@jbrowse/bandage-core 9.2.0 → 9.4.0

package/dist/bubbles/bubbleHalos.js

@@ -1,14 +1,16 @@
 import {
+  SMALL_VARIANT_BP,
   WHOLE_FRACTION,
   bubbleHalos,
   coversGraph
-} from "../chunks/chunk-2AWUWGAD.js";
+} from "../chunks/chunk-REM73HCU.js";
 import "../chunks/chunk-XKWD2RY3.js";
 import "../chunks/chunk-FX4RDMDN.js";
 import "../chunks/chunk-2CVHXFK7.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {
+  SMALL_VARIANT_BP,
   WHOLE_FRACTION,
   bubbleHalos,
   coversGraph

package/dist/bubbles/superbubbles.js

@@ -1,10 +1,9 @@
 import {
-  MAX_SUPERBUBBLES,
   graphBubbles,
   superbubblesFromGraph
-} from "../chunks/chunk-ZDJDM77V.js";
+} from "../chunks/chunk-TF7H5LQS.js";
 import "../chunks/chunk-VHW7FDHU.js";
-import "../chunks/chunk-2AWUWGAD.js";
+import "../chunks/chunk-REM73HCU.js";
 import "../chunks/chunk-XKWD2RY3.js";
 import "../chunks/chunk-GOZYKNQ2.js";
 import "../chunks/chunk-FX4RDMDN.js";
@@ -15,7 +14,6 @@ import "../chunks/chunk-2CVHXFK7.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {
-  MAX_SUPERBUBBLES,
   graphBubbles,
   superbubblesFromGraph
 };

package/dist/chunks/{chunk-HOOVOF2Y.js → chunk-4DEOECM3.js}

@@ -45,7 +45,7 @@ import {
 } from "./chunk-BR25DGIJ.js";
 import {
   version
-} from "./chunk-FM6XRXPX.js";
+} from "./chunk-BIGORSXS.js";
 import {
   walkRowLabels,
   walkRowsExtent
@@ -62,7 +62,7 @@ import {
 } from "./chunk-RAKOB6IV.js";
 import {
   geneLabelCandidates
-} from "./chunk-GJMC3PGM.js";
+} from "./chunk-DRG4236Y.js";
 import {
   nodesUnderBox
 } from "./chunk-FP4H7SFT.js";

package/dist/chunks/{chunk-FM6XRXPX.js → chunk-BIGORSXS.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "9.2.0";
+var version = "9.4.0";
 
 export {
   version

package/dist/chunks/{chunk-GJMC3PGM.js → chunk-DRG4236Y.js}

@@ -21,6 +21,7 @@ var LEGEND_INSET_PX = 6;
 var ROUTE_STACK = 8;
 var GENE_PIN_DROP_PX = 18;
 var GENE_STACK = 2;
+var BUBBLE_STACK = 3;
 var TOPMOST_BASELINE = LABEL_PX + LABEL_PAD;
 function geneCoverageNote(pin) {
   const length = pin.gene.end - pin.gene.start;
@@ -92,24 +93,31 @@ function layoutLabels(m) {
   const onRows = m.drawnRowLabels.length > 0;
   const rowsTop = onRows ? Math.min(...m.drawnRowLabels.map((r) => r.y)) : Infinity;
   const halo = m.contigThickness * HALO_FACTOR;
-  const byBubble = byExtent(m.bubbleHalos, (h) => h.members);
+  const above = (h, gap) => {
+    const { x, y } = screen({
+      x: h.labelAt.x,
+      y: Math.min(h.labelAt.y, rowsTop)
+    });
+    const baseline = y - halo / 2 - gap;
+    return { x, y: onRows ? Math.max(baseline, TOPMOST_BASELINE) : baseline };
+  };
+  const byBubble = byExtent(
+    m.bubbleHalos.filter((h) => !h.tick),
+    (h) => h.whole ? -1 : h.members
+  );
   const bubbles = placeLabels(
-    byBubble.map((h) => {
-      const { x, y } = screen({
-        x: h.labelAt.x,
-        y: Math.min(h.labelAt.y, rowsTop)
-      });
-      const baseline = y - halo / 2 - 6;
-      return {
-        item: h,
-        x,
-        y: onRows ? Math.max(baseline, TOPMOST_BASELINE) : baseline,
-        text: h.label
-      };
-    }),
+    byBubble.map((h) => ({
+      item: h,
+      ...above(h, 6),
+      text: h.label,
+      // `0 bp–11 kb superbubble` where `…, 1198 segments, 5 routes` does not fit
+      fallback: h.label.includes(",") ? h.label.split(",")[0] : void 0,
+      stack: BUBBLE_STACK
+    })),
     frame,
     take
   );
+  const ticks = m.bubbleHalos.filter((h) => h.tick && !h.whole).map((h) => ({ item: h, ...above(h, 2) })).filter((t) => t.x >= 0 && t.x <= width && t.y >= 0 && t.y <= height);
   const genes = placeLabels(
     geneLabelCandidates(
       m.genePins,
@@ -162,6 +170,7 @@ function layoutLabels(m) {
   );
   return {
     bubbles,
+    ticks,
     genes,
     routes,
     sizes: [...deletionLabels, ...nodeLabels]

