NAME

       map_coords  -  Map  coordinates  from  one  genome  to  another  using a Mercator multiple
       alignment

SYNOPSIS

       map_coords [options] <source genome> <chromosome> <start> <end> <strand> <target genome>

DESCRIPTION

       map_coords from FSA 1.15.9

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

OPTIONS

       -h, --help
              show this message

       -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

       Assumes that coordinates are 1-based and fully-closed, therefore representing the interval
       [start, end].

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

AUTHOR

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