NAME

       map_gff_coords  -  Map  coordinates  of  GFF  features  from one genome to another using a
       Mercator multiple alignment

SYNOPSIS

       map_gff_coords [options] <source genome> <source GFF file> <target genome>

DESCRIPTION

       map_gff_coords from FSA 1.15.9

       Map coordinates of GFF features from one genome  to  another  using  a  Mercator  multiple
       alignment.

OPTIONS

       -h, --help
              show this message

       -t, --type <string>
              only look at features of particular type

       -D, --data <directory>
              path to map, genome and alignment files

       -M, --map <directory>
              path to map and genome files

       -A, --align <directory>
              path to alignment files

       -L, --lazy
              warn, rather than die, if the subalignment can't be obtained

       -U, --truncate
              truncate unmappable sequence (rather than skipping) and show truncated subalignment

       -f, --force-entry
              if  a feature can't be mapped, then add an empty entry to the GFF file (rather than
              skipping it entirely); implies --lazy

       -e, --verbose
              report progress

       PLEASE NOTE: While this program is reasonably fast if  the  GFF  is  properly  ordered  by
       chromosome  and  the  start and end coordinates of features, it will be *very slow* if the
       GFF is not sorted.  Assumes that the "seqid" or "name" field (the first field) of the  GFF
       entries holds the chromosome name.

       Note  that  the  GFF  specification  defines  coordinates  to be 1-based and fully-closed,
       therefore representing the interval [start, end].  Conformance to  this  specification  is
       assumed internally.

       If requested, unmappable sequence will be truncated to the mappable portion; note that the
       truncation will favor the beginning of the requested sequence.

       If a GFF feature is on the + strand for the source genome but the corresponding homologous
       region  in  the  target  genome  is  on  the - strand, then the mapped GFF feature will be
       reported as on the - strand.

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.