer.appendString("Mate Inferred Size "+mate.getInferredInsertSize()+"\n", Level.DEBUG);
+ viewer.appendString("Mate Mapping Quality "+mate.getMappingQuality()+"\n", Level.DEBUG);
+ viewer.appendString("Mate Cigar String "+mate.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);
+ viewer.appendString("Mate Start Coordinate "+sam.getMateAlignmentStart()+"\n", Level.DEBUG);
+ viewer.appendString("Mate Reference Name "+sam.getMateReferenceName()+"\n", Level.DEBUG);
}
- viewDetail.appendString("Mate Strand "+
- (thisSAMRecord.getMateNegativeStrandFlag() ? "-" : "+"), Level.DEBUG);
+ viewer.appendString("Mate Strand "+
+ (sam.getMateNegativeStrandFlag() ? "-" : "+"), Level.DEBUG);
}
- else
- {
- viewDetail.appendString("Mate Unmapped ", Level.DEBUG);
- }
-
- viewDetail.appendString("\n\nFlags:", Level.INFO);
- viewDetail.appendString("\nDuplicate Read "+
- (thisSAMRecord.getDuplicateReadFlag() ? "yes" : "no"), Level.DEBUG);
+
+ viewer.appendString("\n\nFlags:", Level.INFO);
+ viewer.appendString("\nDuplicate Read "+
+ (sam.getDuplicateReadFlag() ? "yes" : "no"), Level.DEBUG);
- viewDetail.appendString("\nRead Paired "+
- (thisSAMRecord.getReadPairedFlag() ? "yes" : "no"), Level.DEBUG);
- if(thisSAMRecord.getReadPairedFlag())
+ viewer.appendString("\nRead Paired "+
+ (sam.getReadPairedFlag() ? "yes" : "no"), Level.DEBUG);
+ if(sam.getReadPairedFlag())
{
- viewDetail.appendString("\nFirst of Pair "+
- (thisSAMRecord.getFirstOfPairFlag() ? "yes" : "no"), Level.DEBUG);
- viewDetail.appendString("\nMate Unmapped "+
- (thisSAMRecord.getMateUnmappedFlag() ? "yes" : "no"), Level.DEBUG);
- viewDetail.appendString("\nProper Pair "+
- (thisSAMRecord.getProperPairFlag() ? "yes" : "no"), Level.DEBUG);
+ viewer.appendString("\nFirst of Pair "+
+ (sam.getFirstOfPairFlag() ? "yes" : "no"), Level.DEBUG);
+ viewer.appendString("\nMate Unmapped "+
+ (sam.getMateUnmappedFlag() ? "yes" : "no"), Level.DEBUG);
+ viewer.appendString("\nProper Pair "+
+ (sam.getProperPairFlag() ? "yes" : "no"), Level.DEBUG);
}
- viewDetail.appendString("\nRead Fails Vendor\nQuality Check "+
- (thisSAMRecord.getReadFailsVendorQualityCheckFlag() ? "yes" : "no"), Level.DEBUG);
- viewDetail.appendString("\nRead Unmapped "+
- (thisSAMRecord.getReadUnmappedFlag() ? "yes" : "no"), Level.DEBUG);
+ viewer.appendString("\nRead Fails Vendor\nQuality Check "+
+ (sam.getReadFailsVendorQualityCheckFlag() ? "yes" : "no"), Level.DEBUG);
+ viewer.appendString("\nRead Unmapped "+
+ (sam.getReadUnmappedFlag() ? "yes" : "no"), Level.DEBUG);
- if(thisSAMRecord.getReadPairedFlag())
- viewDetail.appendString("\nSecond Of Pair "+
- (thisSAMRecord.getSecondOfPairFlag() ? "yes" : "no"), Level.DEBUG);
+ if(sam.getReadPairedFlag())
+ viewer.appendString("\nSecond Of Pair "+
+ (sam.getSecondOfPairFlag() ? "yes" : "no"), Level.DEBUG);
- viewDetail.appendString("\n\nRead Bases:\n", Level.INFO);
+ viewer.appendString("\n\nRead Bases:\n", Level.INFO);
+ wrapReadBases(sam, viewer);
- // wrap the read bases
- String seq = new String(thisSAMRecord.getReadBases());
- int MAX_SEQ_LINE_LENGTH = 100;
+ if(sam.getReadPairedFlag() && mate != null)
+ {
+ viewer.appendString("\nMate Read Bases:\n", Level.INFO);
+ wrapReadBases(mate, viewer);
+ }
+ }
+
+ private static void wrapReadBases(final SAMRecord sam,
+ final FileViewer viewer)
+ {
+ final String seq = new String(sam.getReadBases());
+ final 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);
+ iend = seq.length();
+ viewer.appendString(seq.substring(i, iend)+"\n", Level.DEBUG);
}
}
@@ -3905,8 +3911,7 @@ public class BamView extends JPanel
*/
protected SAMRecord getMate(BamViewRecord thisSAMRecord)
{
- if(!thisSAMRecord.sam.getReadPairedFlag() || // read is not paired in sequencing
- thisSAMRecord.sam.getMateUnmappedFlag())
+ if(!thisSAMRecord.sam.getReadPairedFlag()) // read is not paired in sequencing
return null;
SAMRecord mate = null;
--
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