pangyplot preprocess

Interactively generate a shell (or SLURM) script that preprocesses a GFA or OG file with odgi into the sorted GFA plus layout TSV inputs expected by pangyplot add.

SYNOPSIS

pangyplot preprocess

DESCRIPTION

Runs an interactive prompt that asks for the input file, reference path names, thread count, GPU availability, and (optionally) SLURM job parameters, then writes a self-contained bash script that:

1. Converts the input GFA to ODGI .og format.

2. Optionally sorts the graph with a prioritized list of reference paths.

3. Runs odgi layout (with optional GPU acceleration) to produce the 2D coordinates TSV.

4. Writes the sorted GFA back out.

The generated script’s outputs — a sorted .gfa and a layout .tsv — are the two files that pangyplot add expects via --gfa and --layout.

This command does not run odgi itself; it just produces the script, so the preprocessing can run on a workstation or compute cluster independent of where PangyPlot is installed.

OPTIONS

No command-line options. All parameters are collected via interactive prompts.