public CRAMIterator(final InputStream inputStream, final CRAMReferenceSource referenceSource, final ValidationStringency validationStringency) throws IOException { if (null == referenceSource) { throw new CRAMException("A reference source is required for CRAM files"); } this.countingInputStream = new CountingInputStream(inputStream); this.referenceSource = referenceSource; this.validationStringency = validationStringency; final CramContainerIterator containerIterator = new CramContainerIterator(this.countingInputStream); cramHeader = containerIterator.getCramHeader(); this.containerIterator = containerIterator; firstContainerOffset = this.countingInputStream.getCount(); records = new ArrayList<SAMRecord>(CRAMContainerStreamWriter.DEFAULT_RECORDS_PER_SLICE); normalizer = new CramNormalizer(cramHeader.getSamFileHeader(), referenceSource); parser = new ContainerParser(cramHeader.getSamFileHeader()); }
public CRAMIterator(final SeekableStream seekableStream, final CRAMReferenceSource referenceSource, final long[] coordinates, final ValidationStringency validationStringency) throws IOException { if (null == referenceSource) { throw new CRAMException("A reference source is required for CRAM files"); } this.countingInputStream = new CountingInputStream(seekableStream); this.referenceSource = referenceSource; this.validationStringency = validationStringency; final CramSpanContainerIterator containerIterator = CramSpanContainerIterator.fromFileSpan(seekableStream, coordinates); cramHeader = containerIterator.getCramHeader(); this.containerIterator = containerIterator; firstContainerOffset = containerIterator.getFirstContainerOffset(); records = new ArrayList<SAMRecord>(CRAMContainerStreamWriter.DEFAULT_RECORDS_PER_SLICE); normalizer = new CramNormalizer(cramHeader.getSamFileHeader(), referenceSource); parser = new ContainerParser(cramHeader.getSamFileHeader()); }
public CRAMIterator(final InputStream inputStream, final CRAMReferenceSource referenceSource, final ValidationStringency validationStringency) { if (null == referenceSource) { throw new CRAMException("A reference source is required for CRAM files"); } this.countingInputStream = new CountingInputStream(inputStream); this.referenceSource = referenceSource; this.validationStringency = validationStringency; final CramContainerIterator containerIterator = new CramContainerIterator(this.countingInputStream); cramHeader = containerIterator.getCramHeader(); this.containerIterator = containerIterator; firstContainerOffset = this.countingInputStream.getCount(); records = new ArrayList<>(CRAMContainerStreamWriter.DEFAULT_RECORDS_PER_SLICE); normalizer = new CramNormalizer(cramHeader.getSamFileHeader(), referenceSource); parser = new ContainerParser(cramHeader.getSamFileHeader()); }
public CRAMIterator(final SeekableStream seekableStream, final CRAMReferenceSource referenceSource, final long[] coordinates, final ValidationStringency validationStringency) { if (null == referenceSource) { throw new CRAMException("A reference source is required for CRAM files"); } this.countingInputStream = new CountingInputStream(seekableStream); this.referenceSource = referenceSource; this.validationStringency = validationStringency; final CramSpanContainerIterator containerIterator = CramSpanContainerIterator.fromFileSpan(seekableStream, coordinates); cramHeader = containerIterator.getCramHeader(); this.containerIterator = containerIterator; firstContainerOffset = containerIterator.getFirstContainerOffset(); records = new ArrayList<>(CRAMContainerStreamWriter.DEFAULT_RECORDS_PER_SLICE); normalizer = new CramNormalizer(cramHeader.getSamFileHeader(), referenceSource); parser = new ContainerParser(cramHeader.getSamFileHeader()); }
CramToBam_OBA_Function(CramHeader header, ReferenceSource referenceSource) { this.header = header; parser = new ContainerParser(header.getSamFileHeader()); f = new Cram2SamRecordFactory(header.getSamFileHeader()); codec = new BAMRecordCodec(header.getSamFileHeader()); n = new CramNormalizer(header.getSamFileHeader(), referenceSource); log.info("converter created"); }
ArrayList<CramCompressionRecord> cramRecords = new ArrayList<CramCompressionRecord>(10000); CramNormalizer n = new CramNormalizer(cramHeader.getSamFileHeader(), referenceSource);