odgi heaps

Path pangenome coverage permutations.


odgi heaps [-i, --idx=FILE] [OPTION]…


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



-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).


-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.