Java Code Examples for htsjdk.samtools.SAMRecord#setCigarString()
The following examples show how to use
htsjdk.samtools.SAMRecord#setCigarString() .
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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: PalindromeArtifactClipReadTransformerUnitTest.java From gatk with BSD 3-Clause "New" or "Revised" License | 6 votes |
|
private static GATKRead makeRead(final SAMFileHeader header, final String contig, final int readStart, final int fragmentLength, final byte[] bases, final byte[] qual, final String cigar) {
final SAMRecord read = new SAMRecord(header);
read.setReferenceName(contig);
read.setAlignmentStart(readStart);
read.setReadPairedFlag(true);
read.setReadUnmappedFlag(false);
read.setMateUnmappedFlag(false);
read.setMateReferenceName("Mate");
read.setReadNegativeStrandFlag(false);
read.setMateNegativeStrandFlag(true);
read.setReadBases(bases);
read.setBaseQualities(qual);
final int mateStart = readStart + fragmentLength - bases.length;
read.setMateAlignmentStart(mateStart);
read.setInferredInsertSize(fragmentLength);
read.setProperPairFlag(true);
read.setCigarString(cigar);
return new SAMRecordToGATKReadAdapter(read);
}
Example 3
| 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 4
| Source File: SAMRecordUtilsTest.java From abra2 with MIT License | 5 votes |
|
@Test (groups = "unit" )
public void testRemoveSoftClips_withDeletionAndSoftClipAtStart() {
SAMRecord read = new SAMRecord(null);
read.setReadName("TEST1");
read.setCigarString("2S5M2D3M");
read.setReadString("CCCCCCAGCC");
SAMRecordUtils.removeSoftClips(read);
Assert.assertEquals(read.getCigarString(), "5M2D3M");
Assert.assertEquals(read.getReadString(), "CCCCAGCC");
}
Example 5
| 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 6
| Source File: TagReadWithGeneFunctionTest.java From Drop-seq with MIT License | 5 votes |
|
private SAMRecord getFakeRecord (final File testBAMFile, final int start, final int end, final boolean negativeStrand) {
SamReader inputSam = SamReaderFactory.makeDefault().open(testBAMFile);
SAMRecord r = inputSam.iterator().next();
r.setAlignmentStart(start);
int length = (end -start) +1;
r.setCigarString(length+"M");
r.setMappingQuality(255);
r.setReadNegativeStrandFlag(negativeStrand);
r.setReadBases(Arrays.copyOf(r.getReadBases(), length));
r.setBaseQualities(Arrays.copyOf(r.getBaseQualities(), length));
return (r);
}
Example 7
| Source File: SAMRecordUtilsTest.java From abra2 with MIT License | 5 votes |
|
@Test (groups = "unit" )
public void testRemoveSoftClips_withDeletionAndSoftClipAtEnd() {
SAMRecord read = new SAMRecord(null);
read.setReadName("TEST1");
read.setCigarString("5M2D3M2S");
read.setReadString("CCCCCCAGCC");
SAMRecordUtils.removeSoftClips(read);
Assert.assertEquals(read.getCigarString(), "5M2D3M");
Assert.assertEquals(read.getReadString(), "CCCCCCAG");
}
Example 8
| Source File: AbstractAlignmentMergerTest.java From picard with MIT License | 5 votes |
|
@Test(dataProvider = "readPositionIgnoringSoftClips")
public void testGetReadPositionIgnoringSoftClips(final String cigarString, final int startPosition, final int queryPosition, final int expectedReadPosititon) {
final SAMFileHeader newHeader = SAMRecordSetBuilder.makeDefaultHeader(SAMFileHeader.SortOrder.queryname, 100000,false);
final SAMRecord rec = new SAMRecord(newHeader);
rec.setCigarString(cigarString);
rec.setAlignmentStart(startPosition);
final int readPosition = AbstractAlignmentMerger.getReadPositionAtReferencePositionIgnoreSoftClips(rec, queryPosition);
