@Override public GATKSAMRecord next() { SAMRecord next = it.next(); if (next instanceof GATKSAMRecord) { return (GATKSAMRecord)next; } else { return new GATKSAMRecord(next); } } @Override public void remove() { it.remove(); }
(refIndex != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart == SAMRecord.NO_ALIGNMENT_START)) throw new ReviewedGATKException("Invalid alignment start for artificial read, start = " + alignmentStart); GATKSAMRecord record = new GATKSAMRecord(header); record.setReadName(name); record.setReferenceIndex(refIndex);
@Test public void testUnmappedReadsDoNotFail() { // create an unmapped read final GATKSAMRecord read = new GATKSAMRecord(ArtificialSAMUtils.createArtificialSamHeader()); read.setReadName("foo"); read.setReferenceName("*"); read.setAlignmentStart(100); read.setCigarString("*"); read.setReadUnmappedFlag(true); // try to add it to the manager final OverhangFixingManager manager = new OverhangFixingManager(null, null, null, 100, 1, 30, false); manager.addRead(read); // we just want to make sure that the following call does not fail Assert.assertTrue(true); } }
@Test public void testSecondaryAlignmentsDoNotCauseAccidentalRemovalOfMate() { final List<GATKSAMRecord> properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 530, 1594, true, false); final GATKSAMRecord read1 = properReads.get(0); read1.setFlags(99); // first in proper pair, mate negative strand final GATKSAMRecord read2Primary = properReads.get(1); read2Primary.setFlags(147); // second in pair, mate unmapped, not primary alignment read2Primary.setAlignmentStart(1596); // move the read final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary); read2NonPrimary.setReadName("foo"); read2NonPrimary.setFlags(393); // second in proper pair, on reverse strand read2NonPrimary.setAlignmentStart(451); read2NonPrimary.setMateAlignmentStart(451); final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 10000, 200, 10000); manager.addRead(read2NonPrimary, false, false); manager.addRead(read1, false, false); for ( int i = 0; i < ConstrainedMateFixingManager.EMIT_FREQUENCY; i++ ) manager.addRead(ArtificialSAMUtils.createArtificialRead(header, "foo" + i, 0, 1500, 10), false, false); Assert.assertTrue(manager.forMateMatching.containsKey("foo")); }
@Test public void testSecondaryAlignmentsDoNotInterfere() { final List<GATKSAMRecord> properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 10, 30, true, false); final GATKSAMRecord read1 = properReads.get(0); read1.setAlignmentStart(8); // move the read read1.setFlags(99); // first in proper pair, mate negative strand final GATKSAMRecord read2Primary = properReads.get(1); read2Primary.setFlags(147); // second in pair, mate unmapped, not primary alignment Assert.assertEquals(read1.getInferredInsertSize(), 21); final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary); read2NonPrimary.setFlags(393); // second in proper pair, on reverse strand final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 1000, 1000, 1000); manager.addRead(read1, true, false); manager.addRead(read2NonPrimary, false, false); manager.addRead(read2Primary, false, false); Assert.assertEquals(manager.getNReadsInQueue(), 3); for ( final SAMRecord read : manager.getReadsInQueueForTesting() ) { if ( read.getFirstOfPairFlag() ) { Assert.assertEquals(read.getFlags(), 99); Assert.assertEquals(read.getInferredInsertSize(), 23); } else if ( read.getNotPrimaryAlignmentFlag() ) { Assert.assertEquals(read.getFlags(), 393); Assert.assertEquals(read.getInferredInsertSize(), -21); } else { Assert.assertEquals(read.getFlags(), 147); Assert.assertEquals(read.getInferredInsertSize(), -23); } } }
read2.setFlags(161); // second in pair, mate negative strand final GATKSAMRecord read2Supp = new GATKSAMRecord(read2); read2Supp.setReadName("foo"); read2Supp.setFlags(2209); // second in pair, mate negative strand, supplementary
protected GATKSAMRecord buildSAMRecord(final String readName, final String contig, final int alignmentStart) { GATKSAMRecord record = new GATKSAMRecord(header); record.setReadName(readName); record.setReferenceIndex(dictionary.getSequenceIndex(contig)); record.setAlignmentStart(alignmentStart); record.setCigarString("1M"); record.setReadString("A"); record.setBaseQualityString("A"); record.setReadGroup(readGroup); return record; }
