Java Code Examples for htsjdk.samtools.SAMRecord#setSecondOfPairFlag()
The following examples show how to use
htsjdk.samtools.SAMRecord#setSecondOfPairFlag() .
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Example 1
| Source File: MergeBamAlignmentTest.java From picard with MIT License | 6 votes |
|
private void addAlignmentsForBestFragmentMapqStrategy(
final SAMFileWriter writer, final SAMRecord unmappedRecord, final String sequence, final int[] mapqs) {
boolean reverse = false;
int alignmentStart = 1;
for (final int mapq : mapqs) {
final SAMRecord alignedRecord = new SAMRecord(writer.getFileHeader());
alignedRecord.setReadName(unmappedRecord.getReadName());
alignedRecord.setReadBases(unmappedRecord.getReadBases());
alignedRecord.setBaseQualities(unmappedRecord.getBaseQualities());
alignedRecord.setReferenceName(sequence);
alignedRecord.setAlignmentStart(alignmentStart);
alignmentStart += 10; // Any old position will do
alignedRecord.setReadNegativeStrandFlag(reverse);
reverse = !reverse;
alignedRecord.setCigarString(unmappedRecord.getReadBases().length + "M");
alignedRecord.setMappingQuality(mapq);
alignedRecord.setReadPairedFlag(unmappedRecord.getReadPairedFlag());
alignedRecord.setFirstOfPairFlag(unmappedRecord.getFirstOfPairFlag());
alignedRecord.setSecondOfPairFlag(unmappedRecord.getSecondOfPairFlag());
alignedRecord.setMateUnmappedFlag(true);
writer.addAlignment(alignedRecord);
}
}
Example 2
| Source File: MergeBamAlignmentTest.java From picard with MIT License | 6 votes |
|
private void addAlignmentForMostStrategy(
final SAMFileWriter writer, final SAMRecord unmappedRecord, final MostDistantStrategyAlignmentSpec spec,
final boolean reverse) {
final SAMRecord alignedRecord = new SAMRecord(writer.getFileHeader());
alignedRecord.setReadName(unmappedRecord.getReadName());
alignedRecord.setReadBases(unmappedRecord.getReadBases());
alignedRecord.setBaseQualities(unmappedRecord.getBaseQualities());
alignedRecord.setReferenceName(spec.sequence);
alignedRecord.setAlignmentStart(spec.alignmentStart);
alignedRecord.setReadNegativeStrandFlag(reverse);
alignedRecord.setCigarString(unmappedRecord.getReadBases().length + "M");
alignedRecord.setMappingQuality(spec.mapQ);
alignedRecord.setReadPairedFlag(unmappedRecord.getReadPairedFlag());
alignedRecord.setFirstOfPairFlag(unmappedRecord.getFirstOfPairFlag());
alignedRecord.setSecondOfPairFlag(unmappedRecord.getSecondOfPairFlag());
alignedRecord.setMateUnmappedFlag(true);
writer.addAlignment(alignedRecord);
}
Example 3
| Source File: ClippingUtilityTest.java From picard with MIT License | 6 votes |
|
@Test(dataProvider="clipPairedTestData")
public void testPairedEndClip(final String testName, final String read1, final String read2, final AdapterPair expected) {
final SAMRecord rec1 = new SAMRecord(new SAMFileHeader());
rec1.setReadString(read1);
rec1.setFirstOfPairFlag(true);
final SAMRecord rec2 = new SAMRecord(new SAMFileHeader());
rec2.setReadString(read2);
rec2.setSecondOfPairFlag(true);
final AdapterPair result = ClippingUtility.adapterTrimIlluminaPairedReads(rec1, rec2,
IlluminaAdapterPair.INDEXED, IlluminaAdapterPair.PAIRED_END);
