@jbrowse/bandage-core 6.0.0 → 6.0.2

package/README.md

@@ -23,7 +23,7 @@ npm install @jbrowse/bandage-core
 - Figures: `figureSvg` draws a graph and its lifted walks to a standalone SVG,
   and the `bandage-figure` CLI makes one from a JSON spec with no browser:
   `npx -p @jbrowse/bandage-core bandage-figure spec.json -o figure.svg`. See
-  [docs/figures.md](https://github.com/GMOD/jbrowse-plugin-graphgenomeviewer/blob/main/docs/figures.md)
+  [docs/figures.md](docs/figures.md)
 
 Nothing here imports React, MobX or a JBrowse host. BandageJS's
 [`src/main.ts`](https://github.com/cmdcolin/BandageJS/blob/main/src/main.ts) is
@@ -31,10 +31,26 @@ the worked example.
 
 ## Developing
 
-Lives in the plugin repo as a pnpm workspace package. The plugin imports its
-source directly, so a change here needs no publish to reach the plugin.
+```
+pnpm install
+pnpm test          # unit tests
+pnpm build         # dist/ with declarations
+pnpm test:wasm     # the committed layout engine still loads
+```
+
+The Bandage layout engine is OGDF's FMMM compiled to WASM and committed at
+`src/bandage/bandage-layout.js`; [src/bandage/README.md](src/bandage/README.md)
+says how to rebuild it from `src/bandage/native` and the vendored `vendor/ogdf`.
+A weekly workflow proves the committed artifact still reproduces.
+
+CI also packs the core and runs
+[BandageJS](https://github.com/cmdcolin/BandageJS) and
+[jbrowse-plugin-graphgenomeviewer](https://github.com/GMOD/jbrowse-plugin-graphgenomeviewer)
+against it. An API change lands with the consumer's side on a `core-next` branch
+in that repo, which CI tests in place of `main` until the release.
+
+Release with `pnpm version patch`: it lints, tests, stamps `src/version.ts`,
+writes the changelog with git-cliff and pushes the `v*` tag, and `publish.yml`
+publishes to npm with trusted publishing.
 
-The core releases with the plugin, at the plugin's version: `pnpm version patch`
-at the repo root sets both, and `publish.yml` and `publish-core.yml` each
-publish one from the `v*` tag. `publish-core.yml` also runs by hand to publish a
-version a failed run left behind.
+Both Bandage and OGDF are GPL, which is why this package is GPL-3.0-or-later.

package/dist/alleleProjection/projectAlleles.js

@@ -0,0 +1,10 @@
+import {
+  parsePanSN,
+  projectAlleles
+} from "../chunks/chunk-RVS2QCOX.js";
+import "../chunks/chunk-ES2N6V56.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  parsePanSN,
+  projectAlleles
+};

package/dist/anchoredNodes.js

@@ -0,0 +1,24 @@
+import {
+  REFERENCE_RANK,
+  backboneNodes,
+  backbonePositions,
+  backboneSpan,
+  firstNodeAtOrAfter,
+  isAnchored,
+  isBackbone,
+  isOffReference,
+  overlapsWindow,
+  referenceSpan
+} from "./chunks/chunk-FYQWPEEY.js";
+export {
+  REFERENCE_RANK,
+  backboneNodes,
+  backbonePositions,
+  backboneSpan,
+  firstNodeAtOrAfter,
+  isAnchored,
+  isBackbone,
+  isOffReference,
+  overlapsWindow,
+  referenceSpan
+};

package/dist/bubbleSpreads.js

@@ -0,0 +1,11 @@
+import {
+  BUBBLE_SPREADS,
+  BUBBLE_SPREAD_VALUES,
+  spreadFor
+} from "./chunks/chunk-UVBGRJQX.js";
+import "./chunks/chunk-6JEWNXCQ.js";
+export {
+  BUBBLE_SPREADS,
+  BUBBLE_SPREAD_VALUES,
+  spreadFor
+};

package/dist/bubbles/bubbleHalos.js

@@ -0,0 +1,11 @@
+import {
+  bubbleHalos
+} from "../chunks/chunk-3C2LGJKY.js";
+import "../chunks/chunk-WOO7QYKB.js";
+import "../chunks/chunk-MFKORG3F.js";
+import "../chunks/chunk-3PLYZLYV.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  bubbleHalos
+};

package/dist/bubbles/bubbleLine.js

@@ -0,0 +1,14 @@
+import {
+  SATURATED_PATH_COUNT,
+  bubbleDescription,
+  bubbleLabel,
+  parseBubbleLine,
+  sameBubble
+} from "../chunks/chunk-MFKORG3F.js";
+export {
+  SATURATED_PATH_COUNT,
+  bubbleDescription,
+  bubbleLabel,
+  parseBubbleLine,
+  sameBubble
+};

