Java Code Examples for htsjdk.samtools.SAMRecord#setBaseQualityString()
The following examples show how to use
htsjdk.samtools.SAMRecord#setBaseQualityString() .
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Example 1
| Source File: ReadContextCounterTest.java From hmftools with GNU General Public License v3.0 | 6 votes |
|
@NotNull
public static SAMRecord buildSamRecord(final int alignmentStart, @NotNull final String cigar, @NotNull final String readString,
@NotNull final String qualities) {
final SAMRecord record = new SAMRecord(null);
record.setAlignmentStart(alignmentStart);
record.setCigarString(cigar);
record.setReadString(readString);
record.setReadNegativeStrandFlag(false);
record.setBaseQualityString(qualities);
record.setMappingQuality(20);
record.setDuplicateReadFlag(false);
record.setReadUnmappedFlag(false);
record.setProperPairFlag(true);
record.setReadPairedFlag(true);
return record;
}
Example 2
| Source File: SmartSamWriterTest.java From rtg-tools with BSD 2-Clause "Simplified" License | 6 votes |
|
private static SAMRecord createRecord(int position, String ref) {
final SAMFileHeader header = new SAMFileHeader();
header.getSequenceDictionary().addSequence(new SAMSequenceRecord("A", 100000));
header.getSequenceDictionary().addSequence(new SAMSequenceRecord("B", 100000));
final SAMRecord rec = new SAMRecord(header);
rec.setReferenceName(ref);
rec.setReadName("read");
rec.setReadString("ACGT");
rec.setBaseQualityString("####");
if (ref.equals(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME)) {
rec.setReadUnmappedFlag(true);
} else {
rec.setCigarString("4=");
rec.setAlignmentStart(position);
}
return rec;
}
Example 3
| Source File: SAMRecordsTest.java From hmftools with GNU General Public License v3.0 | 5 votes |
|
@NotNull
public static SAMRecord buildSamRecord(final int alignmentStart, @NotNull final String cigar, @NotNull final String readString,
@NotNull final String qualities) {
final SAMRecord record = new SAMRecord(null);
record.setAlignmentStart(alignmentStart);
record.setCigarString(cigar);
record.setReadString(readString);
record.setReadNegativeStrandFlag(false);
record.setBaseQualityString(qualities);
record.setMappingQuality(20);
record.setDuplicateReadFlag(false);
record.setReadUnmappedFlag(false);
return record;
}
Example 4
| Source File: RefSequenceTest.java From hmftools with GNU General Public License v3.0 | 5 votes |
|
@NotNull
public static SAMRecord buildSamRecord(final int alignmentStart, @NotNull final String cigar, @NotNull final String readString,
@NotNull final String qualities) {
final SAMRecord record = new SAMRecord(null);
record.setAlignmentStart(alignmentStart);
record.setCigarString(cigar);
record.setReadString(readString);
record.setReadNegativeStrandFlag(false);
record.setBaseQualityString(qualities);
record.setMappingQuality(20);
record.setDuplicateReadFlag(false);
record.setReadUnmappedFlag(false);
return record;
}
Example 5
| Source File: ReadContextFactoryTest.java From hmftools with GNU General Public License v3.0 | 5 votes |
|
@NotNull
static SAMRecord buildSamRecord(@NotNull final String cigar, @NotNull final String readString, @NotNull final String qualities) {
final SAMRecord record = new SAMRecord(null);
record.setAlignmentStart(1000);
record.setCigarString(cigar);
record.setReadString(readString);
record.setReadNegativeStrandFlag(false);
record.setBaseQualityString(qualities);
record.setMappingQuality(20);
record.setDuplicateReadFlag(false);
record.setReadUnmappedFlag(false);
return record;
}
Example 6
| Source File: TestUtils.java From hmftools with GNU General Public License v3.0 | 5 votes |
|
@NotNull
public static SAMRecord buildSamRecord(final int alignmentStart, @NotNull final String cigar, @NotNull final String readString,
@NotNull final String qualities, final boolean negativeStrand) {
final SAMRecord record = new SAMRecord(null);
record.setAlignmentStart(alignmentStart);
record.setCigarString(cigar);
record.setReadString(readString);
record.setReadNegativeStrandFlag(negativeStrand);
record.setBaseQualityString(qualities);
record.setMappingQuality(20);
record.setDuplicateReadFlag(false);
record.setReadUnmappedFlag(false);
return record;
}
Example 7
| Source File: SortedSAMWriter.java From abra2 with MIT License | 5 votes |
|
public void addAlignment(int sampleIdx, SAMRecordWrapper samRecord, int chromosomeChunkIdx) {
Feature chunk = this.chromosomeChunker.getChunks().get(chromosomeChunkIdx);
SAMRecord read = samRecord.getSamRecord();
// Only output reads with original start pos within specified chromosomeChunk
// Avoids reads being written in 2 different chunks
int origAlignmentStart = read.getAlignmentStart();
String yo = read.getStringAttribute("YO");
if (yo != null) {
String[] fields = yo.split(":");
origAlignmentStart = Integer.parseInt(fields[1]);
}
if (origAlignmentStart >= chunk.getStart() && origAlignmentStart <= chunk.getEnd()) {
if (samRecord.isUnalignedRc() && read.getReadUnmappedFlag()) {
// This read was reverse complemented, but not updated.
