@jbrowse/bandage-core 10.2.7 → 10.3.1

package/dist/chunks/{chunk-QBHPHLAQ.js → chunk-EWLXU3UG.js}

@@ -1,19 +1,19 @@
 import {
   svgCanvas
-} from "./chunk-RUCH6ZFL.js";
+} from "./chunk-V4YML3GR.js";
 import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-WBSWROE6.js";
+} from "./chunk-SFP3E4RI.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-EFQLEGWM.js";
+} from "./chunk-ZJBOM73S.js";
 import {
   Canvas2DRenderer
-} from "./chunk-QLWI2PZ3.js";
+} from "./chunk-EJRJAAN7.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -21,43 +21,45 @@ import {
 } from "./chunk-JSUCGZ6K.js";
 import {
   genePins
-} from "./chunk-RPRHR56C.js";
+} from "./chunk-BS6HPYCZ.js";
 import {
   geneLabelCandidates
-} from "./chunk-KC7T5RWG.js";
+} from "./chunk-PSCSZSVK.js";
 import {
   nodesUnderBox
-} from "./chunk-4HWM3FNK.js";
+} from "./chunk-OMUPUB4J.js";
 import {
   escapeAttr,
   serializeEl
 } from "./chunk-H2H4Y3TV.js";
 import {
   version
-} from "./chunk-CG35S2S2.js";
+} from "./chunk-AQCOIE5R.js";
 import {
   axisScaleOf
-} from "./chunk-A7CFWFQS.js";
-import {
-  rangeText,
-  walkKey
-} from "./chunk-4ETPXDO6.js";
+} from "./chunk-BKEZLETL.js";
 import {
   figureScene
-} from "./chunk-23YFB5BB.js";
+} from "./chunk-QH2MIXBA.js";
 import {
   encodingStops
-} from "./chunk-VQC7KELB.js";
+} from "./chunk-DO62DG26.js";
+import {
+  rangeText
+} from "./chunk-CGFPFBT2.js";
 import {
   walkRowLabels
-} from "./chunk-L2HDM2R3.js";
+} from "./chunk-A2TJ5UX6.js";
 import {
   nodeInk
-} from "./chunk-JBCZIBFC.js";
+} from "./chunk-CRCD3ODN.js";
+import {
+  FIGURE_DEFAULTS
+} from "./chunk-D7WIYPG3.js";
 import {
   FIT_PADDING,
   fitTransform
-} from "./chunk-QXUEF3AJ.js";
+} from "./chunk-KMBE2Q42.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -69,9 +71,8 @@ import {
   FACET_GAP_PX,
   FACET_PAD_PX,
   FACET_TITLE_PX,
-  facetCells,
   facetGrid
-} from "./chunk-XV4P5KEQ.js";
+} from "./chunk-TGUFT6KK.js";
 
 // src/figure.ts
 var FONT = 'font-family="Helvetica, Arial, sans-serif" font-size="11"';
@@ -100,15 +101,14 @@ function exonKeySvg(x, y) {
     markup: `<g transform="translate(${x} ${y})" ${FONT}><rect x="1" y="4" width="${SWATCH_PX - 2}" height="10" rx="4" fill="none" stroke="${EXON_COLOR}" stroke-width="2"/><text x="${SWATCH_PX + 5}" y="13">exon</text></g>`
   };
 }
-function walkKeySvg(id, x, y, walk, label, reference) {
-  const key = walkKey(walk, reference);
+function walkKeySvg(id, x, y, walk, label, key) {
   return keySvg(
     id,
     x,
     y,
     encodingStops(walk.encoding),
     label,
-    key.delta + key.outside + key.reversed,
+    key.note,
     key.scale
   );
 }
@@ -122,8 +122,8 @@ function chip(x, y, w, name, note) {
   return `<rect x="${x - w / 2}" y="${y - LABEL_PX - LABEL_PAD + 2}" width="${w}" height="${LABEL_PX + LABEL_PAD * 2 - 2}" rx="3" fill="#fff" fill-opacity="0.85" stroke="${EXON_COLOR}"/><text x="${x}" y="${y}" font-family="Helvetica, Arial, sans-serif" font-size="${LABEL_PX}" fill="${GENE_INK}" text-anchor="middle"><tspan font-style="italic" font-weight="600">${escapeAttr(name)}</tspan>${note ? escapeAttr(note) : ""}</text>`;
 }
 function figureSvg(graph, layout, o = {}) {
-  const width = o.width ?? 1200;
-  const room = o.height ?? 800;
+  const width = o.width ?? FIGURE_DEFAULTS.width;
+  const room = o.height ?? FIGURE_DEFAULTS.height;
   const rows = o.walkRows;
   const {
     bounds,
@@ -132,10 +132,10 @@ function figureSvg(graph, layout, o = {}) {
     layers,
     lift,
     facet,
-    panels,
+    facets,
     labelOf,
     referenceName,
-    reference,
+    keyText,
     contigThickness,
     nodeWidth,
     geometry
@@ -209,7 +209,7 @@ function figureSvg(graph, layout, o = {}) {
       w,
       h,
       pixelRows,
-      panels ? {
+      facets ? {
         padLeft: FACET_PAD_PX,
         padTop: FACET_PAD_PX,
         padRight: FACET_PAD_PX,
@@ -235,12 +235,8 @@ function figureSvg(graph, layout, o = {}) {
   }
   const parts = [];
   let height;
-  if (panels) {
-    const place = facetCells(
-      panels.map((p) => p.walks[0].name),
-      facet.field || "walk",
-      facet.domain
-    );
+  if (facets) {
+    const { panels, place } = facets;
     const grid = facetGrid({
       count: place.count,
       bounds,
@@ -255,7 +251,14 @@ function figureSvg(graph, layout, o = {}) {
       const y = Math.floor(cell / grid.columns) * (grid.height + FACET_TITLE_PX + FACET_GAP_PX);
       const walk = panel.walks[0];
       parts.push(
-        walkKeySvg(`key${i}`, x + 6, y + 2, walk, labelOf(walk.name), reference).markup,
+        walkKeySvg(
+          `key${i}`,
+          x + 6,
+          y + 2,
+          walk,
+          labelOf(walk.name),
+          keyText(walk)
+        ).markup,
         `<svg x="${x}" y="${y + FACET_TITLE_PX}" width="${grid.width}" height="${grid.height}">${drawing(panel, grid.width, grid.height)}</svg>`
       );
     });
@@ -268,7 +271,9 @@ function figureSvg(graph, layout, o = {}) {
     };
     if (lift) {
       lift.walks.forEach((walk, i) => {
-        push(walkKeySvg(`key${i}`, x, 2, walk, labelOf(walk.name), reference));
+        push(
+          walkKeySvg(`key${i}`, x, 2, walk, labelOf(walk.name), keyText(walk))
+        );
       });
       push(
         keySvg(