package/dist/bubbles/bubblesFromGraph.js

@@ -0,0 +1,10 @@
+import {
+  bubblesFromGraph
+} from "../chunks/chunk-4S47XRYA.js";
+import "../chunks/chunk-MFKORG3F.js";
+import "../chunks/chunk-HNQPEMYE.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  bubblesFromGraph
+};

package/dist/bubbles/classifyBubble.js

@@ -0,0 +1,15 @@
+import {
+  BUBBLE_KIND_COLORS,
+  BUBBLE_KIND_NAMES,
+  bubbleSegmentIds,
+  classifyBubble,
+  formatBp
+} from "../chunks/chunk-WOO7QYKB.js";
+import "../chunks/chunk-MFKORG3F.js";
+export {
+  BUBBLE_KIND_COLORS,
+  BUBBLE_KIND_NAMES,
+  bubbleSegmentIds,
+  classifyBubble,
+  formatBp
+};

package/dist/bubbles/popBubble.js

@@ -0,0 +1,9 @@
+import {
+  bubbleSubgraph
+} from "../chunks/chunk-VHW7FDHU.js";
+import "../chunks/chunk-ST2IBUAN.js";
+import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  bubbleSubgraph
+};

package/dist/chunks/chunk-3C2LGJKY.js

@@ -0,0 +1,108 @@
+import {
+  bubbleSegmentIds,
+  classifyBubble,
+  formatBp
+} from "./chunk-WOO7QYKB.js";
+import {
+  svgPath
+} from "./chunk-3PLYZLYV.js";
+import {
+  isBackbone
+} from "./chunk-FYQWPEEY.js";
+
+// src/bubbles/bubbleHalos.ts
+var WHOLE_FRACTION = 0.9;
+var NAMED_WALKS = 2;
+var MIN_CHIPPED_BP = 1e3;
+function bubbleHalos(graph, bubbles, positions, walkLabel = (name) => name, repeats = []) {
+  const byName = new Map(graph.nodes.map((n) => [n.name, n]));
+  const halos = [];
+  for (const bubble of bubbles) {
+    const parts = [];
+    let minX = Infinity;
+    let maxX = -Infinity;
+    let minY = Infinity;
+    const nodeIds = [];
+    const ends = [];
+    for (const name of bubbleSegmentIds(bubble)) {
+      const node = byName.get(name);
+      const line = node && positions[node.id];
+      if (!node || !line?.length) {
+        continue;
+      }
+      if (isBackbone(node) && (node.stable.start < bubble.start || node.stable.start >= bubble.end)) {
+        ends.push(line[Math.floor(line.length / 2)]);
+        continue;
+      }
+      nodeIds.push(node.id);
+      parts.push(svgPath(line.length === 1 ? [line[0], line[0]] : line));
+      for (const p of line) {
+        minX = Math.min(minX, p.x);
+        maxX = Math.max(maxX, p.x);
+        minY = Math.min(minY, p.y);
+      }
+    }
+    if (nodeIds.length === 0) {
+      continue;
+    }
+    const labelAt = { x: (minX + maxX) / 2, y: minY };
+    const anchor = ends.length ? {
+      x: ends.reduce((s, p) => s + p.x, 0) / ends.length,
+      y: ends.reduce((s, p) => s + p.y, 0) / ends.length
+    } : labelAt;
+    const sharing = /* @__PURE__ */ new Map();
+    for (const route of bubble.routes ?? []) {
+      for (const id of new Set(route.steps)) {
+        sharing.set(id, (sharing.get(id) ?? 0) + 1);
+      }
+    }
+    const routes = [];
+    for (const route of bubble.routes ?? []) {
+      if (bubble.longestAlleleLength < MIN_CHIPPED_BP) {
+        break;
+      }
+      if (route.steps.length === 0) {
+        continue;
+      }
+      const rarest = Math.min(...route.steps.map((id) => sharing.get(id)));
+      let at;
+      let far = -1;
+      for (const id of route.steps) {
+        if (sharing.get(id) !== rarest) {
+          continue;
+        }
+        for (const p of positions[id] ?? []) {
+          const d = Math.hypot(p.x - anchor.x, p.y - anchor.y);
+          if (d > far) {
+            far = d;
+            at = p;
+          }
+        }
+      }
+      if (at) {
+        routes.push({ route, at, text: routeText(route, walkLabel) });
+      }
+    }
+    halos.push({
+      bubble,
+      ...classifyBubble(bubble, repeats),
+      path: parts.join(""),
+      labelAt,
+      members: nodeIds.length,
+      nodeIds,
+      whole: nodeIds.length >= WHOLE_FRACTION * graph.nodes.length,
+      routes
+    });
+  }
+  return halos;
+}
+function routeText(route, walkLabel) {
+  const names = [...new Set(route.walks.map(walkLabel))].sort();
+  const shown = names.slice(0, NAMED_WALKS).join(", ");
+  const more = names.length > NAMED_WALKS ? ` +${names.length - NAMED_WALKS}` : "";
+  return `${shown}${more} \xB7 ${formatBp(route.bp)}`;
+}
+
+export {
+  bubbleHalos
+};