// Change it back to its original state.
read.setReadString(rc.reverseComplement(read.getReadString()));
read.setBaseQualityString(rc.reverse(read.getBaseQualityString()));
read.setReadNegativeStrandFlag(!read.getReadNegativeStrandFlag());
}
writers[sampleIdx][chromosomeChunkIdx].addAlignment(read);
}
}
Example 8
| Source File: SamOutputTest.java From rtg-tools with BSD 2-Clause "Simplified" License | 5 votes |
|
public void test() throws IOException {
final SAMFileHeader header = new SAMFileHeader();
header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
header.getSequenceDictionary().addSequence(new SAMSequenceRecord("seq", 1000000));
final SAMRecord rec = new SAMRecord(header);
rec.setAlignmentStart(500000);
rec.setReferenceName("seq");
rec.setReadName("read");
rec.setReadString("acgt");
rec.setBaseQualityString("####");
rec.setCigarString("4=");
try (TestDirectory dir = new TestDirectory()) {
final MemoryPrintStream mps = new MemoryPrintStream();
try (SamOutput out = SamOutput.getSamOutput(new File(dir, "foo"), mps.outputStream(), header, true, true, null)) {
out.getWriter().addAlignment(rec);
}
mNano.check("samoutput_expected_1.sam", MainResult.run(new ExtractCli(), "--header", new File(dir, "foo.bam").getPath(), "seq:500000+1").out());
assertTrue(new File(dir, "foo.bam.bai").exists());
assertEquals("", mps.toString());
try (SamOutput out = SamOutput.getSamOutput(new File(dir, "foo.sam"), mps.outputStream(), header, true, true, null)) {
out.getWriter().addAlignment(rec);
}
mNano.check("samoutput_expected_1.sam", MainResult.run(new ExtractCli(), "--header", new File(dir, "foo.sam.gz").getPath(), "seq:500000+1").out());
assertTrue(new File(dir, "foo.sam.gz.tbi").exists());
assertEquals("", mps.toString());
try (SamOutput out = SamOutput.getSamOutput(new File(dir, "foo.sam"), mps.outputStream(), header, false, true, null)) {
out.getWriter().addAlignment(rec);
}
mNano.check("samoutput_expected_1.sam", FileHelper.fileToString(new File(dir, "foo.sam")));
assertFalse(new File(dir, "foo.sam.tbi").exists());
assertEquals("", mps.toString());
try (SamOutput out = SamOutput.getSamOutput(new File("-"), mps.outputStream(), header, true, true, null)) {
out.getWriter().addAlignment(rec);
}
mNano.check("samoutput_expected_1.sam", mps.toString());
}
}
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: BAMRecordViewTest.java From cramtools with Apache License 2.0 | 5 votes |
|
@Test
public void test() {
SAMFileHeader header = new SAMFileHeader();
SAMRecord r1 = new SAMRecord(header);
r1.setReadName("readName");
r1.setFlags(4);
r1.setReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
r1.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
r1.setMappingQuality(SAMRecord.NO_MAPPING_QUALITY);
r1.setCigar(new Cigar());
r1.setMateReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
r1.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
r1.setReadBases("A".getBytes());
r1.setBaseQualityString("!");
BAMRecordView view = new BAMRecordView(new byte[1024]);
translate(r1, view);
r1.setReadName("2");
translate(r1, view);
List<SAMRecord> list = toSAMRecord(view, header);
assertEquals(2, list.size());
Iterator<SAMRecord> iterator = list.iterator();
SAMRecord r2 = iterator.next();
r1.setReadName("readName");
compare(r1, r2);
r1.setReadName("2");
r2 = iterator.next();
compare(r1, r2);
}
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 |
|
/**
* @return a 2-element array in which the first element is the unmapped SAM, and the second the mapped SAM.
*/
private File[] createSamFilesToBeMerged(final MultipleAlignmentSpec[] specs) {
try {
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 SAMRecord unmappedRecord = new SAMRecord(header);
unmappedRecord.setReadName("theRead");
unmappedRecord.setReadString("ACGTACGTACGTACGT");
unmappedRecord.setBaseQualityString("5555555555555555");
unmappedRecord.setReadUnmappedFlag(true);
final SAMFileWriter unmappedWriter = factory.makeSAMWriter(header, false, unmappedSam);
unmappedWriter.addAlignment(unmappedRecord);
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);
for (final MultipleAlignmentSpec spec : specs) {
final SAMRecord alignedRecord = new SAMRecord(header);
alignedRecord.setReadName(unmappedRecord.getReadName());
alignedRecord.setReadBases(unmappedRecord.getReadBases());
alignedRecord.setBaseQualities(unmappedRecord.getBaseQualities());
alignedRecord.setReferenceName(sequence);
alignedRecord.setAlignmentStart(1);
alignedRecord.setReadNegativeStrandFlag(spec.reverseStrand);
alignedRecord.setCigarString(spec.cigar);
alignedRecord.setMappingQuality(spec.mapQ);
if (spec.oneOfTheBest) {
alignedRecord.setAttribute(ONE_OF_THE_BEST_TAG, 1);
}
alignedWriter.addAlignment(alignedRecord);
}
alignedWriter.close();
return new File[]{unmappedSam, alignedSam};
} catch (IOException e) {
throw new PicardException(e.getMessage(), e);
}
}
Example 13
| 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));
}
}
