@jbrowse/bandage-core 10.2.6 → 10.3.0

package/dist/chunks/{chunk-ABUIN5AK.js → chunk-EHXBZ5JZ.js}

@@ -1,24 +1,28 @@
 import {
   bubblesFromGraph,
+  derivedBubble,
   relax,
   walkIndexOf,
   walkRoutes
-} from "./chunk-CQHUZHET.js";
+} from "./chunk-RFG42VIO.js";
 import {
   bubbleSubgraph
-} from "./chunk-T6V4KI2L.js";
+} from "./chunk-PPDE4IVT.js";
 import {
   coversGraph
-} from "./chunk-JA2HJIYS.js";
+} from "./chunk-E4ZM4OOJ.js";
 import {
   bubbleSegmentIds
-} from "./chunk-URZ3CH2R.js";
+} from "./chunk-A4JDEUAI.js";
 import {
   strandSides
-} from "./chunk-7SRWJLSC.js";
+} from "./chunk-UBQSRCWR.js";
+import {
+  pushTo
+} from "./chunk-BSOZW3FC.js";
 import {
   isBackbone
-} from "./chunk-FYQWPEEY.js";
+} from "./chunk-RJWPJCIB.js";
 
 // src/bubbles/superbubbles.ts
 function slotGraph(graph, index) {
@@ -207,8 +211,7 @@ function superbubblesFromGraph(graph, span) {
   const holders = /* @__PURE__ */ new Map();
   members.forEach((vs, i) => {
     for (const v of vs) {
-      ;
-      (holders.get(v) ?? holders.set(v, []).get(v)).push(i);
+      pushTo(holders, v, i);
     }
   });
   const nested = (f, i) => holders.get(f.inside[0] >> 1).some(
@@ -226,24 +229,26 @@ function superbubblesFromGraph(graph, span) {
   return outermost.map((f) => {
     const source = nodes[f.source >> 1];
     const sink = nodes[f.sink >> 1];
-    const walked = walkIndex && walkRoutes(graph, byId, walkIndex, source.id, sink.id);
-    const crossed = walked?.n ? walked : void 0;
-    const routes = crossed ?? routesThrough(nodes, offset, next, f);
+    const walked = walkRoutes(
+      graph,
+      byId,
+      walkIndex,
+      source.id,
+      sink.id,
+      () => routesThrough(nodes, offset, next, f)
+    );
     const placedOn = onReference(source, sink);
     return {
-      refName: placedOn ? source.stable.refName : span.refName,
-      start: placedOn ? source.stable.start + source.length : span.start,
-      end: placedOn ? sink.stable.start : span.end,
-      segmentCount: f.inside.length + 2,
-      pathCount: routes.n,
-      inversion: false,
-      shortestAlleleLength: routes.min,
-      longestAlleleLength: routes.max,
-      segments: nodesOf(f).map((v) => nodes[v].name).join(","),
-      shortestAllele: void 0,
-      longestAllele: void 0,
-      partial: walked !== void 0 && walked.left > 0,
-      routes: crossed?.routes,
+      ...derivedBubble(
+        {
+          refName: placedOn ? source.stable.refName : span.refName,
+          start: placedOn ? source.stable.start + source.length : span.start,
+          end: placedOn ? sink.stable.start : span.end
+        },
+        nodesOf(f).map((v) => nodes[v]),
+        walked,
+        walked.walksLeave
+      ),
       key: `${source.name}>${sink.name}`,
       ...placedOn ? {} : { offReference: true }
     };

