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.