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.