if (result != null) {
Assert.assertEquals(result.getName(), expected.getName(), testName);
}
else {
Assert.assertNull(expected, testName);
}
}
Example 4
| Source File: Read.java From cramtools with Apache License 2.0 | 6 votes |
|
SAMRecord firstSAMRecord(SAMFileHeader header) {
SAMRecord r = new SAMRecord(header);
r.setReadName(evidenceRecord.getReadName());
r.setReferenceName(evidenceRecord.Chromosome);
r.setAlignmentStart(Integer.valueOf(evidenceRecord.OffsetInReference) + 1);
r.setMappingQuality(Integer.valueOf(evidenceRecord.ScoreAllele0));
r.setReadPairedFlag(true);
r.setReadUnmappedFlag(false);
r.setReadNegativeStrandFlag(negative);
r.setFirstOfPairFlag(evidenceRecord.side == 0);
r.setSecondOfPairFlag(!r.getFirstOfPairFlag());
r.setCigar(new Cigar(Utils.toCigarOperatorList(firstHalf.samCigarElements)));
r.setReadBases(Utils.toByteArray(firstHalf.readBasesBuf));
r.setBaseQualities(Utils.toByteArray(firstHalf.readScoresBuf));
r.setAttribute("GC", Utils.toString(firstHalf.gcList));
r.setAttribute("GS", Utils.toString(firstHalf.gsBuf));
r.setAttribute("GQ", SAMUtils.phredToFastq(Utils.toByteArray(firstHalf.gqBuf)));
return r;
}
Example 5
| Source File: Read.java From cramtools with Apache License 2.0 | 6 votes |
|
SAMRecord secondSAMRecord(SAMFileHeader header) {
SAMRecord r = new SAMRecord(header);
r.setReadName(evidenceRecord.getReadName());
r.setReferenceName(evidenceRecord.Chromosome);
r.setAlignmentStart(Integer.valueOf(evidenceRecord.MateOffsetInReference) + 1);
r.setMappingQuality(Integer.valueOf(evidenceRecord.ScoreAllele0));
r.setReadPairedFlag(true);
r.setReadUnmappedFlag(false);
r.setReadNegativeStrandFlag(negative);
r.setFirstOfPairFlag(evidenceRecord.side == 1);
r.setSecondOfPairFlag(!r.getFirstOfPairFlag());
r.setCigar(new Cigar(Utils.toCigarOperatorList(secondHalf.samCigarElements)));
r.setReadBases(Utils.toByteArray(secondHalf.readBasesBuf));
r.setBaseQualities(Utils.toByteArray(secondHalf.readScoresBuf));
r.setAttribute("GC", Utils.toString(secondHalf.gcList));
r.setAttribute("GS", Utils.toString(secondHalf.gsBuf));
r.setAttribute("GQ", SAMUtils.phredToFastq(Utils.toByteArray(secondHalf.gqBuf)));
return r;
}
Example 6
| Source File: FilterBamByTagTest.java From Drop-seq with MIT License | 5 votes |
|
@Test
public void filterByReadNumberTest() {
FilterBamByTag t = new FilterBamByTag();
// record paired and read is 1st
List<SAMRecord> recs = getPairedRead ();
SAMRecord recFirstPaired = recs.get(0);
SAMRecord recSecondPaired = recs.get(1);
boolean flag1= t.retainByReadNumber(recFirstPaired, 1);
boolean flag2= t.retainByReadNumber(recFirstPaired, 2);
Assert.assertTrue(flag1);
Assert.assertFalse(flag2);
// record paired and read is 2st
recSecondPaired.setProperPairFlag(true);
recSecondPaired.setSecondOfPairFlag(true);
flag1= t.retainByReadNumber(recSecondPaired, 1);
flag2= t.retainByReadNumber(recSecondPaired, 2);
Assert.assertTrue(flag2);
Assert.assertFalse(flag1);
// record unpaired and read is 1st
SAMRecordSetBuilder builder = new SAMRecordSetBuilder();
builder.addUnmappedFragment("foo");
SAMRecord recFirstUnPaired = builder.getRecords().iterator().next();
flag1= t.retainByReadNumber(recFirstUnPaired, 1);