package/dist/chunks/{chunk-QLWI2PZ3.js → chunk-EJRJAAN7.js}

@@ -46,18 +46,22 @@ var Canvas2DRenderer = class {
     this.highlightFactor = factor;
   }
   updateTransform(transform) {
+    this.transform = transform;
+  }
+  fitted() {
+    const t = this.transform;
     const k = this.fit;
-    this.transform = k === 1 ? transform : {
-      ...transform,
-      scaleX: transform.scaleX * k,
-      scaleY: transform.scaleY * k,
-      translateX: transform.translateX * k,
-      translateY: transform.translateY * k,
-      dpr: transform.dpr * k
+    return !t || k === 1 ? t : {
+      ...t,
+      scaleX: t.scaleX * k,
+      scaleY: t.scaleY * k,
+      translateX: t.translateX * k,
+      translateY: t.translateY * k,
+      dpr: t.dpr * k
     };
   }
   render(clearColor) {
-    const t = this.transform;
+    const t = this.fitted();
     if (!t) {
       return;
     }
@@ -84,7 +88,7 @@ var Canvas2DRenderer = class {
       weight: e.thickness,
       last: inRun(edgeRun, i)
     }))) {
-      this.strokeCurves(items, color);
+      this.strokeCurves(items, color, t);
     }
     const lifted = this.liftedStrokes(batch);
     for (const { color, items } of groupByPaint(batch.nodeStrokes, (s, i) => {
@@ -95,7 +99,7 @@ var Canvas2DRenderer = class {
         last: f !== void 0
       };
     })) {
-      this.strokeNodes(items, color);
+      this.strokeNodes(items, color, t);
     }
     const arrowRun = this.edgeRun(batch.arrowRuns);
     for (const { color, items } of groupByPaint(batch.arrows, (a, i) => ({
@@ -103,7 +107,7 @@ var Canvas2DRenderer = class {
       weight: 0,
       last: inRun(arrowRun, i)
     }))) {
-      this.fillArrows(items, color);
+      this.fillArrows(items, color, t);
     }
   }
   // Only what the highlights lift, over a transparent clear, for a hover layer
@@ -113,7 +117,8 @@ var Canvas2DRenderer = class {
     const ctx = this.ctx;
     ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height);
     const batch = this.batch;
-    if (!this.transform || !batch) {
+    const t = this.fitted();
+    if (!t || !batch) {
       return;
     }
     ctx.lineCap = "round";
@@ -125,7 +130,7 @@ var Canvas2DRenderer = class {
       weight: e.thickness,
       last: false
     }))) {
-      this.strokeCurves(items, color);
+      this.strokeCurves(items, color, t);
     }
     const lifted = [...this.liftedStrokes(batch)];
     for (const { color, items } of groupByPaint(lifted, ([i, f]) => ({
@@ -135,7 +140,8 @@ var Canvas2DRenderer = class {
     }))) {
       this.strokeNodes(
         items.map(([i]) => batch.nodeStrokes[i]),
-        color
+        color,
+        t
       );
     }
     const arrows = runItems(batch.arrows, this.edgeRun(batch.arrowRuns));
@@ -144,7 +150,7 @@ var Canvas2DRenderer = class {
       weight: 0,
       last: false
     }))) {
-      this.fillArrows(items, color);
+      this.fillArrows(items, color, t);
     }
   }
   edgeRun(runs) {
@@ -163,8 +169,7 @@ var Canvas2DRenderer = class {
     }
     return lifted;
   }
-  strokeCurves(items, color) {
-    const t = this.transform;
+  strokeCurves(items, color, t) {
     const ctx = this.ctx;
     ctx.strokeStyle = abgrToCssRgba(color);
     ctx.lineWidth = items[0].thickness * 2 * t.dpr;
@@ -188,8 +193,7 @@ var Canvas2DRenderer = class {
     }
     ctx.stroke();
   }
-  strokeNodes(items, color) {
-    const t = this.transform;
+  strokeNodes(items, color, t) {
     const ctx = this.ctx;
     ctx.strokeStyle = abgrToCssRgba(color);
     ctx.lineWidth = items[0].thickness * 2 * t.dpr;
@@ -204,8 +208,7 @@ var Canvas2DRenderer = class {
     }
     ctx.stroke();
   }
-  fillArrows(items, color) {
-    const t = this.transform;
+  fillArrows(items, color, t) {
     const ctx = this.ctx;
     ctx.fillStyle = abgrToCssRgba(color);
     ctx.beginPath();

package/dist/chunks/{chunk-Q7LYHGGQ.js → chunk-GIHTHYXY.js}

@@ -1,16 +1,16 @@
 import {
   joinCuts
-} from "./chunk-WSIFAZU7.js";
+} from "./chunk-HNWJ4B7S.js";
 import {
   wellKnownSample
-} from "./chunk-RAKOB6IV.js";
+} from "./chunk-234NFZS4.js";
 import {
   gfaTables
-} from "./chunk-G45YY72K.js";
+} from "./chunk-Z6XZWPXK.js";
 import {
   panSNMatchesPrefix,
   panSNSample
-} from "./chunk-BPLIXMH7.js";
+} from "./chunk-4XWZNPQ2.js";
 