Assert.assertEquals(readPosition, expectedReadPosititon);
}
Example 9
| 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 10
| 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 11
| 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 12
| Source File: TagReadWithGeneExonFunctionTest.java From Drop-seq with MIT License | 5 votes |
|
private SAMRecord getFakeRecord (final File testBAMFile, final int start, final int end, final boolean negativeStrand) {
SamReader inputSam = SamReaderFactory.makeDefault().open(testBAMFile);
SAMRecord r = inputSam.iterator().next();
r.setAlignmentStart(start);
int length = (end -start) +1;
r.setCigarString(length+"M");
r.setMappingQuality(255);
r.setReadNegativeStrandFlag(negativeStrand);
r.setReadBases(Arrays.copyOf(r.getReadBases(), length));
r.setBaseQualities(Arrays.copyOf(r.getBaseQualities(), length));
return (r);
}
Example 13
| Source File: TagReadWithGeneFunctionTest.java From Drop-seq with MIT License | 5 votes |
|
private SAMRecord getFakeSplitRecord (final File testBAMFile, final int start1, final int end1, final int start2, final int end2, final boolean negativeStrand) {
SamReader inputSam = SamReaderFactory.makeDefault().open(testBAMFile);
SAMRecord r = inputSam.iterator().next();
r.setAlignmentStart(start1);
int length = (end1 -start1) +1;
int gap = ((start2-1)-(end1+1)) +1;
int length2 = (end2 -start2) +1;
r.setCigarString(length+"M"+gap+"N"+length2+"M");
r.setMappingQuality(255);
r.setReadNegativeStrandFlag(negativeStrand);
r.setReadBases(Arrays.copyOf(r.getReadBases(), length+length2));
r.setBaseQualities(Arrays.copyOf(r.getBaseQualities(), length+length2));
return (r);
}
Example 14
| Source File: SAMRecordUtilsTest.java From abra2 with MIT License | 4 votes |
|
private Cigar getCigar(String str) {
SAMRecord read = new SAMRecord(null);
read.setCigarString(str);
return read.getCigar();
}
Example 15
| Source File: AlignmentsTagsTest.java From cramtools with Apache License 2.0 | 4 votes |
|
private void doTest(byte[] ref, int alignmentStart, byte[] readBases) throws IOException,
CloneNotSupportedException {
SAMSequenceRecord sequenceRecord = new SAMSequenceRecord("1", ref.length);
SAMSequenceDictionary sequenceDictionary = new SAMSequenceDictionary();
sequenceDictionary.addSequence(sequenceRecord);
SAMFileHeader header = new SAMFileHeader();
header.setSequenceDictionary(sequenceDictionary);
SAMRecord samRecord = new SAMRecord(header);
samRecord.setReadUnmappedFlag(false);
samRecord.setAlignmentStart(alignmentStart);
samRecord.setReferenceIndex(0);
samRecord.setReadBases(readBases);
samRecord.setCigarString(samRecord.getReadLength() + "M");
ReferenceSource referenceSource = new ReferenceSource() {
@Override
public synchronized ReferenceRegion getRegion(SAMSequenceRecord record, int start_1based,
int endInclusive_1based) throws IOException {
int zbInclusiveStart = start_1based - 1;
int zbExlcusiveEnd = endInclusive_1based;
return new ReferenceRegion(Arrays.copyOfRange(ref, zbInclusiveStart, zbExlcusiveEnd),
sequenceRecord.getSequenceIndex(), sequenceRecord.getSequenceName(), start_1based);
}
};
AlignmentsTags.calculateMdAndNmTags(samRecord, referenceSource, sequenceDictionary, true, true);
SAMRecord checkRecord = (SAMRecord) samRecord.clone();
SequenceUtil.calculateMdAndNmTags(checkRecord, ref, true, true);
// System.out.printf("TEST: ref %s, start %d, read bases %s\n", new
// String(ref), alignmentStart, new String(
// readBases));
// System.out
// .println(referenceSource.getRegion(sequenceRecord, alignmentStart,
// alignmentStart + readBases.length));