flag2= t.retainByReadNumber(recFirstPaired, 2);
Assert.assertTrue(flag1);
Assert.assertFalse(flag2);
}
Example 7
| Source File: FastqToSam.java From picard with MIT License | 5 votes |
|
/** More complicated method that takes two fastq files and builds pairing information in the SAM. */
protected int doPaired(final FastqReader freader1, final FastqReader freader2, final SAMFileWriter writer) {
int readCount = 0;
final ProgressLogger progress = new ProgressLogger(LOG);
for ( ; freader1.hasNext() && freader2.hasNext() ; readCount++) {
final FastqRecord frec1 = freader1.next();
final FastqRecord frec2 = freader2.next();
final String frec1Name = SequenceUtil.getSamReadNameFromFastqHeader(frec1.getReadHeader());
final String frec2Name = SequenceUtil.getSamReadNameFromFastqHeader(frec2.getReadHeader());
final String baseName = getBaseName(frec1Name, frec2Name, freader1, freader2);
final SAMRecord srec1 = createSamRecord(writer.getFileHeader(), baseName, frec1, true) ;
srec1.setFirstOfPairFlag(true);
srec1.setSecondOfPairFlag(false);
writer.addAlignment(srec1);
progress.record(srec1);
final SAMRecord srec2 = createSamRecord(writer.getFileHeader(), baseName, frec2, true) ;
srec2.setFirstOfPairFlag(false);
srec2.setSecondOfPairFlag(true);
writer.addAlignment(srec2);
progress.record(srec2);
}
if (freader1.hasNext() || freader2.hasNext()) {
throw new PicardException("Input paired fastq files must be the same length");
}
return readCount;
}
Example 8
| Source File: MergeBamAlignmentTest.java From picard with MIT License | 5 votes |
|
private SAMRecord makeRead(final SAMFileHeader alignedHeader, final SAMRecord unmappedRec, final HitSpec hitSpec,
final boolean firstOfPair, final int hitIndex) {
if (hitSpec == null) return null;
final SAMRecord rec = makeRead(alignedHeader, unmappedRec, hitSpec, hitIndex);
rec.setReadPairedFlag(true);
if (firstOfPair) {
rec.setFirstOfPairFlag(true);
rec.setAlignmentStart(hitIndex + 1);
} else {
rec.setSecondOfPairFlag(true);
rec.setAlignmentStart(hitIndex + 201);
}
return rec;
}
Example 9
| Source File: FastqRead.java From cramtools with Apache License 2.0 | 5 votes |
|
public SAMRecord toSAMRecord(SAMFileHeader header) {
SAMRecord record = new SAMRecord(header);
String name = null;
if (data[nameLen - 1] == '/' && Character.isDigit(data[nameLen]))
name = new String(data, 1, nameLen - 2);
else
name = new String(data, 1, nameLen - 2);
record.setReadName(name);
int readLen = (data.length - this.nameLen - 4 - 1) / 2;
byte[] bases = Arrays.copyOfRange(data, nameLen + 2, nameLen + 2 + readLen);
record.setReadBases(bases);
byte[] scores = Arrays.copyOfRange(data, nameLen + 3 + 1 + readLen + 1, nameLen + 3 + 1 + 2 * readLen + 1);
record.setBaseQualityString(new String(scores));
record.setReadUnmappedFlag(true);
switch (templateIndex) {
case 0:
record.setReadPairedFlag(false);
break;
case 1:
record.setReadPairedFlag(true);
record.setFirstOfPairFlag(true);
break;
case 2:
record.setReadPairedFlag(true);
record.setSecondOfPairFlag(true);
break;
default:
break;
}
return record;
}
Example 10
| Source File: ClusterDataToSamConverter.java From picard with MIT License | 4 votes |
