map_coords1
Map coordinates from one genome to another using a mercator multiple alignment
Usage
map_coords [options]
<source
genome>
<chromosome>
<start>
<end>
<strand>
<target
genome>
Overview
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.