 // src/gbzWindow.ts
 import { isReverse, nodeId } from "@gmod/gbz-base";
@@ -210,6 +210,7 @@ export {
   haplotypePrefix,
   haplotypeWanted,
   referenceSamplesOf,
+  aliasedSample,
   resolveReferenceSample,
   referencePathQuery,
   nodeLimitError,

package/dist/chunks/{chunk-L3O7AWLI.js → chunk-GJLZ2MKE.js}

@@ -1,6 +1,6 @@
 import {
   placeOffReference
-} from "./chunk-TZFWUT2C.js";
+} from "./chunk-MYLAJDKB.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";
@@ -8,7 +8,7 @@ import {
   backboneNodes,
   backbonePositions,
   referenceSpan
-} from "./chunk-FYQWPEEY.js";
+} from "./chunk-RJWPJCIB.js";
 
 // src/layout/anchoredLayout.ts
 function rankRows(graph) {

package/dist/chunks/{chunk-LOEA5IHZ.js → chunk-GJU6BJJA.js}

@@ -1,9 +1,6 @@
 import {
   placeOffReference
-} from "./chunk-TZFWUT2C.js";
-import {
-  parsePanSN
-} from "./chunk-RVS2QCOX.js";
+} from "./chunk-MYLAJDKB.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";
@@ -12,14 +9,17 @@ import {
   backbonePositions,
   isOffReference,
   referenceSpan
-} from "./chunk-FYQWPEEY.js";
+} from "./chunk-RJWPJCIB.js";
+import {
+  panSNSample
+} from "./chunk-4XWZNPQ2.js";
 
 // src/layout/sampleRowLayout.ts
 function contributingSamples(graph, keep) {
   const carried = /* @__PURE__ */ new Map();
   for (const node of graph.nodes) {
     if (isOffReference(node)) {
-      const { sample } = parsePanSN(node.stable.refName);
+      const sample = panSNSample(node.stable.refName);
       carried.set(sample, (carried.get(sample) ?? 0) + node.length);
     }
   }
@@ -43,12 +43,12 @@ function sampleRowLayout(graph, region, keep = []) {
     span,
     rowY: (node) => {
       const stable = node.stable;
-      const row = stable ? rowOf.get(parsePanSN(stable.refName).sample) : void 0;
+      const row = stable ? rowOf.get(panSNSample(stable.refName)) : void 0;
       return (row ?? spareRow) * ROW_HEIGHT_PX;
     },
     positions: nodePositions
   });
-  const referenceSample = parsePanSN(backbone[0].stable.refName).sample;
+  const referenceSample = panSNSample(backbone[0].stable.refName);
   const rowLabels = [
     { label: referenceSample, y: 0 },
     ...samples.map((sample) => ({

package/dist/chunks/{chunk-XL472HHD.js → chunk-GQZVR5DW.js}

@@ -1,15 +1,16 @@
-import {
-  REFERENCE_RAMP_MAX_HUE
-} from "./chunk-A4PFFC4Q.js";
-
 // src/referenceRampCss.ts
+var REFERENCE_RAMP_MAX_HUE = 300;
+var REFERENCE_RAMP_SATURATION = 0.7;
+var REFERENCE_RAMP_LIGHTNESS = 0.5;
 function rampHueCss(hue) {
-  return `hsl(${hue}, 70%, 50%)`;
+  return `hsl(${hue}, ${REFERENCE_RAMP_SATURATION * 100}%, ${REFERENCE_RAMP_LIGHTNESS * 100}%)`;
 }
-function rampHue(bp, domain) {
-  const frac = (bp - domain.start) / (domain.end - domain.start);
+function rampHueAt(frac) {
   return Math.max(0, Math.min(1, frac)) * REFERENCE_RAMP_MAX_HUE;
 }
+function rampHue(bp, domain) {
+  return rampHueAt((bp - domain.start) / (domain.end - domain.start));
+}
 var HUE_STOP_DEG = 30;
 function rampStops({ start, bp, reversed }, domain) {
   const low = rampHue(start, domain);
@@ -32,7 +33,11 @@ var RAMP_GRADIENT_CSS = `linear-gradient(to right, ${RAMP_GRADIENT_STOPS.map(
 ).join(", ")})`;
 
