@jbrowse/bandage-core 6.0.4 → 6.1.1

package/dist/chunks/{chunk-IO2PCPZI.js → chunk-7UIMNBJT.js}

@@ -11,10 +11,11 @@ import {
   parseGFA
 } from "./chunk-CDLPYR5O.js";
 import {
+  closableDeletions,
   routeNodes,
   takeRoutes,
   withDeletionRoutes
-} from "./chunk-MI35EUIE.js";
+} from "./chunk-STNG3Y5X.js";
 import {
   anchorGraph
 } from "./chunk-ST2IBUAN.js";
@@ -79,12 +80,14 @@ function engineRequest(graph, scaling, settings) {
 }
 function engineKey(graph, settings) {
   const anchored = graph.nodes.some(isBackbone);
-  return `${settings.quality}|${settings.linearLayout}|${settings.bubbleSpread}|${settings.spacing ?? 1}|${settings.componentSeparation ?? 1}|${anchored}|${graph.referencePath ?? ""}`;
+  return `${settings.quality}|${settings.linearLayout}|${settings.bubbleSpread}|${settings.spacing ?? 1}|${settings.componentSeparation ?? 1}|${settings.showDeletionEdges !== false}|${anchored}|${graph.referencePath ?? ""}`;
 }
 async function forceLayout(graph, settings, engine) {
   const spread = spreadFor(settings.bubbleSpread);
-  const deletions = deletionEdges(graph);
-  const routed = withDeletionRoutes(graph, deletions);
+  const found = deletionEdges(graph);
+  const dropped = settings.showDeletionEdges === false ? closableDeletions(graph, found) : /* @__PURE__ */ new Set();
+  const deletions = found.filter((d) => !dropped.has(d.edgeIndex));
+  const routed = withDeletionRoutes(graph, deletions, dropped);
   const merged = mergeRuns(routed.graph, routed.ids);
   const runs = {
     ...merged.graph,

package/dist/chunks/{chunk-FZCOVJAL.js → chunk-OSDI57GY.js}

@@ -24,10 +24,10 @@ import {
 } from "./chunk-3S3YVOJ7.js";
 import {
   version
-} from "./chunk-QFBZQJFK.js";
+} from "./chunk-XH43CLO2.js";
 import {
   axisScaleOf
-} from "./chunk-MQJUG2D2.js";
+} from "./chunk-XJWN753L.js";
 import {
   facetLifts,
   walkLift
@@ -43,7 +43,7 @@ import {
   FIT_PADDING,
   drawingBounds,
   fitTransform
-} from "./chunk-IO2PCPZI.js";
+} from "./chunk-7UIMNBJT.js";
 import {
   buildGeometry,
   computeReferenceRamp

package/dist/chunks/{chunk-MI35EUIE.js → chunk-STNG3Y5X.js}

@@ -1,13 +1,16 @@
 // src/layout/deletionRoutes.ts
 var ROUTE_ID = "\0deletion:";
 var ROUTE_FRACTION = 0.5;
-function withDeletionRoutes(graph, deletions) {
+function withDeletionRoutes(graph, deletions, dropped = /* @__PURE__ */ new Set()) {
   const routes = new Map(
     deletions.map((d) => [d.edgeIndex, `${ROUTE_ID}${d.edgeIndex}`])
   );
   const edges = [];
   graph.edges.forEach((edge, ei) => {
     const id = routes.get(ei);
+    if (dropped.has(ei)) {
+      return;
+    }
     if (id === void 0) {
       edges.push(edge);
     } else {
@@ -36,6 +39,35 @@ function withDeletionRoutes(graph, deletions) {
     ids: new Set(routes.values())
   };
 }
+function closableDeletions(graph, deletions) {
+  const parent = /* @__PURE__ */ new Map();
+  const root = (id) => {
+    let r = id;
+    while (parent.has(r)) {
+      r = parent.get(r);
+    }
+    if (r !== id) {
+      parent.set(id, r);
+    }
+    return r;
+  };
+  const join = (a, b) => {
+    const [ra, rb] = [root(a), root(b)];
+    if (ra !== rb) {
+      parent.set(ra, rb);
+    }
+    return ra !== rb;
+  };
+  const candidates = new Set(deletions.map((d) => d.edgeIndex));
+  graph.edges.forEach((e, ei) => {
+    if (!candidates.has(ei)) {
+      join(e.from, e.to);
+    }
+  });
+  return new Set(
+    deletions.filter((d) => !join(d.from, d.to)).map((d) => d.edgeIndex)
+  );
+}
 function routeNodes(graph, deletions, routes, drawnOf, opts) {
   const lengths = new Map(graph.nodes.map((n) => [n.id, n.length]));
   return deletions.map((d) => {
@@ -71,6 +103,7 @@ function takeRoutes(positions, routes) {
 
