@Override public void setBaseQualities(final byte[] value) { super.setBaseQualities(value); mBinaryDataStale = true; }
@Override public void setBaseQualities(final byte[] value) { super.setBaseQualities(value); mBinaryDataStale = true; }
@Override public void setBaseQualities(final byte[] value) { super.setBaseQualities(value); mBinaryDataStale = true; }
@Override public void setBaseQualities(final byte[] value) { if (!initializedFields.contains(LazyField.QUALS)) { initializedFields.add(LazyField.QUALS); } super.setBaseQualities(value); }
@Override public void setBaseQualities(final byte[] value) { if (!initializedFields.contains(LazyField.QUALS)) { initializedFields.add(LazyField.QUALS); } super.setBaseQualities(value); }
public void setBaseQualityString(final String value) { if (NULL_QUALS_STRING.equals(value)) { setBaseQualities(NULL_QUALS); } else { setBaseQualities(SAMUtils.fastqToPhred(value)); } }
public void setBaseQualityString(final String value) { if (NULL_QUALS_STRING.equals(value)) { setBaseQualities(NULL_QUALS); } else { setBaseQualities(SAMUtils.fastqToPhred(value)); } }
public void setBaseQualityString(final String value) { if (NULL_QUALS_STRING.equals(value)) { setBaseQualities(NULL_QUALS); } else { setBaseQualities(SAMUtils.fastqToPhred(value)); } }
@Override public byte[] getBaseQualities() { byte[] ret = super.getBaseQualities(); if (mRestOfBinaryData != null && ret == null) { ret = decodeBaseQualities(); super.setBaseQualities(ret); } return ret; }
@Override public byte[] getBaseQualities() { byte[] ret = super.getBaseQualities(); if (mRestOfBinaryData != null && ret == null) { ret = decodeBaseQualities(); super.setBaseQualities(ret); } return ret; }
@Override public byte[] getBaseQualities() { byte[] ret = super.getBaseQualities(); if (mRestOfBinaryData != null && ret == null) { ret = decodeBaseQualities(); super.setBaseQualities(ret); } return ret; }
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 public void canShadeBaseQuality() throws InvalidGenomicCoordsException, IOException, InvalidColourException { GenomicCoords gc= new GenomicCoords("chr7:1-80", 80, null, null); SAMRecord rec= new SAMRecord(null); rec.setAlignmentStart(1); rec.setCigarString("2M3D8M"); rec.setMappingQuality(30); rec.setReadBases("AAAAATTTTT".getBytes()); rec.setBaseQualities("!!!!!IIIII".getBytes()); System.err.println(rec.getSAMString()); TextRead tr= new TextRead(rec, gc, false); System.err.println(Splitter.on("m").omitEmptyStrings().splitToList(tr.getPrintableTextRead(false, false, false))); }
public static void trim(SAMRecord read, int startCount, int endCount) { int readLength = read.getReadLength(); read.setReadBases(Arrays.copyOfRange(read.getReadBases(), startCount, readLength - endCount)); read.setBaseQualities(Arrays.copyOfRange(read.getBaseQualities(), startCount, readLength - endCount)); if (read.getCigar() != null && read.getCigar().getCigarElements().size() > 0) { read.setAlignmentStart(read.getAlignmentStart() + CigarUtil.offsetOf(read.getCigar(), startCount)); read.setCigar(CigarUtil.trimReadBases(read.getCigar(), startCount, endCount)); assert (read.getReadLength() == read.getCigar().getReadLength()); } }
private SAMRecord generateRecord(String name) { SAMRecord record = new SAMRecord(new SAMFileHeader()); record.setReadName(name); record.setBaseQualities(highQualities); record.setReadBases(refBases); return record; }
@BeforeTest public void setUp(){ record = new SAMRecord(new SAMFileHeader()); record.setReadName("testRecord"); record.setReadBases(bases); record.setBaseQualities(qualities); }
@Test public void testCigarNoSeqValidation() throws Exception { final SAMRecordSetBuilder samBuilder = new SAMRecordSetBuilder(); samBuilder.addFrag("name", 0, 1, false); samBuilder.iterator().next().setReadBases(SAMRecord.NULL_SEQUENCE); samBuilder.iterator().next().setBaseQualities(SAMRecord.NULL_SEQUENCE); final Histogram<String> results = executeValidation(samBuilder.getSamReader(), null, IndexValidationStringency.EXHAUSTIVE); Assert.assertNull(results.get(SAMValidationError.Type.MISMATCH_CIGAR_SEQ_LENGTH .getHistogramString())); }
@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); }