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Commit 15355f51 authored by tcarver's avatar tcarver
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show read mate sequence if available

parent 83157825
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uk/ac/sanger/artemis/components/alignment/BamView.java
+ 67
− 62
View file @ 15355f51
......@@ -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);
}
else
{
viewDetail.appendString("Mate Unmapped ", Level.DEBUG);
viewer.appendString("Mate Strand "+
(sam.getMateNegativeStrandFlag() ? "-" : "+"), 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(sam.getReadPairedFlag())
viewer.appendString("\nSecond Of Pair "+
(sam.getSecondOfPairFlag() ? "yes" : "no"), Level.DEBUG);
if(thisSAMRecord.getReadPairedFlag())
viewDetail.appendString("\nSecond Of Pair "+
(thisSAMRecord.getSecondOfPairFlag() ? "yes" : "no"), Level.DEBUG);
viewer.appendString("\n\nRead Bases:\n", Level.INFO);
wrapReadBases(sam, viewer);
viewDetail.appendString("\n\nRead Bases:\n", Level.INFO);
if(sam.getReadPairedFlag() && mate != null)
{
viewer.appendString("\nMate Read Bases:\n", Level.INFO);
wrapReadBases(mate, viewer);
}
}
// wrap the read bases
String seq = new String(thisSAMRecord.getReadBases());
int MAX_SEQ_LINE_LENGTH = 100;
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);
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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