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

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

map_coords 1.15.9                                 December 2015                                    MAP_COORDS(1)

       map_coords from FSA 1.15.9

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

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

-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.

map_coords [options] <sourcegenome><chromosome><start><end><strand><targetgenome>