package/dist/chunks/{chunk-2AWUWGAD.js → chunk-REM73HCU.js}

@@ -15,6 +15,7 @@ var WHOLE_FRACTION = 0.9;
 function coversGraph(members, nodes) {
   return members + 2 >= nodes || members >= WHOLE_FRACTION * nodes;
 }
+var SMALL_VARIANT_BP = 50;
 var NAMED_WALKS = 2;
 var MIN_CHIPPED_BP = 1e3;
 function bubbleHalos(graph, bubbles, positions, walkLabel = (name) => name, repeats = []) {
@@ -87,6 +88,7 @@ function bubbleHalos(graph, bubbles, positions, walkLabel = (name) => name, repe
         routes.push({ route, at, text: routeText(route, walkLabel) });
       }
     }
+    const whole = bubble.covering === true || coversGraph(nodeIds.length, graph.nodes.length);
     halos.push({
       bubble,
       ...classifyBubble(bubble, repeats),
@@ -94,7 +96,10 @@ function bubbleHalos(graph, bubbles, positions, walkLabel = (name) => name, repe
       labelAt,
       members: nodeIds.length,
       nodeIds,
-      whole: coversGraph(nodeIds.length, graph.nodes.length),
+      whole,
+      // The drawing's own bubble keeps its name however small. A partial
+      // bubble's lengths are a floor, so it may be no small variant.
+      tick: !whole && !bubble.partial && bubble.longestAlleleLength < SMALL_VARIANT_BP,
       routes
     });
   }
@@ -110,5 +115,6 @@ function routeText(route, walkLabel) {
 export {
   WHOLE_FRACTION,
   coversGraph,
+  SMALL_VARIANT_BP,
   bubbleHalos
 };

package/dist/chunks/{chunk-ZDJDM77V.js → chunk-TF7H5LQS.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-VHW7FDHU.js";
 import {
   coversGraph
-} from "./chunk-2AWUWGAD.js";
+} from "./chunk-REM73HCU.js";
 import {
   bubbleSegmentIds
 } from "./chunk-XKWD2RY3.js";
@@ -23,7 +23,6 @@ import {
 } from "./chunk-FYQWPEEY.js";
 
