@jbrowse/bandage-core 9.4.0 → 9.6.0

package/dist/bubbles/bubbleHalos.js

@@ -3,7 +3,7 @@ import {
   WHOLE_FRACTION,
   bubbleHalos,
   coversGraph
-} from "../chunks/chunk-REM73HCU.js";
+} from "../chunks/chunk-EHUBJDDB.js";
 import "../chunks/chunk-XKWD2RY3.js";
 import "../chunks/chunk-FX4RDMDN.js";
 import "../chunks/chunk-2CVHXFK7.js";

package/dist/bubbles/bubblesFromGraph.js

@@ -2,7 +2,7 @@ import {
   bubblesFromGraph,
   walkIndexOf,
   walkRoutes
-} from "../chunks/chunk-GOZYKNQ2.js";
+} from "../chunks/chunk-CLOP7UVD.js";
 import "../chunks/chunk-FX4RDMDN.js";
 import "../chunks/chunk-HNQPEMYE.js";
 import "../chunks/chunk-CPMHA4W5.js";

package/dist/bubbles/superbubbles.js

@@ -1,11 +1,11 @@
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "../chunks/chunk-TF7H5LQS.js";
+} from "../chunks/chunk-C55SC5AJ.js";
 import "../chunks/chunk-VHW7FDHU.js";
-import "../chunks/chunk-REM73HCU.js";
+import "../chunks/chunk-EHUBJDDB.js";
 import "../chunks/chunk-XKWD2RY3.js";
-import "../chunks/chunk-GOZYKNQ2.js";
+import "../chunks/chunk-CLOP7UVD.js";
 import "../chunks/chunk-FX4RDMDN.js";
 import "../chunks/chunk-HNQPEMYE.js";
 import "../chunks/chunk-ST2IBUAN.js";

package/dist/chunks/{chunk-TF7H5LQS.js → chunk-C55SC5AJ.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-VHW7FDHU.js";
 import {
   coversGraph
-} from "./chunk-REM73HCU.js";
+} from "./chunk-EHUBJDDB.js";
 import {
   bubbleSegmentIds
 } from "./chunk-XKWD2RY3.js";
@@ -11,7 +11,7 @@ import {
   bubblesFromGraph,
   walkIndexOf,
   walkRoutes
-} from "./chunk-GOZYKNQ2.js";
+} from "./chunk-CLOP7UVD.js";
 import {
   SATURATED_PATH_COUNT
 } from "./chunk-FX4RDMDN.js";
@@ -227,7 +227,10 @@ function superbubblesFromGraph(graph, span) {
     (f, i) => !covers[i] && placed(f) && !nested(f, i)
   );
   const byId = new Map(nodes.map((n) => [n.id, n]));
-  const walkIndex = walkIndexOf(graph);
+  const walkIndex = walkIndexOf(
+    graph,
+    outermost.flatMap((f) => [nodes[f.source >> 1].id, nodes[f.sink >> 1].id])
+  );
   return outermost.map((f) => {
     const source = nodes[f.source >> 1];
     const sink = nodes[f.sink >> 1];