|
/**
* Creates a new SAM record from the basecall data
*/
private SAMRecord createSamRecord(final ReadData readData, final String readName, final boolean isPf, final boolean firstOfPair,
final String unmatchedBarcode, final String barcodeQuality,
final List<String> molecularIndexes, final List<String> molecularIndexQualities) {
final SAMRecord sam = new SAMRecord(null);
sam.setReadName(readName);
sam.setReadBases(readData.getBases());
sam.setBaseQualities(readData.getQualities());
// Flag values
sam.setReadPairedFlag(isPairedEnd);
sam.setReadUnmappedFlag(true);
sam.setReadFailsVendorQualityCheckFlag(!isPf);
if (isPairedEnd) {
sam.setMateUnmappedFlag(true);
sam.setFirstOfPairFlag(firstOfPair);
sam.setSecondOfPairFlag(!firstOfPair);
}
if (filters.filterOut(sam)) {
sam.setAttribute(ReservedTagConstants.XN, 1);
}
if (this.readGroupId != null) {
sam.setAttribute(SAMTag.RG.name(), readGroupId);
}
// If it's a barcoded run and it has been decided that the original BC value should be added to the record, do it
if (unmatchedBarcode != null) {
sam.setAttribute(SAMTag.BC.name(), unmatchedBarcode);
if (barcodeQuality != null ) {
sam.setAttribute(SAMTag.QT.name(), barcodeQuality);
}
}
if (!molecularIndexes.isEmpty()) {
if (!this.MOLECULAR_INDEX_TAG.isEmpty()) {
sam.setAttribute(this.MOLECULAR_INDEX_TAG, String.join(MOLECULAR_INDEX_, molecularIndexes));
}
if (!this.MOLECULAR_INDEX_QUALITY_TAG.isEmpty()) {
sam.setAttribute(this.MOLECULAR_INDEX_QUALITY_TAG, String.join(MOLECULAR_INDEX_, molecularIndexQualities));
}
if (!this.tagPerMolecularIndex.isEmpty()) {
if (tagPerMolecularIndex.size() != molecularIndexes.size()) {
throw new PicardException("Found " + molecularIndexes.size() + " molecular indexes but only " + tagPerMolecularIndex.size() + " SAM tags given.");
}
for (int i = 0; i < this.tagPerMolecularIndex.size(); i++) {
sam.setAttribute(this.tagPerMolecularIndex.get(i), molecularIndexes.get(i));
}
}
}
return sam;
}
Example 11
| Source File: MergeBamAlignmentTest.java From picard with MIT License | 4 votes |
|
/**
* Confirm that paired reads are rejected by PrimaryAlignmentStrategy.EarliestFragment.
*/
@Test(expectedExceptions = UnsupportedOperationException.class)
public void testEarliestFragmentStrategyPaired() throws Exception {
final File output = File.createTempFile("mergeTest", ".sam");
output.deleteOnExit();
final File unmappedSam = File.createTempFile("unmapped.", ".sam");
unmappedSam.deleteOnExit();
final SAMFileWriterFactory factory = new SAMFileWriterFactory();
final SAMFileHeader header = new SAMFileHeader();
header.setSortOrder(SAMFileHeader.SortOrder.queryname);
final String cigar = "16M";
final SAMRecord firstOfPair = new SAMRecord(header);
firstOfPair.setReadName("theRead");
firstOfPair.setReadString("ACGTACGTACGTACGT");
firstOfPair.setBaseQualityString("5555555555555555");
firstOfPair.setReadUnmappedFlag(true);
firstOfPair.setReadPairedFlag(true);
firstOfPair.setFirstOfPairFlag(true);
final SAMRecord secondOfPair = new SAMRecord(header);
secondOfPair.setReadName("theRead");
secondOfPair.setReadString("ACGTACGTACGTACGT");
secondOfPair.setBaseQualityString("5555555555555555");
