@Override public void setReadName(final String value) { super.setReadName(value); mBinaryDataStale = true; mReadNameLengthValid = false; }
@Override public void setReadName(final String value) { super.setReadName(value); mBinaryDataStale = true; mReadNameLengthValid = false; }
@Override public void setReadName(final String value) { super.setReadName(value); mBinaryDataStale = true; mReadNameLengthValid = false; }
@Override public SAMRecord next() { final SAMRecord rec = underlyingIterator.next(); final String readName = rec.getReadName(); if (readName.endsWith(suffixToTrim)) { rec.setReadName(readName.substring(0, readName.length() - suffixToTrim.length())); } return rec; }
@Override public SAMRecord next() { final SAMRecord rec = underlyingIterator.next(); final String readName = rec.getReadName(); if (readName.endsWith(suffixToTrim)) { rec.setReadName(readName.substring(0, readName.length() - suffixToTrim.length())); } return rec; }
@Override public String getReadName() { String result = super.getReadName(); if (mRestOfBinaryData != null && result == null) { result = decodeReadName(); super.setReadName(result); } return result; }
@Override public String getReadName() { String result = super.getReadName(); if (mRestOfBinaryData != null && result == null) { result = decodeReadName(); super.setReadName(result); } return result; }
@Override public String getReadName() { String result = super.getReadName(); if (mRestOfBinaryData != null && result == null) { result = decodeReadName(); super.setReadName(result); } return result; }
@Test public void testCompareDifferentNames() throws Exception { final SAMRecord a = new SAMRecord(null); a.setReadName("A"); final SAMRecord b = new SAMRecord(null); b.setReadName("B"); Assert.assertTrue(COMPARATOR.compare(a, b) < 0); Assert.assertTrue(COMPARATOR.compare(b, a) > 0); }
@Test public void testCompareDifferentNames() throws Exception { final SAMRecord a = new SAMRecord(null); a.setReadName("A"); final SAMRecord b = new SAMRecord(null); b.setReadName("B"); // hashes are providing a different order in this case Assert.assertTrue(COMPARATOR.compare(a, b) != 0); Assert.assertTrue(COMPARATOR.compare(b, a) != 0); }
@Test(dataProvider = "testNmFromCigarProvider") public void testNmTagFromCigar(final String cigarString, final int expectedNmValue) { final SAMRecord rec = new SAMRecord(null); rec.setReadName("test"); rec.setCigarString(cigarString); Assert.assertEquals(SequenceUtil.calculateSamNmTagFromCigar(rec),expectedNmValue); }
private static SAMRecord createSAMRecord(SAMFileHeader header, int recordIndex, int seqId, int start) { byte[] bases = "AAAAA".getBytes(); final SAMRecord record = new SAMRecord(header); record.setReferenceIndex(seqId); record.setAlignmentStart(start); record.setReadBases(bases); record.setBaseQualities(bases); record.setReadName(Integer.toString(recordIndex)); return record; }
@Test(dataProvider = "makeReferenceFromAlignment") public void testMakeReferenceFromAlignment(final String seq, final String cigar, final String md, boolean includeReferenceBasesForDeletions, final String expectedReference) { final SAMRecord rec = new SAMRecord(null); rec.setReadName("test"); rec.setReadString(seq); rec.setCigarString(cigar); rec.setAttribute(SAMTag.MD.name(), md); final byte[] refBases = SequenceUtil.makeReferenceFromAlignment(rec, includeReferenceBasesForDeletions); Assert.assertEquals(StringUtil.bytesToString(refBases), expectedReference); }
private SAMRecord generateRecord(String name) { SAMRecord record = new SAMRecord(new SAMFileHeader()); record.setReadName(name); record.setBaseQualities(highQualities); record.setReadBases(refBases); return record; }
private static SAMRecord createRecord(int start, int mappingQuality) { final SAMRecord rec = new SAMRecord(getHeader()); rec.setReadName("read"); rec.setReferenceName("1"); rec.setAlignmentStart(start); rec.setMappingQuality(mappingQuality); return rec; }
@BeforeTest public void setUp(){ record = new SAMRecord(new SAMFileHeader()); record.setReadName("testRecord"); record.setReadBases(bases); record.setBaseQualities(qualities); }
@BeforeTest public void setUp(){ record = new SAMRecord(new SAMFileHeader()); record.setReadName("testRecord"); record.setReadBases(bases); record.setBaseQualities(qualities); }
@BeforeTest public void setUp(){ String referenceString = ">chrM\nACCTACGTTCAATATTCTTCACCTACGTTCAATATTCTTCACCTACGTTCAATATTCTTCACCTACGTTCAATATTCTTCACCTACGTTCAATATTCTTC"; ref = new ReferenceSequence("chrM", 0, referenceString.getBytes()); sequence = new SAMSequenceRecord("chrM", 100); record = new SAMRecord(new SAMFileHeader()); record.setReadName("test"); record.setBaseQualities(qualities); record.setReadBases(refBases); secondRecord = generateRecord("test1"); thirdRecord = generateRecord("test2"); }
@BeforeTest public void setUp() { SAMRecord record = new SAMRecord(new SAMFileHeader()); record.setReadName("testRecord"); record.setReadBases(bases); record.setBaseQualities(qualities); typedRecordAndOffset = EdgingRecordAndOffset.createBeginRecord(record, 10, 10, 10); typedRecordAndOffsetEnd = EdgingRecordAndOffset.createEndRecord(typedRecordAndOffset); }
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); }