package/dist/chunks/{chunk-GOZYKNQ2.js → chunk-CLOP7UVD.js}

@@ -38,7 +38,10 @@ function bubblesFromGraph(graph) {
   const backbone = graph.nodes.filter(isBackbone).sort((a, b) => a.stable.start - b.stable.start);
   const ends = /* @__PURE__ */ new Set([backbone[0].id, backbone.at(-1).id]);
   const boundaries = backbone.map((node) => [node, indexOf.get(node.id)]).filter(([node, i]) => ends.has(node.id) || reach[i] === 0).sort(([a, ia], [b, ib]) => ia - ib || a.stable.start - b.stable.start);
-  const walkIndex = walkIndexOf(graph);
+  const walkIndex = walkIndexOf(
+    graph,
+    boundaries.map(([node]) => node.id)
+  );
   const bubbles = [];
   for (let i = 0; i + 1 < boundaries.length; i++) {
     const [start, i0] = boundaries[i];
@@ -104,47 +107,63 @@ function bubblesFromGraph(graph) {
   }
   return bubbles;
 }
-function walkIndexOf(graph) {
-  return graph.paths?.map((p) => {
-    const at = /* @__PURE__ */ new Map();
-    p.nodeIds.forEach((id, i) => {
-      if (!at.has(id)) {
-        at.set(id, i);
+function walkIndexOf(graph, ids) {
+  const paths = graph.paths;
+  if (!paths) {
+    return void 0;
+  }
+  const index = /* @__PURE__ */ new Map();
+  for (const id of ids) {
+    index.set(id, new Int32Array(paths.length).fill(-1));
+  }
+  paths.forEach((p, k) => {
+    const steps = p.nodeIds;
+    for (let i = 0; i < steps.length; i++) {
+      const at = index.get(steps[i]);
+      if (at?.[k] === -1) {
+        at[k] = i;
       }
-    });
-    return at;
+    }
   });
+  return index;
 }
 function walkRoutes(graph, byId, walkIndex, startId, endId) {
-  const seen = /* @__PURE__ */ new Map();
+  const routes = [];
   let min = Infinity;
   let max = -Infinity;
   let left = 0;
+  const at0 = walkIndex.get(startId);
+  const at1 = walkIndex.get(endId);
   graph.paths.forEach((p, k) => {
-    const i0 = walkIndex[k].get(startId);
-    const i1 = walkIndex[k].get(endId);
-    if (i0 === void 0 || i1 === void 0) {
-      if (i0 !== void 0 || i1 !== void 0) {
+    const i0 = at0[k];
+    const i1 = at1[k];
+    if (i0 < 0 || i1 < 0) {
+      if (i0 >= 0 || i1 >= 0) {
         left++;
       }
       return;
     }
-    const steps = p.nodeIds.slice(Math.min(i0, i1) + 1, Math.max(i0, i1));
-    if (i1 < i0) {
-      steps.reverse();
-    }
-    let bp = 0;
-    for (const id of steps) {
-      bp += byId.get(id)?.length ?? 0;
+    const ids = p.nodeIds;
+    const lo = Math.min(i0, i1) + 1;
+    const hi = Math.max(i0, i1);
+    const step = i1 < i0 ? (j) => ids[hi - 1 - j] : (j) => ids[lo + j];
+    let route = routes.find(
+      (r) => r.steps.length === hi - lo && r.steps.every((id, j) => id === step(j))
+    );
+    if (!route) {
+      const steps = Array.from({ length: hi - lo }, (_, j) => step(j));
+      let bp = 0;
+      for (const id of steps) {
+        bp += byId.get(id)?.length ?? 0;
+      }
+      route = { steps, bp, walks: [] };
+      routes.push(route);
     }
-    const key = steps.join(",");
-    const route = seen.get(key) ?? { steps, bp, walks: [] };
     route.walks.push(p.name);
-    seen.set(key, route);
-    min = Math.min(min, bp);
-    max = Math.max(max, bp);
+    min = Math.min(min, route.bp);
+    max = Math.max(max, route.bp);
   });
-  return seen.size || left ? { min, max, n: seen.size, left, routes: [...seen.values()] } : void 0;
+  return routes.length || left ? { min, max, n: routes.length, left, routes } : void 0;
 }
 
