.. _odgi cover:

#########
odgi cover
#########

find a path cover of the variation graph

SYNOPSIS
========

**odgi cover** [**-i, –idx**\ =\ *FILE*] [**-o, –out**\ =\ *FILE*]
[*OPTION*]…

DESCRIPTION
===========

The odgi cover(1) command finds a path cover of a variation graph, with
a specified number of paths per component.

OPTIONS
=======

Graph Files IO
--------------

| **-i, –idx**\ =\ *FILE*
| File containing the succinct variation graph where find a path cover.
  The file name usually ends with *.og*.

| **-o, –out**\ =\ *FILE*
| Write the succinct variation graph with the generated paths to *FILE*.
  The file name usually ends with *.og*.

Cover Options
-------------

| **-n, –num-paths-per-component**\ =\ *N*
| Number of paths to generate per component.

| **-k, –node-windows-size**\ =\ *N*
| Size of the node window to check each time a new path is extended (it
  has to be greater than or equal to 2).

| **-c, –min-node-coverage**\ =\ *N*
| Minimum node coverage to reach (it has to be greater than 0). There
  will be generated paths until the specified minimum node coverage is
  reached, or until the maximum number of allowed generated paths is
  reached (number of nodes in the input variation graph).

| **-i, –ignore-paths**
| Ignore the paths already embedded in the graph during the nodes
  coverage initialization.

| **-w, –write-node-coverages**\ =\ *FILE*
| Write the node coverages at the end of the paths generation to FILE.
  The file will contain tab-separated values (header included), and have
  3 columns: *component_id*, *node_id*, and *coverage*.

Threading
---------

| **-t, –threads**\ =\ *N*
| Number of threads to use for the parallel sorter.

Processing Information
----------------------

| **-P, –progress**
| Print information about the components and the progress to stderr.

Program Information
-------------------

| **-h, –help**
| Print a help message for **odgi cover**.

..
	EXIT STATUS
	===========
	
	| **0**
	| Success.
	
	| **1**
	| Failure (syntax or usage error; parameter error; file processing
	  failure; unexpected error).
	
	BUGS
	====
	
	Refer to the **odgi** issue tracker at
	https://github.com/pangenome/odgi/issues.