odgi chop

Divide nodes into smaller pieces preserving node topology and order.

SYNOPSIS

odgi chop [-i, --idx=FILE] [-o, --out=FILE] [-c, –chop-to=N] [OPTION]…

DESCRIPTION

The odgi chop command chops long nodes into short ones while preserving the graph topology and node order.

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!

-o, --out=FILE

Write the chopped succinct variation graph in ODGI format to FILE. A file ending of .og is recommended.

-c, --chop-to=N

Divide nodes that are longer than N base pairs into nodes no longer than N while maintaining graph topology.

Threading

-t, --threads=N

Number of threads to use for the parallel operations.

Processing Information

-d, --debug

Print information about the process to stderr.

-P, --progress

Print information about the operations and the progress to stderr.

Program Information

-h, --help

Print a help message for odgi chop.