.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
.TH MAP_COORDS "1" "December 2015" "map_coords 1.15.9" "User Commands"
.SH NAME
map_coords \- Map coordinates from one genome to another using a Mercator multiple alignment
.SH SYNOPSIS
.B map_coords
[\fI\,options\/\fR] \fI\,<source genome> <chromosome> <start> <end> <strand> <target genome>\/\fR
.SH DESCRIPTION
map_coords from FSA 1.15.9
.PP
Map coordinates from one genome to another using a Mercator multiple alignment.
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this message
.TP
\fB\-D\fR, \fB\-\-data\fR <directory>
path to map, genome and alignment files
.TP
\fB\-M\fR, \fB\-\-map\fR <directory>
path to map and genome files
.TP
\fB\-A\fR, \fB\-\-align\fR <directory>
path to alignment files
.TP
\fB\-L\fR, \fB\-\-lazy\fR
warn, rather than die, if the subalignment can't be obtained
.TP
\fB\-U\fR, \fB\-\-truncate\fR
truncate unmappable sequence (rather than skipping) and show truncated subalignment
.PP
Assumes that coordinates are 1\-based and fully\-closed,
therefore representing the interval [start, end].
.PP
If requested, unmappable sequence will be truncated to the mappable portion;
note that the truncation will favor the beginning of the requested sequence.
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.