integrate reverse complement in Apollo

GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.

http://genomearchitect.readthedocs.io/

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integrate reverse complement in Apollo #482

Closed nathandunn closed 7 years ago

nathandunn commented 9 years ago

~~sequence~~ moved to #1273
~~edit functionality~~ moved to #1280
~~nclist (chunks)~~ moved to #1281
- ~~re-assess what is getting reverse and how, could be that chunk 1 is using 2's and vice versa . .. maybe chunk values should be reversed~~
- ~~create integration tests~~
[x] getFeatures
- [x] flip strands on projection
[x] nclist (trackData)
- ~~11.4 case~~ moved to #1270

https://trello.com/c/3tMaHPcQ/100-reverse-complement-hard

Please add additional visualizations as you have time.

Related somewhat to #481 . . . .

nathandunn commented 8 years ago

Just wanted to add this from @cmdcolin . . I think that it still needs to be completed for other track types and tested for annotation and Apollo integration (we should automatically over-ride and flip these tracks), but overall it works well within JBrowse.

cmdcolin commented 8 years ago

@nathandunn thanks. I think that should be possible. Automatically "upgrading" the store types to use projection types should be possible too

The currently implemented ones in the plugin are BAM, BigWig, NCList, Sequence

A remaining store class is the one used for the annotation track on Apollo (that uses a store class called scratchpad)

nathandunn commented 8 years ago

Updated interfaces @selewis @monicacecilia

This implies that the scaffolds are ordered and the entire scaffold is reversed or not.

nathandunn commented 7 years ago

It should be noted that a lot of this might already be done.

nathandunn commented 7 years ago

moved mega-issue to other issues