// System.out.printf("NM: %s x %s\n", samRecord.getAttribute("NM"),
// checkRecord.getAttribute("NM"));
// System.out.printf("MD: %s x %s\n", samRecord.getAttribute("MD"),
// checkRecord.getAttribute("MD"));
Assert.assertEquals(checkRecord.getAttribute("NM"), samRecord.getAttribute("NM"));
Assert.assertEquals(checkRecord.getAttribute("MD"), samRecord.getAttribute("MD"));
}
Example 16
| Source File: TestBAMRecordView.java From cramtools with Apache License 2.0 | 4 votes |
|
@Test
public void test() throws IOException {
byte[] buf = new byte[1024];
BAMRecordView view = new BAMRecordView(buf);
view.setRefID(0);
view.setAlignmentStart(77);
view.setMappingScore(44);
view.setIndexBin(99);
view.setFlags(555);
view.setMateRefID(0);
view.setMateAlStart(78);
view.setInsertSize(133);
view.setReadName("name1");
view.setCigar(TextCigarCodec.decode("10M"));
view.setBases("AAAAAAAAAA".getBytes());
view.setQualityScores("BBBBBBBBBB".getBytes());
int id = 'A' << 16 | 'M' << 8 | 'A';
view.addTag(id, "Q".getBytes(), 0, 1);
int len = view.finish();
System.out.println(Arrays.toString(Arrays.copyOf(buf, len)));
ByteArrayOutputStream baos = new ByteArrayOutputStream();
SAMFileHeader header = new SAMFileHeader();
header.addSequence(new SAMSequenceRecord("14", 14));
ByteArrayOutputStream baos2 = new ByteArrayOutputStream();
SAMFileWriter writer = new SAMFileWriterFactory().makeBAMWriter(header, true, baos2);
SAMRecord record = new SAMRecord(header);
record.setReferenceIndex(0);
record.setAlignmentStart(1);
record.setCigarString("10M");
record.setFlags(555);
record.setMappingQuality(44);
record.setMateReferenceIndex(0);
record.setMateAlignmentStart(0);
record.setInferredInsertSize(133);
record.setReadName("name1");
record.setReadBases("AAAAAAAAAA".getBytes());
record.setBaseQualities("BBBBBBBBBB".getBytes());
record.setAttribute("AM", 'Q');
System.out.println("BAMFileWriter.addAlignment():");
writer.addAlignment(record);
System.out.println(".");
writer.close();
System.out.println("------------------------------------------");
System.out.println();
System.out.println(new String(baos2.toByteArray()));
System.out.println();
SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
SAMFileReader reader2 = new SAMFileReader(new ByteArrayInputStream(baos2.toByteArray()));
SAMRecordIterator iterator = reader2.iterator();
while (iterator.hasNext()) {
record = iterator.next();
System.out.println(record.getSAMString());
}
System.out.println("------------------------------------------");
BlockCompressedOutputStream bcos = new BlockCompressedOutputStream(baos, null);
bcos.write("BAM\1".getBytes());
bcos.write(toByteArray(header));
CramInt.writeInt32(header.getSequenceDictionary().size(), bcos);
for (final SAMSequenceRecord sequenceRecord : header.getSequenceDictionary().getSequences()) {
byte[] bytes = sequenceRecord.getSequenceName().getBytes();
CramInt.writeInt32(bytes.length + 1, bcos);
bcos.write(sequenceRecord.getSequenceName().getBytes());
bcos.write(0);
CramInt.writeInt32(sequenceRecord.getSequenceLength(), bcos);
}
bcos.write(buf, 0, len);
bcos.close();
System.out.println(new String(baos.toByteArray()));
SAMFileReader reader = new SAMFileReader(new ByteArrayInputStream(baos.toByteArray()));
iterator = reader.iterator();
while (iterator.hasNext()) {
record = iterator.next();
System.out.println(record.getSAMString());
}
reader.close();
}
Example 17
| Source File: RevertSam.java From picard with MIT License | 4 votes |
|
/**
* Takes an individual SAMRecord and applies the set of changes/reversions to it that
* have been requested by program level options.
