@jbrowse/bandage-core 9.6.0 → 9.7.0

package/dist/chunks/chunk-5QOMIEHX.js

@@ -0,0 +1,81 @@
+import {
+  pathSteps
+} from "./chunk-6N7H22SS.js";
+import {
+  pathOrigin
+} from "./chunk-ST2IBUAN.js";
+
+// src/tubeMap/bundle.ts
+function bundleRoutes(graph, groupOf = () => "", merge = true) {
+  const paths = graph.paths ?? [];
+  const steps = pathSteps(graph);
+  const routes = /* @__PURE__ */ new Map();
+  paths.forEach((path, i) => {
+    const walk = pathOrigin(path.name).name;
+    const route = steps[i].map((s) => `${s.node.id}${s.strand}`).join(",");
+    const pieces = routes.get(walk);
+    if (pieces) {
+      pieces.push(route);
+    } else {
+      routes.set(walk, [route]);
+    }
+  });
+  const routeRank = /* @__PURE__ */ new Map();
+  const bundles = /* @__PURE__ */ new Map();
+  for (const [walk, pieces] of routes) {
+    const route = walk === graph.referencePath ? `\0${walk}` : pieces.join("|");
+    const group = groupOf(walk);
+    const rank = routeRank.get(route) ?? routeRank.size;
+    routeRank.set(route, rank);
+    const key = `${route}	${group}`;
+    const bundle = bundles.get(key);
+    if (bundle) {
+      bundle.walks.push(walk);
+    } else {
+      bundles.set(key, { rank, group, walks: [walk] });
+    }
+  }
+  if (merge && bundles.size === routes.size) {
+    return graph;
+  }
+  const ordered = [...bundles.values()].sort(
+    (a, b) => a.rank - b.rank || a.group.localeCompare(b.group)
+  );
+  const recordsOf = /* @__PURE__ */ new Map();
+  for (const path of paths) {
+    const walk = pathOrigin(path.name).name;
+    const records = recordsOf.get(walk);
+    if (records) {
+      records.push(path);
+    } else {
+      recordsOf.set(walk, [path]);
+    }
+  }
+  if (!merge) {
+    return {
+      ...graph,
+      paths: ordered.flatMap(
+        ({ walks }) => walks.flatMap((walk) => recordsOf.get(walk))
+      )
+    };
+  }
+  const kept = ordered.flatMap(
+    ({ walks }) => recordsOf.get(walks[0]).map((path) => walks.length > 1 ? { ...path, members: walks } : path)
+  );
+  const keptWalks = new Set(ordered.map((b) => b.walks[0]));
+  return {
+    ...graph,
+    paths: kept,
+    anchorPaths: graph.anchorPaths?.filter((p) => keptWalks.has(p.name)),
+    pathVisits: graph.pathVisits ? new Map(
+      [...graph.pathVisits].map(([segment, visits]) => [
+        segment,
+        visits.filter((v) => keptWalks.has(v.path))
+      ])
+    ) : void 0
+  };
+}
+
+export {
+  bundleRoutes
+};

package/dist/chunks/{chunk-INJ2UVOT.js → chunk-6N7H22SS.js}

@@ -59,7 +59,8 @@ function tubeMapTracks(graph) {
         name: path.name,
         sequence,
         sourceTrackID: 0,
-        type: "haplotype"
+        type: "haplotype",
+        ...path.members ? { freq: path.members.length } : {}
       }
     ] : [];
   });
@@ -218,9 +219,12 @@ function runTubeMap(graph) {
   const reads = graph.reads ? tubeMapReads(graph, graph.reads, paths.length) : [];
   const tubeColor = reads.length > 0 ? pathGreyCssColor : pathCssColor;
   const pathColors = paths.map((_, i) => tubeColor(i, paths.length));
+  const bundled = paths.some((p) => p.members);
+  const walks = paths.reduce((n, p) => n + (p.members?.length ?? 1), 0);
   const layout = layoutTubeMap(tubeMapNodes(graph), tracks, reads, {
     nodeWidthOption: "compressed",
-    trackWidth: tubeWidth(tracks.length)
+    trackWidth: tubeWidth(bundled ? walks : tracks.length),
+    ...bundled ? { freqWidth: "linear" } : {}
   });
   if (!layout) {
     return void 0;

package/dist/chunks/{chunk-WVPC3JVY.js → chunk-7FARTP3U.js}

@@ -45,7 +45,7 @@ import {
 } from "./chunk-BR25DGIJ.js";
 import {
   version
-} from "./chunk-YSQMOOHY.js";
+} from "./chunk-ESRCSSS2.js";
 import {
   walkRowLabels,
   walkRowsExtent

