public int computeId(BitSet activeMatches,IReadBlock readBlock){
  if (name2id != null) {
    final String name=readBlock.getReadName();
    final Integer id=name2id.get(name);
    if (id != null && id > 0)     return id;
  }
  if (activeMatches.cardinality() == 0)   return IdMapper.NOHITS_ID;
  for (int i=activeMatches.nextSetBit(0); i != -1; i=activeMatches.nextSetBit(i + 1)) {
    IMatchBlock match=readBlock.getMatchBlock(i);
    int id=match.getId(cName);
    if (id > 0)     return id;
  }
  return IdMapper.UNASSIGNED_ID;
}

public int computeId ( BitSet activeMatches , IReadBlock readBlock ) { if ( name2id != null ) { final String name = readBlock . getReadName ( ) ; final Integer id = name2id . get ( name ) ; if ( id != null && id > 0 ) return id ; } if ( activeMatches . cardinality ( ) == 0 ) return IdMapper . NOHITS_ID ; for ( int i = activeMatches . nextSetBit ( 0 ) ; i != - 1 ; i = activeMatches . nextSetBit ( i + 1 ) ) { IMatchBlock match = readBlock . getMatchBlock ( i ) ; int id = match . getId ( cName ) ; if ( id > 0 ) return id ; } return IdMapper . UNASSIGNED_ID ; }
computes the id for a read from its matches matches