package/dist/chunks/{chunk-XI3ZUTWF.js → chunk-FW2R7UDZ.js}

@@ -2,21 +2,27 @@ import {
   canonicalStrand,
   stepName,
   tubeMapReads
-} from "./chunk-CWFNEKST.js";
+} from "./chunk-A7H753BA.js";
+import {
+  referenceWalkName
+} from "./chunk-OOIOX36I.js";
 import {
   pathCssColor,
   pathGreyCssColor
-} from "./chunk-3XSM4OZU.js";
+} from "./chunk-3GP3KT5L.js";
 import {
   pathOrigin
-} from "./chunk-M6LK4GII.js";
+} from "./chunk-B5X2RLJG.js";
 import {
   ownStrand,
   strandSides
-} from "./chunk-7SRWJLSC.js";
+} from "./chunk-UBQSRCWR.js";
+import {
+  groupBy
+} from "./chunk-BSOZW3FC.js";
 import {
   isBackbone
-} from "./chunk-FYQWPEEY.js";
+} from "./chunk-RJWPJCIB.js";
 
 // src/layout/tubeMapLayout.ts
 import { forward, isReverse, layoutTubeMap } from "@jbrowse/tubemap-core";
@@ -53,9 +59,8 @@ function tubeMapTracks(graph) {
       }
     ] : [];
   });
-  const reference = tracks.findIndex(
-    (t) => pathOrigin(t.name).name === graph.referencePath
-  );
+  const name = referenceWalkName(graph);
+  const reference = tracks.findIndex((t) => pathOrigin(t.name).name === name);
   if (reference > 0) {
     tracks.unshift(...tracks.splice(reference, 1));
   }
@@ -279,15 +284,7 @@ function tubeMapLayout(graph) {
 }
 function tubeMapColumns(graph, layout) {
   const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));
-  const byOrder = /* @__PURE__ */ new Map();
-  for (const node of drawnNodes(layout)) {
-    const list = byOrder.get(node.order);
-    if (list) {
-      list.push(node);
-    } else {
-      byOrder.set(node.order, [node]);
-    }
-  }
+  const byOrder = groupBy(drawnNodes(layout), (node) => node.order);
   const columns = [];
   let end = -Infinity;
   for (const order of [...byOrder.keys()].sort((a, b) => a - b)) {
@@ -355,9 +352,6 @@ export {
   pathSteps,
   tubeMapTracks,
   hasTubeMapPaths,
-  tubeWidth,
-  mergedRuns,
-  boxGraph,
   tubeMapLayout,
   hasTubeMapBackbone,
   tubeMapReferenceLayout

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-QXUEF3AJ.js → chunk-KMBE2Q42.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-NZTYV3JL.js";
 import {
   parseGFA
 } from "./chunk-5I3K4R2G.js";
 import {
   graphFromTables
-} from "./chunk-OIV2GBAJ.js";
+} from "./chunk-DBLV7PGG.js";
 import {
   anchorGraph
-} from "./chunk-M6LK4GII.js";
+} from "./chunk-B5X2RLJG.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);