NAME

       delta2blocks - extra tool for mummer from patch of mugsy to sort alignments
       delta2maf - extra tool for mummer from patch of mugsy to sort alignments

SYNOPSIS

       delta2blocks [options]<deltafile><refID><qryID>
       delta2maf [options]<deltafile><refID><qryID>

DESCRIPTION

       -h     Display help information

       -q     Sort alignments by the query start coordinate

       -r     Sort alignments by the reference start coordinate

       -w int Set the screen width - default is 60

       -x int Set  the matrix type - default is 2 (BLOSUM 62), other options include 1 (BLOSUM 45) and 3 (BLOSUM
              80)
              note: only has effect on amino acid alignments

       Input is the .delta output of either the "nucmer" or the "promer" program passed on the command line.

       Output is to stdout, and consists of all  the  alignments  between  the  query  and  reference  sequences
       identified on the command line.

       NOTE: No sorting is done by default, therefore the alignments will be ordered as found in the <deltafile>
       input.

SEE ALSO

       This tool originates from mugsy that provides a code copy of mummer with additional patches.  The  source
       can be found in SVN svn://svn.code.sf.net/p/mugsy/code/trunk