---
name: "map_coords"
section: "1"
platform: "linux"
package: "fsa"
version: "1.15.9+dfsg-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/map_coords"
---

# map\_coords(1)

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

## 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.