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