secondOfPair.setReadUnmappedFlag(true);
secondOfPair.setReadPairedFlag(true);
secondOfPair.setSecondOfPairFlag(true);
SamPairUtil.setMateInfo(firstOfPair, secondOfPair);
final SAMFileWriter unmappedWriter = factory.makeSAMWriter(header, false, unmappedSam);
unmappedWriter.addAlignment(firstOfPair);
unmappedWriter.addAlignment(secondOfPair);
unmappedWriter.close();
final File alignedSam = File.createTempFile("aligned.", ".sam");
alignedSam.deleteOnExit();
// Populate the header with SAMSequenceRecords
header.setSequenceDictionary(SAMSequenceDictionaryExtractor.extractDictionary(sequenceDict2.toPath()));
// Create 2 alignments for each end of pair
final SAMFileWriter alignedWriter = factory.makeSAMWriter(header, false, alignedSam);
for (int i = 1; i <= 2; ++i) {
final SAMRecord firstOfPairAligned = new SAMRecord(header);
firstOfPairAligned.setReadName(firstOfPair.getReadName());
firstOfPairAligned.setReadBases(firstOfPair.getReadBases());
firstOfPairAligned.setBaseQualities(firstOfPair.getBaseQualities());
firstOfPairAligned.setReferenceName("chr1");
firstOfPairAligned.setAlignmentStart(i);
firstOfPairAligned.setCigarString(cigar);
firstOfPairAligned.setMappingQuality(100);
firstOfPairAligned.setReadPairedFlag(true);
firstOfPairAligned.setFirstOfPairFlag(true);
firstOfPairAligned.setAttribute(SAMTag.HI.name(), i);
final SAMRecord secondOfPairAligned = new SAMRecord(header);
secondOfPairAligned.setReadName(secondOfPair.getReadName());
secondOfPairAligned.setReadBases(secondOfPair.getReadBases());
secondOfPairAligned.setBaseQualities(secondOfPair.getBaseQualities());
secondOfPairAligned.setReferenceName("chr1");
secondOfPairAligned.setAlignmentStart(i + 10);
secondOfPairAligned.setCigarString(cigar);
secondOfPairAligned.setMappingQuality(100);
secondOfPairAligned.setReadPairedFlag(true);
secondOfPairAligned.setSecondOfPairFlag(true);
secondOfPairAligned.setAttribute(SAMTag.HI.name(), i);
SamPairUtil.setMateInfo(firstOfPairAligned, secondOfPairAligned);
alignedWriter.addAlignment(firstOfPairAligned);
alignedWriter.addAlignment(secondOfPairAligned);
}
alignedWriter.close();
doMergeAlignment(unmappedSam, Collections.singletonList(alignedSam),
null, null, null, null,
false, true, false, 1,
"0", "1.0", "align!", "myAligner",
true,
fasta, output,
SamPairUtil.PairOrientation.FR,
MergeBamAlignment.PrimaryAlignmentStrategy.EarliestFragment,
null, null, null, null);
Assert.fail("Exception was not thrown");
}
Example 12
| Source File: MergeBamAlignmentTest.java From picard with MIT License | 4 votes |
|
private void testBestFragmentMapqStrategy(final String testName, final int[] firstMapQs, final int[] secondMapQs,
final boolean includeSecondary, final int expectedFirstMapq,
final int expectedSecondMapq) throws Exception {
final File unmappedSam = File.createTempFile("unmapped.", ".sam");
unmappedSam.deleteOnExit();
final SAMFileWriterFactory factory = new SAMFileWriterFactory();
final SAMFileHeader header = new SAMFileHeader();
header.setSortOrder(SAMFileHeader.SortOrder.queryname);
final String readName = "theRead";
final SAMRecord firstUnmappedRead = new SAMRecord(header);
firstUnmappedRead.setReadName(readName);
