jbrowse-plugin-graphgenomeviewer 4.0.7 → 4.0.9

package/README.md

@@ -1,31 +1,21 @@
 # jbrowse-plugin-graphgenomeviewer
 
-A JBrowse 2 plugin that draws a pangenome graph (GFA / rGFA, or a gbz-base
-database) as a track of a linear genome view, and as a **GraphGenomeView** of
-its own for a whole file.
+Pangenome graphs in JBrowse 2.
 
 ![KIV-2, force-directed, with its bubbles marked](img/force_kiv2.png)
 
-The LPA KIV-2 window of the HPRC release 2 graph: the GRCh38 backbone runs left
-to right, and the kringle repeat array forms the loops in the middle.
+![Tube maps, and a tube map track under a linear view](img/tube_map.png)
 
-## Core ideas
-
-- **Six layouts, one graph.** Force-directed (Bandage's OGDF FMMM, compiled to
-  wasm) shows the graph's shape; the variant map, ordered, anchored, sample-row
-  and walk-row layouts put it on reference coordinates so it lines up under a
-  linear view.
-- **Bubbles are the unit.** The plugin reads `gfatools bubble` output beside an
-  rGFA index, or derives bubbles from the graph itself, then marks them and
-  opens any one level by level.
-- **Haplotypes as walks.** Over gbz-base a node draws thicker the more
-  haplotypes carry it, and picking one walk lifts its route out of the drawing
-  with its length against the reference.
-
-![HG00133's walk lifted out of the KIV-2 cut](img/force_kiv2_walk.png)
+- Eight layouts: force-directed (Bandage FMMM), variant map, ordered, anchored,
+  sample rows, walk rows, and sequenceTubeMap's tube map on its own axis or the
+  reference's
+- Bubbles from `gfatools bubble` or the graph itself, opened level by level
+- gbz-base haplotypes as walks: carriage as node thickness, one walk lifted out
 
 ## Usage
 
+Needs JBrowse 5.0.0-beta.9 or later.
+
 ```json
 {
   "plugins": [
@@ -37,15 +27,14 @@ to right, and the kringle repeat array forms the loops in the middle.
 }
 ```
 
-The plugin needs a JBrowse host of 5.0.0-beta.9 or later. **File → Open track**
-takes a `.segs.bed.gz` url from `build_rgfa_tabix.sh` and opens it as a graph
-track with no config. A hand-written track needs only the adapter; a
-`FeatureTrack` over an rGFA opens as `LinearGraphDisplay` unless its config
-lists `displays`:
+- **File → Open track** opens an rGFA index (`.segs.bed.gz` from
+  `build_rgfa_tabix.sh`) or a gbz-base database (`.gbz.db`) as a `GraphTrack`
+- **Add → Graph genome view** opens a whole GFA file
+- A hand-written track needs only the adapter:
 
 ```json
 {
-  "type": "FeatureTrack",
+  "type": "GraphTrack",
   "trackId": "hprc_graph",
   "name": "HPRC release 2 graph",
   "assemblyNames": ["hg38"],
@@ -60,27 +49,21 @@ lists `displays`:
 }
 ```
 
-The display cuts the visible window plus one window-width each side, up to 5 Mb.
-Past `aboveBpPerPx` it cuts the optional `coarse` tier instead, one node per
-bubble with no size cap, built by `build_bubble_tier.sh` in jbrowse-components.
-Layouts on reference bp pan and zoom with the view; the force-directed and
-ordered layouts fit the track and zoom from its menu. The track menu picks the
-layout, colour and walk, and switches to the segments lane, one block per
-segment.
-
-**Add → Graph genome view** opens a whole GFA file in its own view.
+- The track menu picks layout, colour and walk, and switches to the segments
+  lane or, for gbz-base, the haplotype lanes
+- Cuts the window plus a window each side, up to 5 Mb; past `aboveBpPerPx`, the
+  `coarse` tier (`build_bubble_tier.sh` in jbrowse-components)
+- gbz-base swaps in `{ "type": "GbzBaseSyntenyAdapter", "uri": "….gbz.db" }`; an
+  `hg38` or `hs1` track finds the graph's GRCh38 or CHM13 reference sample, and
+  `assemblyNameToPanSN` covers other names
 
 ## Docs
 
-- [docs/layouts.md](docs/layouts.md) — every layout, bubbles, walks, genes on
-  the graph, and the demonstration loci
-- [docs/developing.md](docs/developing.md) — dev server, building, the Bandage
-  engine, testing and `host-compat`
-- [docs/layout-experiments.md](docs/layout-experiments.md) — all six loci in
-  every layout, current and proposed
+- [docs/layouts.md](docs/layouts.md) — layouts, bubbles, walks, genes, loci
+- [docs/developing.md](docs/developing.md) — building, testing, `host-compat`
+- [docs/layout-experiments.md](docs/layout-experiments.md) — every locus in
+  every layout
 
 ## License
 
-GPL-3.0-or-later, because the force-directed layout runs a wasm build of
-Bandage's FMMM layout from [OGDF](https://ogdf.github.io/), and both are GPL.
-JBrowse stays Apache-2.0, since configs load this plugin separately at runtime.
+GPL-3.0-or-later (the wasm FMMM engine is OGDF, GPL).

package/dist/chunks/AddTrackWorkflow-LRRSAVSX.js

@@ -0,0 +1,2 @@
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+//# sourceMappingURL=AddTrackWorkflow-LRRSAVSX.js.map

package/dist/chunks/{AddTrackWorkflow-J44PELJE.js.map → AddTrackWorkflow-LRRSAVSX.js.map}

@@ -2,6 +2,6 @@
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