NAME

       delta-filter  -  read  a delta alignment file from either nucmer or promer and filters the
       alignments

SYNOPSIS

       delta-filter [options]<deltafile>

DESCRIPTION

       -1     1-to-1 alignment allowing for rearrangements (intersection of -r and -q alignments)

       -g     1-to-1 global alignment not allowing rearrangements

       -h     Display help information

       -i float
              Set the minimum alignment identity [0, 100], default 0

       -l int Set the minimum alignment length, default 0

       -m     Many-to-many alignment allowing for rearrangements (union of -r and -q alignments)

       -q     Maps each position of each query to its best hit in  the  reference,  allowing  for
              reference overlaps

       -r     Maps  each  position  of  each reference to its best hit in the query, allowing for
              query overlaps

       -u float      Set the minimum alignment uniqueness, i.e. percent of

              the alignment matching to unique reference AND query sequence [0, 100], default 0

       -o float
              Set the maximum alignment overlap for -r  and  -q  options  as  a  percent  of  the
              alignment length [0, 100], default 100

       -v     Print the discarded alignments instead of those that pass filters

       -b     Maps duplications (XOR of -r and -q alignments, one or the other but not both)

       Reads a delta alignment file from either nucmer or promer and filters the alignments based
       on the command-line switches, leaving only the desired  alignments  which  are  output  to
       stdout  in  the same delta format as the input. For multiple switches, order of operations
       is as follows: -i -l -u -q -r -g -m -1 -b. If an alignment  is  excluded  by  a  preceding
       operation, it will be ignored by the succeeding operations.

       An  important  distinction  between  the  -g  option  and the -1 and -m options is that -g
       requires the alignments to be mutually consistent in their order,  while  the  -1  and  -m
       options  are not required to be mutually consistent and therefore tolerate translocations,
       inversions, etc. In general cases, the -m option is the best choice,  however  -1  can  be
       handy  for  applications  such as SNP finding which require a 1-to-1 mapping. Finally, for
       mapping  query  contigs,  or  sequencing  reads,  to  a  reference  genome,  use  -q.  The
       duplications  printed  with the -b option are -r and -q alignments that are not present in
       the 1-to-1 alignment. These alignments are also the  difference  between  the  -1  and  -m
       alignments

SEE ALSO

       The  -b  option  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