@jbrowse/bandage-core 5.0.0 → 5.1.0

package/dist/chunks/{chunk-WWH65AAB.js → chunk-Y2MDXT4O.js}

@@ -297,6 +297,16 @@ function attachment(segments, side) {
 }
 var TANGENT_SPAN_FACTOR = 0.5;
 var MAX_TANGENT = 80;
+function ownStrand(id) {
+  return id.endsWith("-") ? "-" : "+";
+}
+function strandSides(edge) {
+  const own = (id, strand) => (strand ?? ownStrand(id)) === ownStrand(id);
+  return {
+    from: own(edge.from, edge.fromStrand) ? "end" : "start",
+    to: own(edge.to, edge.toStrand) ? "start" : "end"
+  };
+}
 function spanOf(segments) {
   let min = Infinity;
   let max = -Infinity;
@@ -409,6 +419,14 @@ function selfLinkOf(edge) {
   }
   return edge.fromStrand && edge.toStrand && edge.fromStrand !== edge.toStrand ? edge.fromStrand === "+" ? "end" : "start" : true;
 }
+function edgeJoinOf(edge, stranded = false) {
+  const self = selfLinkOf(edge);
+  if (!stranded) {
+    return self;
+  }
+  const sides = strandSides(edge);
+  return self === false ? sides : sides.from === sides.to ? sides.from : true;
+}
 function hairpinCurves(attach, reach, offsetX, offsetY) {
   const { at, inward } = attach;
   const dx = inward ? at.x - inward.x : 1;
@@ -447,7 +465,7 @@ function hairpinCurves(attach, reach, offsetX, offsetY) {
     }
   ];
 }
-function computeEdgeCurves(fromSegments, toSegments, selfLink, offsetX, offsetY, axis, bypassed = [], maxBowIn) {
+function computeEdgeCurves(fromSegments, toSegments, join, offsetX, offsetY, axis, bypassed = [], maxBowIn) {
   const scale = axis.scaleX;
   const yToX = yToXOf(axis);
   const maxBow = maxBowIn ?? (axis.pixelRows ? MAX_ROW_BOW_PX : void 0);
@@ -456,7 +474,7 @@ function computeEdgeCurves(fromSegments, toSegments, selfLink, offsetX, offsetY,
       computeEdgeCurves(
         scaleYOf(fromSegments, yToX),
         scaleYOf(toSegments, yToX),
-        selfLink,
+        join,
         offsetX,
         offsetY * yToX,
         { scaleX: scale, scaleY: scale },
@@ -468,15 +486,16 @@ function computeEdgeCurves(fromSegments, toSegments, selfLink, offsetX, offsetY,
       yToX
     );
   }
-  if (typeof selfLink === "string") {
+  if (typeof join === "string") {
     return hairpinCurves(
-      attachment(fromSegments, selfLink),
+      attachment(fromSegments, join),
       selfLoopReach(fromSegments, scale),
       offsetX,
       offsetY
     );
   }
-  const sides = selfLink ? { from: "end", to: "start" } : facingSides(fromSegments, toSegments);
+  const loop = join === true;
+  const sides = loop ? { from: "end", to: "start" } : join || facingSides(fromSegments, toSegments);
   const fromAttach = attachment(fromSegments, sides.from);
   const toAttach = attachment(toSegments, sides.to);
   const fromEnd = fromAttach.at;
@@ -485,7 +504,7 @@ function computeEdgeCurves(fromSegments, toSegments, selfLink, offsetX, offsetY,
   const p1y = fromEnd.y + offsetY;
   const p2x = toStart.x + offsetX;
   const p2y = toStart.y + offsetY;
-  if (selfLink) {
+  if (loop) {
     let segDirX = 1;
     let segDirY = 0;
     if (fromAttach.inward) {
@@ -591,12 +610,15 @@ function nearerEnd(segments, to) {
   const end = segments.at(-1);
   return Math.hypot(start.x - to.x, start.y - to.y) < Math.hypot(end.x - to.x, end.y - to.y) ? "start" : "end";
 }
-function routedEdgeCurves(fromSegments, toSegments, route) {
+function routedEdgeCurves(fromSegments, toSegments, route, sides) {
   const fromAttach = attachment(
     fromSegments,
-    nearerEnd(fromSegments, route[0])
+    sides?.from ?? nearerEnd(fromSegments, route[0])
+  );
+  const toAttach = attachment(
+    toSegments,
+    sides?.to ?? nearerEnd(toSegments, route.at(-1))
   );
-  const toAttach = attachment(toSegments, nearerEnd(toSegments, route.at(-1)));
   const points = [fromAttach.at, ...route, toAttach.at];
   const tangent = (i) => {
     const p = points[i];
@@ -646,16 +668,21 @@ var MIN_DELETION_BP = 1;
 function bypassedPoints(nodePositions, bypassed) {
   return bypassed.flatMap((id) => nodePositions[id] ?? []);
 }
-function deletionArcCurves(nodePositions, deletion, axis, route) {
+function deletionArcCurves(nodePositions, deletion, axis, route, stranded = false) {
   const from = nodePositions[deletion.from];
   const to = nodePositions[deletion.to];
   if (!from?.length || !to?.length) {
     return void 0;
   }
-  return route ? routedEdgeCurves(from, to, route) : computeEdgeCurves(
+  return route ? routedEdgeCurves(
+    from,
+    to,
+    route,
+    stranded ? strandSides(deletion) : void 0
+  ) : computeEdgeCurves(
     from,
     to,
-    deletion.from === deletion.to,
+    edgeJoinOf(deletion, stranded),
     0,
     0,
     axis,
@@ -723,6 +750,8 @@ function deletionEdges(graph) {
           edgeIndex,
           from: edge.from,
           to: edge.to,
+          ...edge.fromStrand ? { fromStrand: edge.fromStrand } : {},
+          ...edge.toStrand ? { toStrand: edge.toStrand } : {},
           refName,
           start,
           end,
@@ -1207,19 +1236,11 @@ function takeRoutes(positions, routes) {
 }
 