 export {

package/dist/chunks/{chunk-REM73HCU.js → chunk-EHUBJDDB.js}

@@ -55,27 +55,11 @@ function bubbleHalos(graph, bubbles, positions, walkLabel = (name) => name, repe
       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)));
+    for (const [route, own] of ownStretches(bubble)) {
       let at;
       let far = -1;
-      for (const id of route.steps) {
-        if (sharing.get(id) !== rarest) {
-          continue;
-        }
+      for (const id of own) {
         for (const p of positions[id] ?? []) {
           const d = Math.hypot(p.x - anchor.x, p.y - anchor.y);
           if (d > far) {
@@ -105,6 +89,37 @@ function bubbleHalos(graph, bubbles, positions, walkLabel = (name) => name, repe
   }
   return halos;
 }
+var stretches = /* @__PURE__ */ new WeakMap();
+function ownStretches(bubble) {
+  const cached = stretches.get(bubble);
+  if (cached) {
+    return cached;
+  }
+  const chipped = bubble.longestAlleleLength < MIN_CHIPPED_BP ? [] : bubble.routes ?? [];
+  const sharing = /* @__PURE__ */ new Map();
+  chipped.forEach((route, r) => {
+    const counted = /* @__PURE__ */ new Map();
+    for (const id of route.steps) {
+      if (counted.get(id) !== r) {
+        counted.set(id, r);
+        sharing.set(id, (sharing.get(id) ?? 0) + 1);
+      }
+    }
+  });
+  const own = /* @__PURE__ */ new Map();
+  for (const route of chipped) {
+    let rarest = Infinity;
+    for (const id of route.steps) {
+      rarest = Math.min(rarest, sharing.get(id));
+    }
+    const steps = new Set(route.steps.filter((id) => sharing.get(id) === rarest));
+    if (steps.size > 0) {
+      own.set(route, [...steps]);
+    }
+  }
+  stretches.set(bubble, own);
+  return own;
+}
 function routeText(route, walkLabel) {
   const names = [...new Set(route.walks.map(walkLabel))].sort();
   const shown = names.slice(0, NAMED_WALKS).join(", ");

package/dist/chunks/{chunk-UNOE2NDN.js → chunk-Q6FRNVDU.js}

@@ -18,6 +18,7 @@ var UNTANGLE_LINKS = 3;
 var UNTANGLE_PUSH = 0.3;
 var SMOOTH_PASSES = 2;
 var MAX_HOPS = 200;
+var REFERENCE_HOPS = 20;
 var EPS = 0.1;
 var WARM = 0.5;
 function flipped(strand, name) {
@@ -238,7 +239,8 @@ function stressLayout(request, opts = {}) {
     let idx = c.indexOf[i];
     let dir = rand() < 0.5 ? -1 : 1;
     let remaining = length;
-    for (let hops = 0; hops < MAX_HOPS; hops++) {
+    const maxHops = refIdx[comp[i]].length >= 2 ? REFERENCE_HOPS : MAX_HOPS;
+    for (let hops = 0; hops < maxHops; hops++) {
       const points = count[chain];
       const step = per[chain];
       const toEnd = (dir > 0 ? points - 1 - idx : idx) * step;

package/dist/chunks/{chunk-6EJIU6IA.js → chunk-VK6XMP6B.js}

@@ -1,6 +1,6 @@
 import {
   stressLayout
-} from "./chunk-UNOE2NDN.js";
+} from "./chunk-Q6FRNVDU.js";
 import {
   loadBandage
 } from "./chunk-7XHHVYG7.js";
@@ -14,7 +14,7 @@ var LAYOUT_ENGINES = [
   },
   {
     value: "stress",
-    label: "Stress (experimental)",
+    label: "Stress",
     description: "Stress layout by stochastic gradient descent in plain JS: distances along the graph become distances on the page, so the reference reads straight and a repeat loop reads as a ring."
   }
 ];

package/dist/chunks/{chunk-4DEOECM3.js → chunk-WVPC3JVY.js}

@@ -45,7 +45,7 @@ import {
 } from "./chunk-BR25DGIJ.js";
 import {
   version
-} from "./chunk-BIGORSXS.js";
+} from "./chunk-YSQMOOHY.js";
 import {
   walkRowLabels,
   walkRowsExtent

