New feature requests.

[EdHarry]

Requests

Feature requests made by Sanger GRIT team on 18/11/2021.

Scaffold Painting

• Paint all option.
• Paint region option, i.e. select a start and an end.

Editing

• Ability to tag regions with extra meta-data (e.g. haplotig).
  • Ability to sort / rearrange map based on meta-data tags.
  • Ability to export meta-data in AGP output.
  • Option to auto-tag painted sequences.
  • Default tags:
    • Haplotig
    • Unloc
    • X
    • Y
    • Z
    • W
• Ability to edit non-contiguous regions.
• Ability to import AGP.
• Option to preserve sequence order in AGP output.

UI

• More accurate position info on tooltip.
• Scaffold lookup menu.

Rendering

• Increased resolution.

Estimated difficulty / priority queue

Easy, ~1 week turnaround time

• Paint all.
• Paint regions.
• More accurate tooltip.
• Auto-tag option.
• New default tags.
• AGP sequence preservation option.

Medium, ~3-4 weeks turnaround time

• Meta-data tags, sorting based on tags, exporting meta-data.
• Non-contiguous editing.
• Scaffold lookup.

Hard, no estimate on turnaround, experimentation required

• Resolution increase.

[atracey99]

Could we have a search box to look up scaffold names please? Looking up via sequence list can be very inefficient with long potentially unsorted lists

[EdHarry]

Could we have a search box to look up scaffold names please? Looking up via sequence list can be very inefficient with long potentially unsorted lists

Sure, I should be able to add something like that.

Update -> added to original comment.

[EdHarry]

Development release: 0.2.5-dev-0

Implemented features:

• More scaffold painting options.
• More accurate tooltip.
• Scaffold lookup.
• Meta data tags.

Any feedback will be appreciated.

[jeramiahsmith]

HI, I have been giving this a try and am loving the interface. One thing I am wondering is if it would somehow be possible to import an external AGP file to aid in initial ordering of scaffolds. Perhaps such a feature already exists though?

[EdHarry]

HI, I have been giving this a try and am loving the interface. One thing I am wondering is if it would somehow be possible to import an external AGP file to aid in initial ordering of scaffolds. Perhaps such a feature already exists though?

I think this should be possible, I'll see if I can get something like this implemented in the next devel release.

[EdHarry]

Development release: 0.2.5-dev-1

New features:

• More default tags.
• Painted sequences auto-tagged in AGP output.
• Higher resolution support (experimental). See PretextMap branch with high resolution option.

[EdHarry]

Development release: 0.2.5-dev-2

New features:

• Option to preserve sequence order in AGP output.
• Option to display embedded graph labels.

Note: Save-states only compatible with previous version (0.2.5-dev-1).

[EdHarry]

Full 0.2.5 release

Unfortunately some requested features weren't able to make this release:

• Non-contiguous editing
• AGP input

This thread will close for now, but may reopen, pending future development work.