readme.md

Waragraph - a variation graph visualizer

Usage

Build with cargo. Only the latest version of Rust is supported.

cargo build --release

Run by providing a GFA file, and, optionally, a TSV layout file from odgi layout. A layout file can also be provided after the program has started, from the settings window.

./target/release/waragraph graph.gfa layout.tsv

Annotations can be loaded at startup using the --bed or --gff (in combination with --gff-attr) command line arguments.

When a GFF file is loaded, the attribute key from --gff-attr is used as the label.

4 column BED files are supported, with the 4th column being used as the label. If the 4th column ends with a space followed by a hex-coded color, e.g. “SomeGene #32ABCD”, that will be the annotation’s highlight color.

./target/release/waragraph graph.gfa layout.tsv --bed some.bed

Global

Press Escape to open and close the settings window. If not provided on startup, a TSV layout file can be loaded under "Graph & Layout" in the "General" tab.

1D

Scroll the path list by scrolling the mouse wheel with the cursor over the path names. Zooming the view can be done by scrolling the wheel over the path visualizations.

Right click on a node to pan the 2D view to that node. This does not zoom the 2D view.

Up and down arrow keys also scroll the list, and the left and right keys pan the view. Press Space to reset the view.

2D

Pan and zoom the view by clicking and dragging with the mouse, and scrolling the mouse wheel.

Right click on a node to pan the 1D view to that node. This does not zoom the 1D view, so if the 1D view is fully zoomed out, nothing will happen.

If annotations are loaded, left clicking an annotation in the sidebar list will pan the view to it, and right clicking it will toggle it so that it’s always highlighted.

Press Space to reset the view.

Project structure

• /lib contains the core graph and related algorithms.
• /app contains the visualizer application.