 export {
+  REFERENCE_RAMP_MAX_HUE,
+  REFERENCE_RAMP_SATURATION,
+  REFERENCE_RAMP_LIGHTNESS,
   rampHueCss,
+  rampHueAt,
   rampHue,
   rampStops,
   RAMP_GRADIENT_STOPS,

package/dist/chunks/{chunk-UVBGRJQX.js → chunk-HKYXWZQS.js}

@@ -1,7 +1,7 @@
 import {
   MEAN_NODE_LENGTH,
   PROPORTIONAL_LENGTH
-} from "./chunk-6JEWNXCQ.js";
+} from "./chunk-34BOZKIE.js";
 
 // src/bubbleSpreads.ts
 var BUBBLE_SPREADS = [

package/dist/chunks/chunk-HMXCN6PG.js

@@ -0,0 +1,17 @@
+// src/util/weakMemo.ts
+function weakMemo() {
+  const cache = /* @__PURE__ */ new WeakMap();
+  return (key, deps, compute) => {
+    const hit = cache.get(key);
+    if (hit?.deps.length === deps.length && hit.deps.every((d, i) => Object.is(d, deps[i]))) {
+      return hit.value;
+    }
+    const value = compute();
+    cache.set(key, { deps, value });
+    return value;
+  };
+}
+
+export {
+  weakMemo
+};

package/dist/chunks/{chunk-WSIFAZU7.js → chunk-HNWJ4B7S.js}

@@ -1,3 +1,7 @@
+import {
+  groupBy
+} from "./chunk-BSOZW3FC.js";
+
 // src/gbzJoin.ts
 var UNKNOWN_SAMPLE = "unknown";
 function parseWalk(line) {
@@ -18,7 +22,7 @@ function segmentLengths(lines) {
       const ln = tags.find((tag) => tag.startsWith("LN:i:"));
       lengths.set(
         id,
-        sequence === "*" && ln ? +ln.slice("LN:i:".length) : sequence.length
+        sequence !== "*" ? sequence.length : ln ? +ln.slice("LN:i:".length) : 0
       );
     }
   }
@@ -94,18 +98,13 @@ function joinCuts(gfas, startsPath) {
     }
     return walks2;
   });
-  const byName = /* @__PURE__ */ new Map();
-  for (const walk of [
-    ...walksByCut.flatMap((walks2) => walks2.slice(0, 1)),
-    ...walksByCut.flatMap((walks2) => walks2.slice(1))
-  ]) {
-    const pieces = byName.get(walk.name);
-    if (pieces) {
-      pieces.push(walk);
-    } else {
-      byName.set(walk.name, [walk]);
-    }
-  }
+  const byName = groupBy(
+    [
+      ...walksByCut.flatMap((walks2) => walks2.slice(0, 1)),
+      ...walksByCut.flatMap((walks2) => walks2.slice(1))
+    ],
+    (walk) => walk.name
+  );
   const walks = [...byName.values()].flatMap(
     (pieces) => joinPieces(pieces, lengths, startsPath)
   );

package/dist/chunks/chunk-HOAIOEI7.js

@@ -0,0 +1,18 @@
+// src/util/partitionPoint.ts
+function partitionPoint(n, pred) {
+  let lo = 0;
+  let hi = n;
+  while (lo < hi) {
+    const mid = lo + hi >> 1;
+    if (pred(mid)) {
+      lo = mid + 1;
+    } else {
+      hi = mid;
+    }
+  }
+  return lo;
+}
+
+export {
+  partitionPoint
+};

package/dist/chunks/{chunk-XMW266WS.js → chunk-HSVFCA2J.js}

@@ -1,9 +1,15 @@
 import {
   formatBp
-} from "./chunk-PTABFYQ7.js";
+} from "./chunk-PFRQBCGC.js";
+import {
+  pushTo
+} from "./chunk-BSOZW3FC.js";
 import {
   isBackbone
-} from "./chunk-FYQWPEEY.js";
+} from "./chunk-RJWPJCIB.js";
+import {
+  partitionPoint
+} from "./chunk-HOAIOEI7.js";
 