package/dist/chunks/{chunk-YSQMOOHY.js → chunk-ESRCSSS2.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "9.6.0";
+var version = "9.7.0";
 
 export {
   version

package/dist/chunks/{chunk-M7SRZJ32.js → chunk-Z7UWHVOM.js}

@@ -6,7 +6,7 @@ import {
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-INJ2UVOT.js";
+} from "./chunk-6N7H22SS.js";
 import {
   anchoredLayout
 } from "./chunk-L3O7AWLI.js";

package/dist/cli/figure.js

@@ -14,9 +14,9 @@ import "../chunks/chunk-LYJ4US66.js";
 import {
   LAYOUT_MODES,
   layoutModeByValue
-} from "../chunks/chunk-M7SRZJ32.js";
+} from "../chunks/chunk-Z7UWHVOM.js";
 import "../chunks/chunk-LOEA5IHZ.js";
-import "../chunks/chunk-INJ2UVOT.js";
+import "../chunks/chunk-6N7H22SS.js";
 import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-L3O7AWLI.js";
 import "../chunks/chunk-TZFWUT2C.js";
@@ -35,7 +35,7 @@ import "../chunks/chunk-LTUWJKHD.js";
 import "../chunks/chunk-WSIFAZU7.js";
 import {
   figureSvg
-} from "../chunks/chunk-WVPC3JVY.js";
+} from "../chunks/chunk-7FARTP3U.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-YSQMOOHY.js";
+import "../chunks/chunk-ESRCSSS2.js";
 import "../chunks/chunk-3C5UXR2U.js";
 import {
   filterSamples,

package/dist/figure.js

@@ -1,6 +1,6 @@
 import {
   figureSvg
-} from "./chunks/chunk-WVPC3JVY.js";
+} from "./chunks/chunk-7FARTP3U.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-YSQMOOHY.js";
+import "./chunks/chunk-ESRCSSS2.js";
 import "./chunks/chunk-3C5UXR2U.js";
 import "./chunks/chunk-MAUEPAMG.js";
 import "./chunks/chunk-7GBL7SJY.js";

package/dist/index.js

@@ -1,15 +1,28 @@
 import {
   wheelZoomFactor
 } from "./chunks/chunk-TDQLINVI.js";
+import {
+  drawTubeMapGenes,
+  tubeMapGenes
+} from "./chunks/chunk-WEDZ76AK.js";
 import {
   tubeMapNodeColors
 } from "./chunks/chunk-A4MYLGKG.js";
+import {
+  bundleRoutes
+} from "./chunks/chunk-5QOMIEHX.js";
 import {
   connectorAt,
   drawLitConnector,
   drawTubeMapConnectors,
   tubeMapConnectors
 } from "./chunks/chunk-2ZT7ZF7A.js";
+import {
+  drawTubeMapRuler,
+  referenceBoxes,
+  rulerBoxes,
+  tubeX
+} from "./chunks/chunk-BPRXQ2SS.js";
 import {
   drawTubeMap,
   drawTubeMapHighlight,
@@ -26,16 +39,6 @@ import {
   referenceKnots,
   warpX
 } from "./chunks/chunk-KQFOCDFY.js";
-import {
-  drawTubeMapGenes,
-  tubeMapGenes
-} from "./chunks/chunk-WEDZ76AK.js";
-import {
-  drawTubeMapRuler,
-  referenceBoxes,
-  rulerBoxes,
-  tubeX
-} from "./chunks/chunk-BPRXQ2SS.js";
 import {
   createForceLayoutCache
 } from "./chunks/chunk-BV64PQ2C.js";
@@ -84,9 +87,9 @@ import {
   LAYOUT_MODES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-M7SRZJ32.js";
+} from "./chunks/chunk-Z7UWHVOM.js";
 import "./chunks/chunk-LOEA5IHZ.js";
-import "./chunks/chunk-INJ2UVOT.js";
+import "./chunks/chunk-6N7H22SS.js";
 import "./chunks/chunk-CWFNEKST.js";
 import "./chunks/chunk-L3O7AWLI.js";
 import "./chunks/chunk-TZFWUT2C.js";
@@ -119,7 +122,7 @@ import {
 } from "./chunks/chunk-AZFVORTC.js";
 import {
   figureSvg
-} from "./chunks/chunk-WVPC3JVY.js";
+} from "./chunks/chunk-7FARTP3U.js";
 import {
   WALK_STRIP_CEILING_PX,
   cutsWholeWalks,
@@ -219,7 +222,7 @@ import {
 import "./chunks/chunk-G2FD7S3C.js";
 import {
   version
-} from "./chunks/chunk-YSQMOOHY.js";
+} from "./chunks/chunk-ESRCSSS2.js";
 import {
   walkRowLabels,
   walkRowsExtent
@@ -387,6 +390,7 @@ export {
   bubbleSubgraph,
   bubblesFromGraph,
   buildGeometry,
+  bundleRoutes,
   callTickInk,
   clampZoom,
   classifyBubble,