*/
public void revertSamRecord(final SAMRecord rec) {
if (RESTORE_ORIGINAL_QUALITIES) {
final byte[] oq = rec.getOriginalBaseQualities();
if (oq != null) {
rec.setBaseQualities(oq);
rec.setOriginalBaseQualities(null);
}
}
if (REMOVE_DUPLICATE_INFORMATION) {
rec.setDuplicateReadFlag(false);
}
if (REMOVE_ALIGNMENT_INFORMATION) {
if (rec.getReadNegativeStrandFlag()) {
rec.reverseComplement(true);
rec.setReadNegativeStrandFlag(false);
}
// Remove all alignment based information about the read itself
rec.setReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
rec.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
rec.setCigarString(SAMRecord.NO_ALIGNMENT_CIGAR);
rec.setMappingQuality(SAMRecord.NO_MAPPING_QUALITY);
rec.setInferredInsertSize(0);
rec.setNotPrimaryAlignmentFlag(false);
rec.setProperPairFlag(false);
rec.setReadUnmappedFlag(true);
// Then remove any mate flags and info related to alignment
rec.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
rec.setMateNegativeStrandFlag(false);
rec.setMateReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
rec.setMateUnmappedFlag(rec.getReadPairedFlag());
if (RESTORE_HARDCLIPS) {
String hardClippedBases = rec.getStringAttribute(AbstractAlignmentMerger.HARD_CLIPPED_BASES_TAG);
String hardClippedQualities = rec.getStringAttribute(AbstractAlignmentMerger.HARD_CLIPPED_BASE_QUALITIES_TAG);
if (hardClippedBases != null && hardClippedQualities != null) {
// Record has already been reverse complemented if this was on the negative strand
rec.setReadString(rec.getReadString() + hardClippedBases);
rec.setBaseQualities(SAMUtils.fastqToPhred(SAMUtils.phredToFastq(rec.getBaseQualities()) + hardClippedQualities));
// Remove hard clipping storage tags
rec.setAttribute(AbstractAlignmentMerger.HARD_CLIPPED_BASES_TAG, null);
rec.setAttribute(AbstractAlignmentMerger.HARD_CLIPPED_BASE_QUALITIES_TAG, null);
}
}
// And then remove any tags that are calculated from the alignment
ATTRIBUTE_TO_CLEAR.forEach(tag -> rec.setAttribute(tag, null));
}
}
Example 18
| Source File: ReorderSam.java From picard with MIT License | 4 votes |
|
/**
* Helper function that writes reads from iterator it into writer out, updating each SAMRecord along the way
* according to the newOrder mapping from dictionary index -> index. Name is used for printing only.
*/
private void writeReads(final SAMFileWriter out,
final SAMRecordIterator it,
final Map<Integer, Integer> newOrder,
final String name) {
long counter = 0;
log.info(" Processing " + name);
while (it.hasNext()) {
counter++;
final SAMRecord read = it.next();
final int oldRefIndex = read.getReferenceIndex();
final int oldMateIndex = read.getMateReferenceIndex();
final int newRefIndex = newOrderIndex(read, oldRefIndex, newOrder);
read.setHeader(out.getFileHeader());
read.setReferenceIndex(newRefIndex);
// read becoming unmapped
if (oldRefIndex != NO_ALIGNMENT_REFERENCE_INDEX &&
newRefIndex == NO_ALIGNMENT_REFERENCE_INDEX) {
read.setAlignmentStart(NO_ALIGNMENT_START);
read.setReadUnmappedFlag(true);
read.setCigarString(SAMRecord.NO_ALIGNMENT_CIGAR);
read.setMappingQuality(SAMRecord.NO_MAPPING_QUALITY);
}
final int newMateIndex = newOrderIndex(read, oldMateIndex, newOrder);
if (oldMateIndex != NO_ALIGNMENT_REFERENCE_INDEX &&
newMateIndex == NO_ALIGNMENT_REFERENCE_INDEX) { // mate becoming unmapped
read.setMateAlignmentStart(NO_ALIGNMENT_START);
read.setMateUnmappedFlag(true);
read.setAttribute(SAMTag.MC.name(), null); // Set the Mate Cigar String to null
}
read.setMateReferenceIndex(newMateIndex);
out.addAlignment(read);
}
it.close();
log.info("Wrote " + counter + " reads");
}
Example 19
| 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 20
| 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);
}
}