 // src/tubeMap/axis.ts
 function referenceBoxes({
@@ -16,8 +22,7 @@ function referenceBoxes({
     const graphNode = nodeById.get(node.name);
     if (node.order >= 0 && graphNode && isBackbone(graphNode)) {
       const { refName, start } = graphNode.stable;
-      const boxes = byRefName.get(refName) ?? byRefName.set(refName, []).get(refName);
-      boxes.push({
+      pushTo(byRefName, refName, {
         name: node.name,
         index,
         bp0: start,
@@ -33,23 +38,15 @@ function referenceBoxes({
   return byRefName;
 }
 function tubeX(boxes, bp, isEnd = false) {
-  let lo = 0;
-  let hi = boxes.length - 1;
-  while (lo < hi) {
-    const mid = lo + hi >> 1;
-    const bp1 = boxes[mid].bp1;
-    if (isEnd ? bp1 < bp : bp1 <= bp) {
-      lo = mid + 1;
-    } else {
-      hi = mid;
-    }
-  }
-  const box = boxes[lo];
-  if (bp <= box.bp0) {
-    return box.x0;
-  }
+  const i = partitionPoint(
+    boxes.length - 1,
+    (j) => isEnd ? boxes[j].bp1 < bp : boxes[j].bp1 <= bp
+  );
+  return boxX(boxes[i], bp);
+}
+function boxX(box, bp) {
   const span = box.bp1 - box.bp0;
-  return span > 0 ? box.x0 + (Math.min(bp, box.bp1) - box.bp0) / span * (box.x1 - box.x0) : box.x0;
+  return bp <= box.bp0 || span <= 0 ? box.x0 : box.x0 + (Math.min(bp, box.bp1) - box.bp0) / span * (box.x1 - box.x0);
 }
 function tubeSpan(boxes, start, end) {
   const a = tubeX(boxes, start);
@@ -199,6 +196,7 @@ function drawTubeMapRuler(ctx, boxes, frame, top, referenceAxis = false) {
 export {
   referenceBoxes,
   tubeX,
+  boxX,
   tubeSpan,
   rulerBoxes,
   rulerInk,

package/dist/chunks/{chunk-3XSM4OZU.js → chunk-IYALCKNB.js}

@@ -1,12 +1,12 @@
 import {
   pathOrigin
-} from "./chunk-M6LK4GII.js";
-import {
-  isGenericSample
-} from "./chunk-BPLIXMH7.js";
+} from "./chunk-LGJBB5BP.js";
 import {
   groupDigits
-} from "./chunk-PTABFYQ7.js";
+} from "./chunk-PFRQBCGC.js";
+import {
+  isGenericSample
+} from "./chunk-4XWZNPQ2.js";
 
 // src/pathColors.ts
 function nameHue(name) {

package/dist/chunks/{chunk-2QLLQJ72.js → chunk-KWHWNOTY.js}

@@ -1,9 +1,9 @@
 import {
   orientToReference
-} from "./chunk-PUG7LXDF.js";
+} from "./chunk-3PZSBNLI.js";
 import {
   seededNodes
-} from "./chunk-IGVV37VI.js";
+} from "./chunk-CKUVEHSS.js";
 import {
   smoothChain
 } from "./chunk-OPPVSPEF.js";
@@ -14,38 +14,38 @@ import {
 } from "./chunk-VPE4AYP7.js";
 import {
   convertGFAToGraph
-} from "./chunk-AR4BUBMU.js";
+} from "./chunk-RWKP7UO4.js";
 import {
   parseGFA
 } from "./chunk-5I3K4R2G.js";
 import {
   graphFromTables
-} from "./chunk-PSMKPSO4.js";
+} from "./chunk-DBLV7PGG.js";
 import {
   anchorGraph
-} from "./chunk-M6LK4GII.js";
+} from "./chunk-LGJBB5BP.js";
 import {
   gfaTables
-} from "./chunk-G45YY72K.js";
+} from "./chunk-Z6XZWPXK.js";
 import {
   mergeRuns,
   splitRuns
-} from "./chunk-N73TI3VG.js";
+} from "./chunk-BZFOFC4D.js";
 import {
   spreadFor
-} from "./chunk-UVBGRJQX.js";
+} from "./chunk-HKYXWZQS.js";
 import {
   drawnLengthOf,
   drawnNodeLength,
   layoutScaling
-} from "./chunk-6JEWNXCQ.js";
+} from "./chunk-34BOZKIE.js";
 import {
   deletionDrawing,
   deletionEdges
-} from "./chunk-24WITXQY.js";
+} from "./chunk-CGMSKIEO.js";
 import {
   isBackbone
-} from "./chunk-FYQWPEEY.js";
+} from "./chunk-RJWPJCIB.js";
 