 export {
   withDeletionRoutes,
+  closableDeletions,
   routeNodes,
   takeRoutes
 };

package/dist/chunks/{chunk-QFBZQJFK.js → chunk-XH43CLO2.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "6.0.4";
+var version = "6.1.1";
 
 export {
   version

package/dist/chunks/{chunk-MQJUG2D2.js → chunk-XJWN753L.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-IO2PCPZI.js";
+} from "./chunk-7UIMNBJT.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {

package/dist/cli/figure.js

@@ -21,7 +21,7 @@ import {
 } from "../chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "../chunks/chunk-FZCOVJAL.js";
+} from "../chunks/chunk-OSDI57GY.js";
 import "../chunks/chunk-47DYCZOK.js";
 import "../chunks/chunk-V5BPIOLS.js";
 import {
@@ -32,21 +32,21 @@ import "../chunks/chunk-CH3DLBUT.js";
 import "../chunks/chunk-4BYTEJGW.js";
 import "../chunks/chunk-BUBZ32IC.js";
 import "../chunks/chunk-3S3YVOJ7.js";
-import "../chunks/chunk-QFBZQJFK.js";
-import "../chunks/chunk-MQJUG2D2.js";
+import "../chunks/chunk-XH43CLO2.js";
+import "../chunks/chunk-XJWN753L.js";
 import "../chunks/chunk-ZKGM7VLA.js";
 import "../chunks/chunk-X4VVPLI5.js";
 import "../chunks/chunk-GOY6REMT.js";
 import {
   forceLayout,
   loadGraph
-} from "../chunks/chunk-IO2PCPZI.js";
+} from "../chunks/chunk-7UIMNBJT.js";
 import "../chunks/chunk-PUG7LXDF.js";
 import "../chunks/chunk-IGVV37VI.js";
 import "../chunks/chunk-72N5DJHZ.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-CDLPYR5O.js";
-import "../chunks/chunk-MI35EUIE.js";
+import "../chunks/chunk-STNG3Y5X.js";
 import "../chunks/chunk-ZHCDYSA5.js";
 import "../chunks/chunk-RX5CSWJW.js";
 import "../chunks/chunk-UMNCCYBN.js";
@@ -241,7 +241,8 @@ async function renderSpec(spec, base) {
       linearLayout: false,
       bubbleSpread: spec.bubbleSpread ?? "auto",
       spacing: spec.spacing,
-      componentSeparation: spec.componentSeparation
+      componentSeparation: spec.componentSeparation,
+      showDeletionEdges: !!spec.showDeletionEdges
     },
     engine
   )).result;

package/dist/figure.js

@@ -1,6 +1,6 @@
 import {
   figureSvg
-} from "./chunks/chunk-FZCOVJAL.js";
+} from "./chunks/chunk-OSDI57GY.js";
 import "./chunks/chunk-47DYCZOK.js";
 import "./chunks/chunk-V5BPIOLS.js";
 import "./chunks/chunk-PJESIRDU.js";
@@ -8,18 +8,18 @@ import "./chunks/chunk-CH3DLBUT.js";
 import "./chunks/chunk-4BYTEJGW.js";
 import "./chunks/chunk-BUBZ32IC.js";
 import "./chunks/chunk-3S3YVOJ7.js";
-import "./chunks/chunk-QFBZQJFK.js";
-import "./chunks/chunk-MQJUG2D2.js";
+import "./chunks/chunk-XH43CLO2.js";
+import "./chunks/chunk-XJWN753L.js";
 import "./chunks/chunk-ZKGM7VLA.js";
 import "./chunks/chunk-X4VVPLI5.js";
 import "./chunks/chunk-GOY6REMT.js";
-import "./chunks/chunk-IO2PCPZI.js";
+import "./chunks/chunk-7UIMNBJT.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-72N5DJHZ.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-MI35EUIE.js";
+import "./chunks/chunk-STNG3Y5X.js";
 import "./chunks/chunk-ZHCDYSA5.js";
 import "./chunks/chunk-RX5CSWJW.js";
 import "./chunks/chunk-UMNCCYBN.js";

