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.

map_coords 1.15.9                                 December 2015                                    MAP_COORDS(1)