 // src/pipeline.ts
 function graphOf(source, name) {
@@ -90,11 +90,12 @@ function engineSettingsOf(s = {}) {
 var COMPONENT_SEPARATION = 15;
 function engineRequest(graph, scaling, settings) {
   const anchored = graph.nodes.some(isBackbone);
+  const s = engineSettingsOf(settings);
   const spaced = {
     ...scaling,
     opts: {
       ...scaling.opts,
-      edgeLength: scaling.opts.edgeLength * (settings.spacing ?? 1)
+      edgeLength: scaling.opts.edgeLength * s.spacing
     }
   };
   return {
@@ -103,18 +104,22 @@ function engineRequest(graph, scaling, settings) {
       edges: graph.edges
     },
     options: {
-      quality: settings.quality,
-      linearLayout: settings.linearLayout,
+      quality: s.quality,
+      linearLayout: s.linearLayout,
       ...spaced.opts,
-      componentSeparation: COMPONENT_SEPARATION * (settings.componentSeparation ?? 1),
+      componentSeparation: COMPONENT_SEPARATION * s.componentSeparation,
       ...anchored ? { rotateComponents: false } : {},
-      engine: settings.engine ?? "fmmm"
+      engine: s.engine
     }
   };
 }
 function engineKey(graph, settings) {
   const anchored = graph.nodes.some(isBackbone);
-  return `${settings.engine ?? "fmmm"}|${settings.quality}|${settings.linearLayout}|${settings.bubbleSpread}|${settings.spacing ?? 1}|${settings.componentSeparation ?? 1}|${settings.showDeletionEdges !== false}|${anchored}|${graph.referencePath ?? ""}`;
+  return [
+    ...Object.values(engineSettingsOf(settings)),
+    anchored,
+    graph.referencePath ?? ""
+  ].join("|");
 }
 async function forceLayout(graph, settings, engine) {
   const spread = spreadFor(settings.bubbleSpread);

package/dist/chunks/{chunk-M6LK4GII.js → chunk-LGJBB5BP.js}

@@ -1,12 +1,15 @@
 import {
   PathVisitsBuilder
-} from "./chunk-RAEABQNW.js";
+} from "./chunk-ZPZ7GNBT.js";
 import {
-  panSNSample
-} from "./chunk-BPLIXMH7.js";
+  groupBy
+} from "./chunk-BSOZW3FC.js";
 import {
   REFERENCE_RANK
-} from "./chunk-FYQWPEEY.js";
+} from "./chunk-RJWPJCIB.js";
+import {
+  panSNSample
+} from "./chunk-4XWZNPQ2.js";
 
 // src/pathAnchoring.ts
 var RANGE_SUFFIX = /:(\d+)-\d+$/;
@@ -132,11 +135,7 @@ function trimOrigins(graph, kept) {
     }
     return sum;
   };
-  const byOrigin = /* @__PURE__ */ new Map();
-  for (const path of graph.paths ?? []) {
-    const origin = pathOrigin(path.name).name;
-    byOrigin.set(origin, [...byOrigin.get(origin) ?? [], path]);
-  }
+  const byOrigin = groupBy(graph.paths ?? [], (p) => pathOrigin(p.name).name);
   return graph.anchorPaths.map((o) => {
     const pieces = byOrigin.get(o.name);
     const path = pieces?.length === 1 ? pieces[0] : void 0;