@Override public void setReadBases(final byte[] value) { super.setReadBases(value); mBinaryDataStale = true; mReadLengthValid = false; }
@Override public void setReadBases(final byte[] value) { super.setReadBases(value); mBinaryDataStale = true; mReadLengthValid = false; }
@Override public void setReadBases(final byte[] value) { super.setReadBases(value); mBinaryDataStale = true; mReadLengthValid = false; }
/** * Randomly fills in the bases for the given record. */ private void fillInBases(final SAMRecord rec){ final int length = this.readLength; final byte[] bases = new byte[length]; for (int i = 0; i < length; ++i) { bases[i] = BASES[this.random.nextInt(BASES.length)]; } rec.setReadBases(bases); }
@Override public void setReadBases(final byte[] value) { if (!initializedFields.contains(LazyField.BASES)) { initializedFields.add(LazyField.BASES); } super.setReadBases(value); }
@Override public void setReadBases(final byte[] value) { if (!initializedFields.contains(LazyField.BASES)) { initializedFields.add(LazyField.BASES); } super.setReadBases(value); }
public void setReadString(final String value) { if (NULL_SEQUENCE_STRING.equals(value)) { mReadBases = NULL_SEQUENCE; } else { final byte[] bases = StringUtil.stringToBytes(value); if (bases != null) { SAMUtils.normalizeBases(bases); } setReadBases(bases); } }
public void setReadString(final String value) { if (NULL_SEQUENCE_STRING.equals(value)) { mReadBases = NULL_SEQUENCE; } else { final byte[] bases = StringUtil.stringToBytes(value); SAMUtils.normalizeBases(bases); setReadBases(bases); } }
public void setReadString(final String value) { if (NULL_SEQUENCE_STRING.equals(value)) { mReadBases = NULL_SEQUENCE; } else { final byte[] bases = StringUtil.stringToBytes(value); if (bases != null) { SAMUtils.normalizeBases(bases); } setReadBases(bases); } }
@Override public byte[] getReadBases() { byte[] result = super.getReadBases(); if (mRestOfBinaryData != null && result == null) { result = decodeReadBases(); super.setReadBases(result); } return result; }
@Override public byte[] getReadBases() { byte[] result = super.getReadBases(); if (mRestOfBinaryData != null && result == null) { result = decodeReadBases(); super.setReadBases(result); } return result; }
@Override public byte[] getReadBases() { byte[] result = super.getReadBases(); if (mRestOfBinaryData != null && result == null) { result = decodeReadBases(); super.setReadBases(result); } return result; }
@Test(dataProvider = "readBasesArrayGetReadLengthData") public void testReadBasesGetReadLength(final byte[] readBases, final int readLength) { final SAMRecord sam = createTestRecordHelper(); sam.setReadBases(readBases); Assert.assertEquals(sam.getReadLength(), readLength); }
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; }
private SAMRecord generateRecord(String name) { SAMRecord record = new SAMRecord(new SAMFileHeader()); record.setReadName(name); record.setBaseQualities(highQualities); record.setReadBases(refBases); return record; }
@Test(dataProvider = "longCigarsData") public void testLongCigarsZerolengthRead(final int numOps) throws Exception { final SAMRecordSetBuilder builder = new SAMRecordSetBuilder(true, SAMFileHeader.SortOrder.coordinate); final Cigar cigar = Cigar.fromCigarOperators(getCigarOperatorsForTest(numOps)); final SAMRecord sam = builder.addFrag("frag1", 0, 1, false, false, cigar.toString(), null, 30); sam.setReadBases(new byte[]{}); sam.setBaseQualityString(""); // in htsjdk only secondary alignments are allowed to have read-length zero (doesn't validate otherwise) sam.setSecondaryAlignment(true); testHelper(builder, SAMFileHeader.SortOrder.coordinate, true); }
@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); }