@Override public long readLong() { readFully(in, tmpBuf.array(), 0, 8); return tmpBuf.getLong(0); }
protected AbstractBAMFileIndex( final SeekableStream stream, final SAMSequenceDictionary dictionary) { mBamDictionary = dictionary; mIndexBuffer = new IndexStreamBuffer(stream); seek(4); sequenceIndexes = new int[readInteger() + 1]; Arrays.fill(sequenceIndexes, -1); }
@Override public void readBytes(final byte[] bytes) { readFully(in, bytes, 0, bytes.length); }
@Override public int readInteger() { readFully(in, tmpBuf.array(), 0, 4); return tmpBuf.getInt(0); }
protected AbstractBAMFileIndex( final SeekableStream stream, final SAMSequenceDictionary dictionary) { mBamDictionary = dictionary; mIndexBuffer = new IndexStreamBuffer(stream); verifyBAMMagicNumber(stream.getSource()); sequenceIndexes = new int[readInteger() + 1]; Arrays.fill(sequenceIndexes, -1); }