@Override public boolean filter(ReferenceContext ref, GATKSAMRecord read) { return ! (read.getReadFailsVendorQualityCheckFlag() || read.getReadUnmappedFlag()); }
private static boolean unclippedReadOverlapsRegion(final GATKSAMRecord sampleRead, final int referenceIndex, final int start, final int end) { final int readReference = sampleRead.getReferenceIndex(); if (readReference != referenceIndex) return false; final int readStart = sampleRead.getUnclippedStart(); if (readStart > end) return false; final int readEnd = sampleRead.getReadUnmappedFlag() ? sampleRead.getUnclippedEnd() : Math.max(sampleRead.getUnclippedEnd(), sampleRead.getUnclippedStart()); return readEnd >= start; }
public void setRead(final GATKSAMRecord read) { if ( !read.isEmpty() ) { this.read = read; if ( ! read.getReadUnmappedFlag() ) loc = genomeLocParser.createGenomeLoc(read.getReferenceName(), read.getSoftStart(), read.getSoftEnd()); } } }
this.duplicates++; if (!read.getReadUnmappedFlag()) { this.mapped++; this.properly_paired++; if (!read.getReadUnmappedFlag() && !read.getMateUnmappedFlag()) { this.with_itself_and_mate_mapped++; if (!read.getReadUnmappedFlag() && read.getMateUnmappedFlag()) { this.singletons++;
private boolean doNotTryToClean(GATKSAMRecord read) { return read.getReadUnmappedFlag() || read.getNotPrimaryAlignmentFlag() || read.getReadFailsVendorQualityCheckFlag() || read.getMappingQuality() == 0 || read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START || ConstrainedMateFixingManager.iSizeTooBigToMove(read, MAX_ISIZE_FOR_MOVEMENT) || ReadUtils.is454Read(read) || ReadUtils.isIonRead(read); // TODO -- it would be nice if we could use indels from 454/Ion reads as alternate consenses }
final CigarShift cigarShift = (read.getReadUnmappedFlag()) ? new CigarShift(new Cigar(), 0, 0) : hardClipCigar(read.getCigar(), start, stop);
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) { // we can not deal with screwy records if ( read.getReadUnmappedFlag() || read.getCigar().numCigarElements() == 0 ) { emit(read); return 0; } // move existing indels (for 1 indel reads only) to leftmost position within identical sequence int numBlocks = AlignmentUtils.getNumAlignmentBlocks(read); if ( numBlocks == 2 ) { Cigar newCigar = AlignmentUtils.leftAlignIndel(IndelRealigner.unclipCigar(read.getCigar()), ref.getBases(), read.getReadBases(), 0, 0, true); newCigar = IndelRealigner.reclipCigar(newCigar, read); read.setCigar(newCigar); } emit(read); return 1; }
if (read.getReadUnmappedFlag()) {
clippedRead = ( clippedRead.getReadUnmappedFlag() ? clippedRead : ReadClipper.hardClipAdaptorSequence( clippedRead ) ); if( !clippedRead.isEmpty() && clippedRead.getCigar().getReadLength() > 0 ) { clippedRead = ReadClipper.hardClipToRegion(clippedRead, activeRegion.getExtendedLoc().getStart(), activeRegion.getExtendedLoc().getStop());
clippedRead = ( clippedRead.getReadUnmappedFlag() ? clippedRead : ReadClipper.hardClipAdaptorSequence( clippedRead ) ); if( !clippedRead.isEmpty() && clippedRead.getCigar().getReadLength() > 0 ) { clippedRead = ReadClipper.hardClipToRegion( clippedRead, activeRegion.getExtendedLoc().getStart(), activeRegion.getExtendedLoc().getStop() );