/** * @param record * @return inclusive 0-based coordinate of the last base alignment */ private int getAlignmentEndForRecord(int record) { view.start = index[record]; return view.calculateAlignmentEnd(); }
public void setData(byte[] buf) { this.buf = buf; reset(); }
private void setMateRefIDForRecord(int record, int refId) { view.start = index[record]; view.setMateRefID(refId); }
private void setFlagsForRecord(int record, int flags) { view.start = index[record]; view.setFlags(flags); }
private void setInsertSizeForRecord(int record, int insertSize) { view.start = index[record]; view.setInsertSize(insertSize); }
@Override protected void ready(BAMRead read) { int streamIndex = getStreamIndex(read.getRecord()); writers[streamIndex].addAlignment(read.getRecord()); ready++; }
public void setAlignmentStart(int alignmenStart) { writeInt(alignmenStart - 1, POS); }
@Override public void add(FastqRead read) { super.add(read); total++; }
public int getMateRefID() { return getInt(MATE_REF_ID); }
private int getAlignmentStartForRecord(int record) { view.start = index[record]; return view.getAlignmentStart(); }
private int getRefIDForRecord(int record) { view.start = index[record]; return view.getRefID(); }
@Override protected AbstractFastqReader newReader() { return new ReaderToFastq(); }
public void setFlags(int flags) { // writeInt(flags, FLAGS); writeUShort(flags, FLAGS); }
public int getFlags() { return getUShort(FLAGS); }
public void setReadLength(int readLength) { writeInt(readLength, READ_LEN); }
@Override public void add(BAMRead read) { super.add(read); total++; }
public int getSequenceId() { return getInt(REF_ID); }
public void setRefID(int id) { writeInt(id, REF_ID); }
public void setMateAlStart(int mateAlStart) { writeInt(mateAlStart - 1, MATE_AL_START); }