Adding additional options for duplicate reads.

igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

https://igv.org

MIT License

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Adding additional options for duplicate reads. #1542

Closed lbergelson closed 3 months ago

lbergelson commented 3 months ago

This is in response to a feature request from @rickymagner. It doesn't seem like there was any way to see which reads are duplicates. Added some new options to help.

new Group By Duplicates option
new Duplicates submenu which allows rapid toggling of duplicates between three states
- Filtered: not visible
- Visible: treated like normal reads
- Textures: rendered with a visible slash texture

Showing the new grouping and cross hatching

The new menu option

lbergelson commented 3 months ago

huh, I seem to have an test failure... I'll look into that...

lbergelson commented 3 months ago

Fixed. I made the faulty assumption that renderOptions wasn't allowed to be null there.

jrobinso commented 3 months ago

I love the feature. I wonder if the options should be verbs, i.e "filter", "show", and "texture". I guess texture isn't a verb, can I texture something? Or space isn't a problem, we could be explict, "filter duplicates", "show duplicates", and "texture duplicates". Again I'm not sure texture is really a verb, but its close enough in context.

rickymagner commented 3 months ago

Apparently it can be used as a verb as well. I like making them verbs since it feels more like an action you're performing in the app.