public byte base(final long alignmentPosition) { return array[arrayPosition(alignmentPosition)]; }
/** * Returns a new object representing the requested region on the reference sequence. * @param name name of the reference sequence * @param start inclusive starting position on the reference sequence * @param stop inclusive end position on the reference sequence * @return a new region object */ public ReferenceRegion getRegion(final String name, final long start, final long stop) { final int index = getSequenceDictionary().getSequenceIndex(name); if (!sequences.containsKey(index)) throw new RuntimeException("Sequence not found: " + name); return new ReferenceRegion(sequences.get(index), index, name, start, stop); }
/** * Returns a new object representing the requested region on the reference sequence. * @param name name of the reference sequence * @param start inclusive starting position on the reference sequence * @param stop inclusive end position on the reference sequence * @return a new region object */ public ReferenceRegion getRegion(final String name, final long start, final long stop) { final int index = getSequenceDictionary().getSequenceIndex(name); if (!sequences.containsKey(index)) throw new RuntimeException("Sequence not found: " + name); return new ReferenceRegion(sequences.get(index), index, name, start, stop); }
public byte base(final long alignmentPosition) { return array[arrayPosition(alignmentPosition)]; }
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); }
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); }