package/dist/chunks/{chunk-BIGORSXS.js → chunk-YSQMOOHY.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "9.4.0";
+var version = "9.6.0";
 
 export {
   version

package/dist/cli/figure.js

@@ -8,8 +8,8 @@ import {
   LAYOUT_ENGINE_VALUES,
   isLayoutEngineKind,
   layoutEngine
-} from "../chunks/chunk-6EJIU6IA.js";
-import "../chunks/chunk-UNOE2NDN.js";
+} from "../chunks/chunk-VK6XMP6B.js";
+import "../chunks/chunk-Q6FRNVDU.js";
 import "../chunks/chunk-LYJ4US66.js";
 import {
   LAYOUT_MODES,
@@ -35,7 +35,7 @@ import "../chunks/chunk-LTUWJKHD.js";
 import "../chunks/chunk-WSIFAZU7.js";
 import {
   figureSvg
-} from "../chunks/chunk-4DEOECM3.js";
+} from "../chunks/chunk-WVPC3JVY.js";
 import "../chunks/chunk-UD5FOCI2.js";
 import "../chunks/chunk-WBCOREDZ.js";
 import "../chunks/chunk-4BYTEJGW.js";
@@ -54,7 +54,7 @@ import "../chunks/chunk-2LQ5BWT7.js";
 import "../chunks/chunk-OXTR3BVF.js";
 import "../chunks/chunk-BR25DGIJ.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-BIGORSXS.js";
+import "../chunks/chunk-YSQMOOHY.js";
 import "../chunks/chunk-3C5UXR2U.js";
 import {
   filterSamples,

package/dist/figure.js

@@ -1,6 +1,6 @@
 import {
   figureSvg
-} from "./chunks/chunk-4DEOECM3.js";
+} from "./chunks/chunk-WVPC3JVY.js";
 import "./chunks/chunk-UD5FOCI2.js";
 import "./chunks/chunk-WBCOREDZ.js";
 import "./chunks/chunk-4BYTEJGW.js";
@@ -16,7 +16,7 @@ import "./chunks/chunk-2LQ5BWT7.js";
 import "./chunks/chunk-OXTR3BVF.js";
 import "./chunks/chunk-BR25DGIJ.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-BIGORSXS.js";
+import "./chunks/chunk-YSQMOOHY.js";
 import "./chunks/chunk-3C5UXR2U.js";
 import "./chunks/chunk-MAUEPAMG.js";
 import "./chunks/chunk-7GBL7SJY.js";

package/dist/index.js

@@ -42,7 +42,7 @@ import {
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "./chunks/chunk-TF7H5LQS.js";
+} from "./chunks/chunk-C55SC5AJ.js";
 import {
   bubbleSubgraph
 } from "./chunks/chunk-VHW7FDHU.js";
@@ -54,7 +54,7 @@ import {
 } from "./chunks/chunk-BXEPA4KS.js";
 import {
   bubbleHalos
-} from "./chunks/chunk-REM73HCU.js";
+} from "./chunks/chunk-EHUBJDDB.js";
 import {
   BUBBLE_KIND_COLORS,
   BUBBLE_KIND_NAMES,
@@ -63,7 +63,7 @@ import {
 } from "./chunks/chunk-XKWD2RY3.js";
 import {
   bubblesFromGraph
-} from "./chunks/chunk-GOZYKNQ2.js";
+} from "./chunks/chunk-CLOP7UVD.js";
 import "./chunks/chunk-FX4RDMDN.js";
 import {
   REFERENCE_STRIP_ZONE_PX,
@@ -74,10 +74,10 @@ import {
 import {
   LAYOUT_ENGINES,
   layoutEngine
-} from "./chunks/chunk-6EJIU6IA.js";
+} from "./chunks/chunk-VK6XMP6B.js";
 import {
   stressLayout
-} from "./chunks/chunk-UNOE2NDN.js";
+} from "./chunks/chunk-Q6FRNVDU.js";
 import "./chunks/chunk-LYJ4US66.js";
 import {
   FORCE_LAYOUT_LABEL,
@@ -119,7 +119,7 @@ import {
 } from "./chunks/chunk-AZFVORTC.js";
 import {
   figureSvg
-} from "./chunks/chunk-4DEOECM3.js";
+} from "./chunks/chunk-WVPC3JVY.js";
 import {
   WALK_STRIP_CEILING_PX,
   cutsWholeWalks,
@@ -219,7 +219,7 @@ import {
 import "./chunks/chunk-G2FD7S3C.js";
 import {
   version
-} from "./chunks/chunk-BIGORSXS.js";
+} from "./chunks/chunk-YSQMOOHY.js";
 import {
   walkRowLabels,
   walkRowsExtent