package/dist/layout/tubeMapLayout.js

@@ -8,7 +8,7 @@ import {
   tubeMapReferenceLayout,
   tubeMapTracks,
   tubeWidth
-} from "../chunks/chunk-INJ2UVOT.js";
+} from "../chunks/chunk-6N7H22SS.js";
 import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
 import "../chunks/chunk-7GBL7SJY.js";

package/dist/layoutModes.js

@@ -4,9 +4,9 @@ import {
   LAYOUT_MODE_VALUES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-M7SRZJ32.js";
+} from "./chunks/chunk-Z7UWHVOM.js";
 import "./chunks/chunk-LOEA5IHZ.js";
-import "./chunks/chunk-INJ2UVOT.js";
+import "./chunks/chunk-6N7H22SS.js";
 import "./chunks/chunk-CWFNEKST.js";
 import "./chunks/chunk-L3O7AWLI.js";
 import "./chunks/chunk-TZFWUT2C.js";

package/dist/tubeMap/bundle.js

@@ -0,0 +1,19 @@
+import {
+  bundleRoutes
+} from "../chunks/chunk-5QOMIEHX.js";
+import "../chunks/chunk-6N7H22SS.js";
+import "../chunks/chunk-CWFNEKST.js";
+import "../chunks/chunk-C44YRP5F.js";
+import "../chunks/chunk-7GBL7SJY.js";
+import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-ST2IBUAN.js";
+import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-TAMCZHLW.js";
+import "../chunks/chunk-N6FECAXP.js";
+import "../chunks/chunk-2CVHXFK7.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  bundleRoutes
+};

package/dist/tubeMap/coarsen.js

@@ -1,6 +1,6 @@
 import {
   pathSteps
-} from "../chunks/chunk-INJ2UVOT.js";
+} from "../chunks/chunk-6N7H22SS.js";
 import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
 import "../chunks/chunk-7GBL7SJY.js";

package/dist/types/index.d.ts

@@ -43,6 +43,7 @@ export { drawTubeMapGenes, tubeMapGenes } from './tubeMap/genes.js';
 export type { TubeMapGene } from './tubeMap/genes.js';
 export { connectorAt, drawLitConnector, drawTubeMapConnectors, tubeMapConnectors, } from './tubeMap/connectors.js';
 export type { Connector } from './tubeMap/connectors.js';
+export { bundleRoutes } from './tubeMap/bundle.js';
 export type { TubeMapColumn, TubeMapDrawing } from './layout/tubeMapLayout.js';
 export { deletionDrawing, deletionEdges } from './deletionEdges.js';
 export type { DeletionDrawing, DeletionEdge } from './deletionEdges.js';

package/dist/types/tubeMap/bundle.d.ts

@@ -0,0 +1,2 @@
+import type { Graph } from '../types.js';
+export declare function bundleRoutes(graph: Graph, groupOf?: (walk: string) => string, merge?: boolean): Graph;

package/dist/types/types.d.ts

@@ -23,6 +23,7 @@ export interface GraphPath {
     sample?: string;
     haplotype?: number;
     contig?: string;
+    members?: string[];
 }
 export interface PathOrigin {
     name: string;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "9.6.0";
+export declare const version = "9.7.0";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-YSQMOOHY.js";
+} from "./chunks/chunk-ESRCSSS2.js";
 export {
   version
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "9.6.0",
+  "version": "9.7.0",
   "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": {
@@ -37,7 +37,7 @@
   "dependencies": {
     "@gmod/gbz-base": "^7.0.0",
     "@gmod/tabix": "^3.9.1",
-    "@jbrowse/tubemap-core": "^0.2.1"
+    "@jbrowse/tubemap-core": "^0.2.2"
   },
   "devDependencies": {
     "@eslint/js": "^10.0.1",