odgi heaps

Path pangenome coverage permutations.

SYNOPSIS

odgi heaps [-i, --idx=FILE] [OPTION]…

DESCRIPTION

Extract matrix of path pangenome coverage permutations for power law regression.

OPTIONS

MANDATORY OPTIONS

-i, --idx=FILE

Load the succinct variation graph in ODGI format from this FILE. The file name usually ends with .og. It also accepts GFAv1, but the on-the-fly conversion to the ODGI format requires additional time!

Heaps Options

-p, --path-groups=FILE

Group paths as described in two-column FILE, with columns path.name and group.name.

-S, --group-by-sample

Following PanSN naming (sample#hap#ctg), group by sample (1st field).

-H, --group-by-haplotype

Following PanSN naming (sample#hap#ctg), group by haplotype (2nd field).

-b, --bed-targets=FILE

BED file over path space of the graph, describing a subset of the graph to consider.

-n, --n-permutations=N

Number of permutations to run.

-d, --min-node-depth=N

Exclude nodes with less than this path depth (default: 0).

Threading

-t, --threads=N

Number of threads to use for parallel operations.

Processing Information

-P, --progress

Print information about the components and the progress to stderr.

Program Information

-h, --help

Print a help message for odgi heaps.