package/dist/layout/stressEngine.js

@@ -1,7 +1,7 @@
 import {
   chains,
   stressLayout
-} from "../chunks/chunk-UNOE2NDN.js";
+} from "../chunks/chunk-Q6FRNVDU.js";
 import "../chunks/chunk-LYJ4US66.js";
 import "../chunks/chunk-JVLURPFW.js";
 import "../chunks/chunk-FYQWPEEY.js";

package/dist/layoutEngines.js

@@ -3,8 +3,8 @@ import {
   LAYOUT_ENGINE_VALUES,
   isLayoutEngineKind,
   layoutEngine
-} from "./chunks/chunk-6EJIU6IA.js";
-import "./chunks/chunk-UNOE2NDN.js";
+} from "./chunks/chunk-VK6XMP6B.js";
+import "./chunks/chunk-Q6FRNVDU.js";
 import "./chunks/chunk-LYJ4US66.js";
 import "./chunks/chunk-7XHHVYG7.js";
 import "./chunks/chunk-JVLURPFW.js";

package/dist/types/bubbles/bubblesFromGraph.d.ts

@@ -6,8 +6,9 @@ export interface Routes {
     n: number;
 }
 export declare function bubblesFromGraph(graph: Graph): MinigraphBubble[];
-export declare function walkIndexOf(graph: Graph): Map<string, number>[] | undefined;
-export declare function walkRoutes(graph: Graph, byId: Map<string, GraphNode>, walkIndex: Map<string, number>[], startId: string, endId: string): (Routes & {
+export type WalkIndex = Map<string, Int32Array>;
+export declare function walkIndexOf(graph: Graph, ids: Iterable<string>): WalkIndex | undefined;
+export declare function walkRoutes(graph: Graph, byId: Map<string, GraphNode>, walkIndex: WalkIndex, startId: string, endId: string): (Routes & {
     left: number;
     routes: BubbleRoute[];
 }) | undefined;

package/dist/types/layoutEngines.d.ts

@@ -5,7 +5,7 @@ export declare const LAYOUT_ENGINES: readonly [{
     readonly description: "Bandage's force-directed layout: OGDF's fast multipole multilevel method, compiled to wasm.";
 }, {
     readonly value: "stress";
-    readonly label: "Stress (experimental)";
+    readonly label: "Stress";
     readonly description: "Stress layout by stochastic gradient descent in plain JS: distances along the graph become distances on the page, so the reference reads straight and a repeat loop reads as a ring.";
 }];
 export type LayoutEngineKind = (typeof LAYOUT_ENGINES)[number]['value'];

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "9.4.0";
+export declare const version = "9.6.0";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-BIGORSXS.js";
+} from "./chunks/chunk-YSQMOOHY.js";
 export {
   version
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "9.4.0",
+  "version": "9.6.0",
   "description": "Pangenome graph layout and drawing with no host: GFA in, the Bandage force-directed engine and reference-anchored layouts, a Canvas2D renderer, hit testing and labels out",
   "license": "GPL-3.0-or-later",
   "repository": {