 // src/bubbles/superbubbles.ts
-var MAX_SUPERBUBBLES = 50;
 function slotGraph(graph, index) {
   const slots = graph.nodes.length * 2;
   const seen = /* @__PURE__ */ new Set();
@@ -224,7 +223,9 @@ function superbubblesFromGraph(graph, span) {
     (j) => j !== i && !covers[j] && members[j].length > members[i].length && members[i].every((v) => holders.get(v).includes(j))
   );
   const placed = (f) => span !== void 0 || onReference(nodes[f.source >> 1], nodes[f.sink >> 1]);
-  const outermost = found.filter((f, i) => !covers[i] && placed(f) && !nested(f, i)).sort((a, b) => b.inside.length - a.inside.length).slice(0, MAX_SUPERBUBBLES);
+  const outermost = found.filter(
+    (f, i) => !covers[i] && placed(f) && !nested(f, i)
+  );
   const byId = new Map(nodes.map((n) => [n.id, n]));
   const walkIndex = walkIndexOf(graph);
   return outermost.map((f) => {
@@ -258,16 +259,22 @@ function superbubblesFromGraph(graph, span) {
 function graphBubbles(graph, span) {
   const n = graph.nodes.length;
   const reach = bubblesFromGraph(graph);
-  return reach.length === 0 ? superbubblesFromGraph(graph, span) : reach.flatMap(
-    (b) => coversGraph(b.segmentCount - 2, n) ? superbubblesFromGraph(
-      b.segmentCount === n ? graph : bubbleSubgraph(graph, bubbleSegmentIds(b)),
-      b
-    ) : [b]
+  if (reach.length === 0) {
+    const inside = superbubblesFromGraph(graph, span);
+    return span ? [...inside, { ...span, covering: true }] : inside;
+  }
+  return reach.flatMap(
+    (b) => coversGraph(b.segmentCount - 2, n) ? [
+      ...superbubblesFromGraph(
+        b.segmentCount === n ? graph : bubbleSubgraph(graph, bubbleSegmentIds(b)),
+        b
+      ),
+      { ...b, covering: true }
+    ] : [b]
   );
 }
 
 export {
-  MAX_SUPERBUBBLES,
   superbubblesFromGraph,
   graphBubbles
 };

package/dist/cli/figure.js

@@ -35,7 +35,7 @@ import "../chunks/chunk-LTUWJKHD.js";
 import "../chunks/chunk-WSIFAZU7.js";
 import {
   figureSvg
-} from "../chunks/chunk-HOOVOF2Y.js";
+} from "../chunks/chunk-4DEOECM3.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-FM6XRXPX.js";
+import "../chunks/chunk-BIGORSXS.js";
 import "../chunks/chunk-3C5UXR2U.js";
 import {
   filterSamples,
@@ -67,7 +67,7 @@ import {
   graphBackbone,
   refNameBinding
 } from "../chunks/chunk-RAKOB6IV.js";
-import "../chunks/chunk-GJMC3PGM.js";
+import "../chunks/chunk-DRG4236Y.js";
 import "../chunks/chunk-FP4H7SFT.js";
 import "../chunks/chunk-MLSWIMZO.js";
 import "../chunks/chunk-WFB5TXRA.js";

package/dist/figure.js

@@ -1,6 +1,6 @@
 import {
   figureSvg
-} from "./chunks/chunk-HOOVOF2Y.js";
+} from "./chunks/chunk-4DEOECM3.js";
 import "./chunks/chunk-UD5FOCI2.js";
 import "./chunks/chunk-WBCOREDZ.js";
 import "./chunks/chunk-4BYTEJGW.js";
@@ -16,13 +16,13 @@ import "./chunks/chunk-2LQ5BWT7.js";
 import "./chunks/chunk-OXTR3BVF.js";
 import "./chunks/chunk-BR25DGIJ.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-FM6XRXPX.js";
+import "./chunks/chunk-BIGORSXS.js";
 import "./chunks/chunk-3C5UXR2U.js";
 import "./chunks/chunk-MAUEPAMG.js";
 import "./chunks/chunk-7GBL7SJY.js";
 import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-RAKOB6IV.js";
-import "./chunks/chunk-GJMC3PGM.js";
+import "./chunks/chunk-DRG4236Y.js";
 import "./chunks/chunk-FP4H7SFT.js";
 import "./chunks/chunk-MLSWIMZO.js";
 import "./chunks/chunk-WFB5TXRA.js";

