@Override public ReferenceSequence getSubsequenceAt(final String name, final long start, final long stop) { final int index = getSequenceDictionary().getSequenceIndex(name); final byte[] bases = Arrays.copyOfRange(sequences.get(index), (int) start, (int) stop + 1); return new ReferenceSequence(name, index, bases); }
@Override public ReferenceSequence getSubsequenceAt(final String name, final long start, final long stop) { final int index = getSequenceDictionary().getSequenceIndex(name); final byte[] bases = Arrays.copyOfRange(sequences.get(index), (int) start, (int) stop + 1); return new ReferenceSequence(name, index, bases); }
/** * 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); }
@Override public ReferenceSequence getSequence(final String name) { final int index = getSequenceDictionary().getSequenceIndex(name); return new ReferenceSequence(name, index, sequences.get(index)); }
@Override public ReferenceSequence getSequence(final String name) { final int index = getSequenceDictionary().getSequenceIndex(name); return new ReferenceSequence(name, index, sequences.get(index)); }
public void addSequence(final String name, final byte[] bases) { final SAMSequenceRecord r = new SAMSequenceRecord(name, bases.length); dictionary.addSequence(r); final int index = getSequenceDictionary().getSequenceIndex(name); sequences.put(index, bases); }
public void addSequence(final String name, final byte[] bases) { final SAMSequenceRecord r = new SAMSequenceRecord(name, bases.length); dictionary.addSequence(r); final int index = getSequenceDictionary().getSequenceIndex(name); sequences.put(index, bases); }