marbl MetagenomeScope issues

marbl / MetagenomeScope

Visualization tool for (meta)genome assembly graphs

https://marbl.github.io/MetagenomeScope/

GNU General Public License v3.0

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issues

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Update DOT parser to optionally allow edge IDs in labels

#246 fedarko opened 3 months ago
0
Adjust max node / max edge counts to consider the top layer of the decomposed graph

#245 fedarko opened 1 year ago
0
[WIP] Support DOT inputs (and multigraphs); much improved boundary node splitting in pattern identification; add back frayed rope support; lots of other improvements

#244 fedarko opened 1 year ago
1
Support general node / edge metadata

#243 fedarko opened 1 year ago
0
Identify cyclic frayed ropes?

#242 fedarko opened 1 year ago
0
Identifying cyclic bubbles?

#241 fedarko opened 1 year ago
1
Draw arrowheads in both directions for self-implying edges

#240 fedarko opened 1 year ago
0
Support duplicate (aka parallel) edges in GFA / FASTG files?

#239 fedarko opened 1 year ago
0
Pass extra GFA segment / link attributes (tags) to the visualization

#238 fedarko opened 1 year ago
0
Compress main.js more

#237 fedarko opened 1 year ago
0
ENH/DOC: no_args_is_help; note in a comment

#236 fedarko closed 1 year ago
0
Fix pygraphviz install; switch to GH Actions

#235 fedarko closed 2 years ago
1
[Feature Request] Output a graph file that could be used elsewhere (e.g., NetworkX, iGraph, or Cytoscape)

#234 jolespin closed 2 years ago
4
set scale in PNG exports to 5: temp #226 fix

#233 fedarko closed 2 years ago
0
Temporarily address #231: thicken duplicate edges

#232 fedarko closed 2 years ago
0
Thicken duplicate edges

#231 fedarko opened 2 years ago
1
Allow searching to return complements if needed

#230 fedarko opened 2 years ago
0
Change chain color to something more neutral: close #221

#229 fedarko closed 2 years ago
0
Pass PATTERN2COLOR from Python to JS?

#228 fedarko opened 2 years ago
0
Automatically cropping screenshots

#227 fedarko opened 2 years ago
1
Blurry exported screenshots

#226 fedarko opened 2 years ago
1
Add "select all" option

#225 fedarko opened 2 years ago
0
Aggregate some statistics in node / edge tables

#224 fedarko opened 2 years ago
0
Better component tiling

#223 fedarko opened 2 years ago
0
New type of pattern: bipartite subgraphs

#222 fedarko opened 2 years ago
1
Change the "chain" color to something more neutral

#221 fedarko closed 2 years ago
1
Prevent long node labels from extending past pattern boundaries

#220 fedarko opened 2 years ago
0
Better selected node/edge/pattern info tables

#219 fedarko opened 2 years ago
0
Fix autoformatting re: ** operator; should un-break CI (for real this time)

#218 fedarko closed 2 years ago
0
STY: Un-break CI

#217 fedarko closed 2 years ago
0
Sanity check with various assemblers' output

#216 fedarko opened 2 years ago
0
DOC: Tidy up README -- filetypes, etc.

#215 fedarko closed 2 years ago
0
Update CI

#214 fedarko closed 2 years ago
0
Corner-case AGP visualization bugs

#213 fedarko opened 2 years ago
0
Documenting gaps in AGP scaffolds

#212 fedarko opened 2 years ago
0
Configurable segment / "node" shapes

#211 fedarko opened 2 years ago
1
Label offsets

#210 fedarko opened 2 years ago
0
Circularized semilinear layout

#209 fedarko opened 3 years ago
0
Detect paths encoded in GFA files and pass to user interface

#208 fedarko closed 1 year ago
1
Support showing extra metadata (length, coverage, etc.) in node / edge labels

#207 fedarko opened 3 years ago
0
Alternate, more intuitive representation of duplicate bubble boundary nodes

#206 fedarko opened 3 years ago
0
[WIP] Add back AGP (scaffold) file visualization; other improvements

#205 fedarko closed 2 years ago
0
Centralize data storage in the Python codebase

#204 fedarko opened 3 years ago
0
For now, just don't detect frayed ropes

#203 fedarko closed 3 years ago
0
Need to set up decomposed graph as a MultiDiGraph

#202 fedarko opened 3 years ago
1
Allow chains to be used as boundary nodes of bubbles

#201 fedarko opened 3 years ago
1
Disallow frayed ropes from being used in other types of patterns in the decomposition

#200 fedarko opened 3 years ago
0
Tidy up docs a bit; remove outdated stuff

#199 fedarko closed 3 years ago
0
Clean up coordinate rotation / conversion code + fix inaccuracies in component tiling

#198 fedarko opened 3 years ago
0
Use a basic grid method for tiling components' bounding boxes; show "N/A" for missing attributes in info tables

#197 fedarko closed 3 years ago
0