public void processAlignment ( final SAMRecord rec ) throws IOException { // write an offset for the first record and for the g-th record thereafter (where // g is the granularity), to be consistent with the index method if ( count == 0 || ( count + 1 ) % granularity == 0 ) { SAMFileSource fileSource = rec . getFileSource ( ) ; SAMFileSpan filePointer = fileSource . getFilePointer ( ) ; writeVirtualOffset ( getPos ( filePointer ) ) ; } count ++ ; }
Process the given record for the index .