package/dist/index.js

@@ -42,7 +42,7 @@ import {
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "./chunks/chunk-ZDJDM77V.js";
+} from "./chunks/chunk-TF7H5LQS.js";
 import {
   bubbleSubgraph
 } from "./chunks/chunk-VHW7FDHU.js";
@@ -54,7 +54,7 @@ import {
 } from "./chunks/chunk-BXEPA4KS.js";
 import {
   bubbleHalos
-} from "./chunks/chunk-2AWUWGAD.js";
+} from "./chunks/chunk-REM73HCU.js";
 import {
   BUBBLE_KIND_COLORS,
   BUBBLE_KIND_NAMES,
@@ -119,7 +119,7 @@ import {
 } from "./chunks/chunk-AZFVORTC.js";
 import {
   figureSvg
-} from "./chunks/chunk-HOOVOF2Y.js";
+} from "./chunks/chunk-4DEOECM3.js";
 import {
   WALK_STRIP_CEILING_PX,
   cutsWholeWalks,
@@ -219,7 +219,7 @@ import {
 import "./chunks/chunk-G2FD7S3C.js";
 import {
   version
-} from "./chunks/chunk-FM6XRXPX.js";
+} from "./chunks/chunk-BIGORSXS.js";
 import {
   walkRowLabels,
   walkRowsExtent
@@ -255,7 +255,7 @@ import {
   LEGEND_INSET_PX,
   geneCoverageNote,
   layoutLabels
-} from "./chunks/chunk-GJMC3PGM.js";
+} from "./chunks/chunk-DRG4236Y.js";
 import {
   findHoveredEdge,
   findHoveredNode

package/dist/labelLayout.js

@@ -4,7 +4,7 @@ import {
   geneCoverageNote,
   geneLabelCandidates,
   layoutLabels
-} from "./chunks/chunk-GJMC3PGM.js";
+} from "./chunks/chunk-DRG4236Y.js";
 import "./chunks/chunk-FP4H7SFT.js";
 import "./chunks/chunk-MLSWIMZO.js";
 import "./chunks/chunk-WFB5TXRA.js";

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

@@ -10,6 +10,7 @@ export interface BubbleHalo {
     members: number;
     nodeIds: string[];
     whole: boolean;
+    tick: boolean;
     routes: RouteLabel[];
 }
 export interface RouteLabel {
@@ -19,4 +20,5 @@ export interface RouteLabel {
 }
 export declare const WHOLE_FRACTION = 0.9;
 export declare function coversGraph(members: number, nodes: number): boolean;
+export declare const SMALL_VARIANT_BP = 50;
 export declare function bubbleHalos(graph: Graph, bubbles: MinigraphBubble[], positions: Record<string, NodeSegment[]>, walkLabel?: (name: string) => string, repeats?: readonly RepeatSpan[]): BubbleHalo[];

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

@@ -14,6 +14,7 @@ export interface MinigraphBubble {
     routes?: BubbleRoute[];
     key?: string;
     offReference?: true;
+    covering?: true;
 }
 export interface BubbleRoute {
     steps: string[];

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

@@ -1,5 +1,4 @@
 import type { MinigraphBubble } from './bubbleLine.js';
 import type { Graph } from '../types.js';
-export declare const MAX_SUPERBUBBLES = 50;
 export declare function superbubblesFromGraph(graph: Graph, span?: MinigraphBubble): MinigraphBubble[];
 export declare function graphBubbles(graph: Graph, span?: MinigraphBubble): MinigraphBubble[];

package/dist/types/labelLayout.d.ts

@@ -38,8 +38,14 @@ export interface LabelLayoutSource {
     alleleDeletions: AlleleDeletion[];
     positionsVersion: number;
 }
+export interface BubbleTick {
+    item: BubbleHalo;
+    x: number;
+    y: number;
+}
 export interface LabelLayout {
     bubbles: PlacedLabel<BubbleHalo>[];
+    ticks: BubbleTick[];
     genes: PlacedLabel<GenePin>[];
     routes: PlacedLabel<{
         halo: BubbleHalo;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "9.2.0";
+export declare const version = "9.4.0";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-FM6XRXPX.js";
+} from "./chunks/chunk-BIGORSXS.js";
 export {
   version
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "9.2.0",
+  "version": "9.4.0",
   "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": {