firstUnmappedRead.setReadString("ACGTACGTACGTACGT");
firstUnmappedRead.setBaseQualityString("5555555555555555");
firstUnmappedRead.setReadUnmappedFlag(true);
firstUnmappedRead.setMateUnmappedFlag(true);
firstUnmappedRead.setReadPairedFlag(true);
firstUnmappedRead.setFirstOfPairFlag(true);
final SAMRecord secondUnmappedRead = new SAMRecord(header);
secondUnmappedRead.setReadName(readName);
secondUnmappedRead.setReadString("TCGAACGTTCGAACTG");
secondUnmappedRead.setBaseQualityString("6666666666666666");
secondUnmappedRead.setReadUnmappedFlag(true);
secondUnmappedRead.setMateUnmappedFlag(true);
secondUnmappedRead.setReadPairedFlag(true);
secondUnmappedRead.setSecondOfPairFlag(true);
final SAMFileWriter unmappedWriter = factory.makeSAMWriter(header, false, unmappedSam);
unmappedWriter.addAlignment(firstUnmappedRead);
unmappedWriter.addAlignment(secondUnmappedRead);
unmappedWriter.close();
final File alignedSam = File.createTempFile("aligned.", ".sam");
alignedSam.deleteOnExit();
final String sequence = "chr1";
// Populate the header with SAMSequenceRecords
header.setSequenceDictionary(SAMSequenceDictionaryExtractor.extractDictionary(sequenceDict2.toPath()));
final SAMFileWriter alignedWriter = factory.makeSAMWriter(header, false, alignedSam);
addAlignmentsForBestFragmentMapqStrategy(alignedWriter, firstUnmappedRead, sequence, firstMapQs);
addAlignmentsForBestFragmentMapqStrategy(alignedWriter, secondUnmappedRead, sequence, secondMapQs);
alignedWriter.close();
final File output = File.createTempFile("testBestFragmentMapqStrategy." + testName, ".sam");
output.deleteOnExit();
doMergeAlignment(unmappedSam, Collections.singletonList(alignedSam),
null, null, null, null,
false, true, false, 1,
"0", "1.0", "align!", "myAligner",
true,
fasta, output,
SamPairUtil.PairOrientation.FR,
MergeBamAlignment.PrimaryAlignmentStrategy.BestEndMapq,
null, includeSecondary, null, null);
final SamReader reader = SamReaderFactory.makeDefault().open(output);
int numFirstRecords = 0;
int numSecondRecords = 0;
int firstPrimaryMapq = -1;
int secondPrimaryMapq = -1;
for (final SAMRecord rec: reader) {
Assert.assertTrue(rec.getReadPairedFlag());
if (rec.getFirstOfPairFlag()) ++numFirstRecords;
else if (rec.getSecondOfPairFlag()) ++ numSecondRecords;
else Assert.fail("unpossible!");
if (!rec.getReadUnmappedFlag() && !rec.getNotPrimaryAlignmentFlag()) {
if (rec.getFirstOfPairFlag()) {
Assert.assertEquals(firstPrimaryMapq, -1);
firstPrimaryMapq = rec.getMappingQuality();
} else {
Assert.assertEquals(secondPrimaryMapq, -1);
secondPrimaryMapq = rec.getMappingQuality();
}
} else if (rec.getNotPrimaryAlignmentFlag()) {
Assert.assertTrue(rec.getMateUnmappedFlag());
}
}
reader.close();
Assert.assertEquals(firstPrimaryMapq, expectedFirstMapq);
Assert.assertEquals(secondPrimaryMapq, expectedSecondMapq);
if (!includeSecondary) {
Assert.assertEquals(numFirstRecords, 1);
Assert.assertEquals(numSecondRecords, 1);
} else {
// If no alignments for an end, there will be a single unmapped record
Assert.assertEquals(numFirstRecords, Math.max(1, firstMapQs.length));
Assert.assertEquals(numSecondRecords, Math.max(1, secondMapQs.length));
}
}