/** * Creates and writes an artificial read given the appropriate data * * @param readBases the bases * @param contig the contig * @param start the read start * @param cigar the cigar string * @param sample the sample name (used to get the right read group) * @param isNegStrand should this read be on the negative strand? */ private void writeRead(final byte[] readBases, final String contig, final int start, final String cigar, final String sample, final boolean isNegStrand) { final GATKSAMRecord read = new GATKSAMRecord(header); read.setBaseQualities(readQuals); read.setReadBases(readBases); read.setReadName("" + readNameCounter++); read.setCigarString(cigar); read.setReadPairedFlag(false); read.setAlignmentStart(start); read.setMappingQuality(60); read.setReferenceName(contig); read.setReadNegativeStrandFlag(isNegStrand); read.setAttribute("RG", sampleRG(sample).getReadGroupId()); readWriter.addAlignment(read); }
Arrays.fill(readQuals, (byte)phredScaledErrorRate); GATKSAMRecord read = new GATKSAMRecord(header); read.setBaseQualities(readQuals); read.setReadBases(readBases);
final GATKSAMRecord returnRead = new GATKSAMRecord( firstRead.getHeader() ); returnRead.setIsStrandless(true); returnRead.setAlignmentStart( firstRead.getAlignmentStart() );
protected GATKSAMRecord buildSAMRecord(String readName, String contig, int alignmentStart, int alignmentEnd) { SAMFileHeader header = ArtificialSAMUtils.createDefaultReadGroup(new SAMFileHeader(), "test", "test"); header.setSequenceDictionary(dictionary); header.setSortOrder(SAMFileHeader.SortOrder.coordinate); GATKSAMRecord record = new GATKSAMRecord(header); record.setReadName(readName); record.setReferenceIndex(dictionary.getSequenceIndex(contig)); record.setAlignmentStart(alignmentStart); Cigar cigar = new Cigar(); int len = alignmentEnd - alignmentStart + 1; cigar.add(new CigarElement(len, CigarOperator.M)); record.setCigar(cigar); record.setReadString(new String(new char[len]).replace("\0", "A")); record.setBaseQualities(new byte[len]); record.setReadGroup(new GATKSAMReadGroupRecord(header.getReadGroup("test"))); return record; }
GATKSAMRecord correctedRead = new GATKSAMRecord(inputRead);
final GATKSAMRecord emptyRead = new GATKSAMRecord(read.getHeader()); emptyRead.setReferenceIndex(read.getReferenceIndex()); emptyRead.setAlignmentStart(0);
/** * Write out a representation of this haplotype as a read * * @param haplotype a haplotype to write out. Cannot be null * @param paddedRefLoc the reference location. Cannot be null * @param isAmongBestHaplotypes true if among the best haplotypes, false if it was just one possible but not so good */ private void writeHaplotype(final Haplotype haplotype, final GenomeLoc paddedRefLoc, final boolean isAmongBestHaplotypes) { final GATKSAMRecord record = new GATKSAMRecord(output.getHeader()); record.setReadBases(haplotype.getBases()); record.setAlignmentStart(paddedRefLoc.getStart() + haplotype.getAlignmentStartHapwrtRef()); record.setBaseQualities(Utils.dupBytes((byte) '!', haplotype.getBases().length)); record.setCigar(AlignmentUtils.consolidateCigar(haplotype.getCigar())); record.setMappingQuality(isAmongBestHaplotypes ? 60 : 0); record.setReadName("HC" + uniqueNameCounter++); record.setAttribute(AlignmentUtils.HAPLOTYPE_TAG,haplotype.hashCode()); record.setReadUnmappedFlag(false); record.setReferenceIndex(paddedRefLoc.getContigIndex()); record.setAttribute(SAMTag.RG.toString(), READ_GROUP_ID); record.setFlags(16); output.add(record); }
/** * Build a SAM record featuring the absolute minimum required dataset. * * @param contig Contig to populate. * @param alignmentStart start of alignment * @param alignmentEnd end of alignment * * @return New SAM Record */ protected GATKSAMRecord buildSAMRecord(String readName, String contig, int alignmentStart, int alignmentEnd) { SAMFileHeader header = new SAMFileHeader(); header.setSequenceDictionary(sequenceSourceFile.getSequenceDictionary()); GATKSAMRecord record = new GATKSAMRecord(header); record.setReadName(readName); record.setReferenceIndex(sequenceSourceFile.getSequenceDictionary().getSequenceIndex(contig)); record.setAlignmentStart(alignmentStart); Cigar cigar = new Cigar(); int len = alignmentEnd - alignmentStart + 1; cigar.add(new CigarElement(len, CigarOperator.M)); record.setCigar(cigar); record.setReadBases(new byte[len]); record.setBaseQualities(new byte[len]); return record; }