@Override public SamReaderFactory referenceSequence(final Path referenceSequence) { this.referenceSource = new ReferenceSource(referenceSequence); return this; }
byte[] getSequence(final String md5) { final int restBetweenTries_ms = 0; final int maxTries = 1; final int timeout_ms = 0; return getSequence(md5, timeout_ms, maxTries, restBetweenTries_ms); }
/** * Create a CRAMFileReader from either a file or input stream using the reference source returned by * {@link ReferenceSource#getDefaultCRAMReferenceSource() getDefaultCRAMReferenceSource}. * * @param cramFile CRAM file to open * @param inputStream CRAM stream to read * * @throws IllegalArgumentException if the {@code cramFile} and the {@code inputStream} are both null * @throws IllegalStateException if a {@link ReferenceSource#getDefaultCRAMReferenceSource() default} * reference source cannot be acquired */ public CRAMFileReader(final File cramFile, final InputStream inputStream) { this(cramFile, inputStream, ReferenceSource.getDefaultCRAMReferenceSource()); }
public void ensure(final int start, final int end) { if (end - start > bases.length) throw new RuntimeException("Window is too small for start " + start + " end " + end); if (position < start) moveForwardTo(start); }
private ReferenceTracks(final int sequenceId, final String sequenceName, final byte[] reference, final int windowSize) { this.sequenceId = sequenceId; this.sequenceName = sequenceName; this.reference = reference; bases = new byte[Math.min(windowSize, reference.length)]; coverage = new short[Math.min(windowSize, reference.length)]; mismatches = new short[Math.min(windowSize, reference.length)]; position = 1; reset(); }
public byte base(final long alignmentPosition) { return array[arrayPosition(alignmentPosition)]; }
public GaveUpException(final String md5) { this.setMd5(md5); }
@Override public SamReaderFactory referenceSequence(final File referenceSequence) { this.referenceSource = new ReferenceSource(referenceSequence); return this; }
public void ensureRange(final int start, final int length) { if (start < position) throw new RuntimeException("Cannot move the window backwards: " + start); if (start > position || start + length > position + bases.length) moveForwardTo(start); }
private ReferenceTracks(final int sequenceId, final String sequenceName, final byte[] reference, final int windowSize) { this.sequenceId = sequenceId; this.sequenceName = sequenceName; this.reference = reference; bases = new byte[Math.min(windowSize, reference.length)]; coverage = new short[Math.min(windowSize, reference.length)]; mismatches = new short[Math.min(windowSize, reference.length)]; position = 1; reset(); }
byte[] getSequence(final String md5) throws GaveUpException { final int restBetweenTries_ms = 0; final int maxTries = 1; final int timeout_ms = 0; return getSequence(md5, timeout_ms, maxTries, restBetweenTries_ms); }
public byte base(final long alignmentPosition) { return array[arrayPosition(alignmentPosition)]; }
/** * Create a CRAMFileReader from either a file or input stream using the reference source returned by * {@link ReferenceSource#getDefaultCRAMReferenceSource() getDefaultCRAMReferenceSource}. * * @param cramFile CRAM file to open * @param inputStream CRAM stream to read * * @throws IllegalArgumentException if the {@code cramFile} and the {@code inputStream} are both null * @throws IllegalStateException if a {@link ReferenceSource#getDefaultCRAMReferenceSource() default} * reference source cannot be acquired */ public CRAMFileReader(final File cramFile, final InputStream inputStream) { this(cramFile, inputStream, ReferenceSource.getDefaultCRAMReferenceSource()); }
@Override public SamReaderFactory referenceSequence(final File referenceSequence) { this.referenceSource = new ReferenceSource(referenceSequence); return this; }
public void ensure(final int start, final int end) { if (end - start > bases.length) throw new RuntimeException("Window is too small for start " + start + " end " + end); if (position < start) moveForwardTo(start); }
private ReferenceTracks(final int sequenceId, final String sequenceName, final byte[] reference, final int windowSize) { this.sequenceId = sequenceId; this.sequenceName = sequenceName; this.reference = reference; bases = new byte[Math.min(windowSize, reference.length)]; coverage = new short[Math.min(windowSize, reference.length)]; mismatches = new short[Math.min(windowSize, reference.length)]; position = 1; reset(); }
public byte[] copy(final long alignmentStart, final int alignmentSpan) { final int from = arrayPosition(alignmentStart); final int to = arrayPosition(alignmentStart + alignmentSpan); return Arrays.copyOfRange(array, from, to); }
@Override public SamReaderFactory referenceSequence(final Path referenceSequence) { this.referenceSource = new ReferenceSource(referenceSequence); return this; }
public void ensure(final int start, final int end) { if (end - start > bases.length) throw new RuntimeException("Window is too small for start " + start + " end " + end); if (position < start) moveForwardTo(start); }
public void ensureRange(final int start, final int length) { if (start < position) throw new RuntimeException("Cannot move the window backwards: " + start); if (start > position || start + length > position + bases.length) moveForwardTo(start); }