package/dist/index.js

@@ -80,7 +80,7 @@ import {
 } from "./chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "./chunks/chunk-FZCOVJAL.js";
+} from "./chunks/chunk-OSDI57GY.js";
 import {
   svgCanvas
 } from "./chunks/chunk-47DYCZOK.js";
@@ -133,7 +133,7 @@ import {
 } from "./chunks/chunk-3S3YVOJ7.js";
 import {
   version
-} from "./chunks/chunk-QFBZQJFK.js";
+} from "./chunks/chunk-XH43CLO2.js";
 import {
   axisScaleOf,
   contains,
@@ -141,7 +141,7 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-MQJUG2D2.js";
+} from "./chunks/chunk-XJWN753L.js";
 import {
   facetLifts,
   walkHighlight,
@@ -170,13 +170,13 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-IO2PCPZI.js";
+} from "./chunks/chunk-7UIMNBJT.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-72N5DJHZ.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-MI35EUIE.js";
+import "./chunks/chunk-STNG3Y5X.js";
 import {
   RAMP_GRADIENT_CSS,
   rampHue,

package/dist/layout/deletionRoutes.js

@@ -1,9 +1,11 @@
 import {
+  closableDeletions,
   routeNodes,
   takeRoutes,
   withDeletionRoutes
-} from "../chunks/chunk-MI35EUIE.js";
+} from "../chunks/chunk-STNG3Y5X.js";
 export {
+  closableDeletions,
   routeNodes,
   takeRoutes,
   withDeletionRoutes

package/dist/pipeline.js

@@ -9,13 +9,13 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-IO2PCPZI.js";
+} from "./chunks/chunk-7UIMNBJT.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-72N5DJHZ.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-MI35EUIE.js";
+import "./chunks/chunk-STNG3Y5X.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-TAMCZHLW.js";

package/dist/types/layout/deletionRoutes.d.ts

@@ -2,7 +2,7 @@ import type { BandageScaleOpts } from './drawnScale.js';
 import type { DeletionEdge } from '../deletionEdges.js';
 import type { Graph, GraphEdge, GraphNode, NodeSegment } from '../types.js';
 export type DeletionRoutes = Record<number, NodeSegment[]>;
-export declare function withDeletionRoutes(graph: Graph, deletions: DeletionEdge[]): {
+export declare function withDeletionRoutes(graph: Graph, deletions: DeletionEdge[], dropped?: Set<number>): {
     graph: {
         nodes: {
             id: string;
@@ -22,6 +22,7 @@ export declare function withDeletionRoutes(graph: Graph, deletions: DeletionEdge
     routes: Map<number, string>;
     ids: Set<string>;
 };
+export declare function closableDeletions(graph: Graph, deletions: DeletionEdge[]): Set<number>;
 export declare function routeNodes(graph: Graph, deletions: DeletionEdge[], routes: Map<number, string>, drawnOf: (bp: number) => number, opts: BandageScaleOpts): GraphNode[];
 export declare function takeRoutes(positions: Record<string, NodeSegment[]>, routes: Map<number, string>): {
     nodePositions: {

package/dist/types/pipeline.d.ts

@@ -29,6 +29,7 @@ export interface EngineSettings {
     bubbleSpread: BubbleSpread;
     spacing?: number;
     componentSeparation?: number;
+    showDeletionEdges?: boolean;
 }
 export declare function engineRequest(graph: Graph, scaling: LayoutScaling, settings: EngineSettings): EngineRequest;
 export declare function engineKey(graph: Graph, settings: EngineSettings): string;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "6.0.4";
+export declare const version = "6.1.1";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-QFBZQJFK.js";
+} from "./chunks/chunk-XH43CLO2.js";
 export {
   version
 };

package/dist/viewport.js

@@ -5,14 +5,14 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-MQJUG2D2.js";
-import "./chunks/chunk-IO2PCPZI.js";
+} from "./chunks/chunk-XJWN753L.js";
+import "./chunks/chunk-7UIMNBJT.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-72N5DJHZ.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-MI35EUIE.js";
+import "./chunks/chunk-STNG3Y5X.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-TAMCZHLW.js";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "6.0.4",
+  "version": "6.1.1",
   "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": {