 // src/layout/mergeRuns.ts
-function ownStrand(id) {
-  return id.endsWith("-") ? "-" : "+";
-}
 function flip(strand) {
   return strand === "+" ? "-" : "+";
 }
-function sidesOf(edge) {
-  const from = (edge.fromStrand ?? ownStrand(edge.from)) === ownStrand(edge.from) ? "end" : "start";
-  const to = (edge.toStrand ?? ownStrand(edge.to)) === ownStrand(edge.to) ? "start" : "end";
-  return { from, to };
-}
 function mergeRuns(graph, alone = /* @__PURE__ */ new Set()) {
-  const sides = graph.edges.map(sidesOf);
+  const sides = graph.edges.map(strandSides);
   const at = /* @__PURE__ */ new Map();
   const attach = (id, side, ei) => {
     const key = `${id}|${side}`;
@@ -1589,24 +1610,33 @@ function loadGraph(text, name, opts = {}) {
   }
   return graph;
 }
+var COMPONENT_SEPARATION = 15;
 function engineRequest(graph, scaling, settings) {
   const anchored = graph.nodes.some(isBackbone);
+  const spaced = {
+    ...scaling,
+    opts: {
+      ...scaling.opts,
+      edgeLength: scaling.opts.edgeLength * (settings.spacing ?? 1)
+    }
+  };
   return {
     graph: {
-      nodes: anchored ? seededNodes(graph, scaling) : scaling.nodes,
+      nodes: anchored ? seededNodes(graph, spaced) : spaced.nodes,
       edges: graph.edges
     },
     options: {
       quality: settings.quality,
       linearLayout: settings.linearLayout,
-      ...scaling.opts,
+      ...spaced.opts,
+      componentSeparation: COMPONENT_SEPARATION * (settings.componentSeparation ?? 1),
       ...anchored ? { rotateComponents: false } : {}
     }
   };
 }
 function engineKey(graph, settings) {
   const anchored = graph.nodes.some(isBackbone);
-  return `${settings.quality}|${settings.linearLayout}|${settings.bubbleSpread}|${anchored}|${graph.referencePath ?? ""}`;
+  return `${settings.quality}|${settings.linearLayout}|${settings.bubbleSpread}|${settings.spacing ?? 1}|${settings.componentSeparation ?? 1}|${anchored}|${graph.referencePath ?? ""}`;
 }
 async function forceLayout(graph, settings, engine) {
   const spread = spreadFor(settings.bubbleSpread);
@@ -1654,6 +1684,7 @@ async function forceLayout(graph, settings, engine) {
     result: {
       ...result,
       nodePositions,
+      stranded: true,
       ...deletions.length ? { deletionRoutes, extent: layoutExtent(deletionRoutes) } : {}
     },
     duration
@@ -1888,10 +1919,10 @@ function labelOrder(nodePositions, nodeLengths) {
   return order;
 }
 var arcCache = /* @__PURE__ */ new WeakMap();
-function arcPlacements(nodePositions, deletions, axis, version2, routes) {
+function arcPlacements(nodePositions, deletions, axis, version2, routes, stranded) {
   const { scaleX, scaleY } = axis;
   const cached2 = arcCache.get(nodePositions);
-  if (cached2?.deletions === deletions && cached2.routes === routes && cached2.scaleX === scaleX && cached2.scaleY === scaleY && cached2.version === version2) {
+  if (cached2?.deletions === deletions && cached2.routes === routes && cached2.stranded === stranded && cached2.scaleX === scaleX && cached2.scaleY === scaleY && cached2.version === version2) {
     return cached2.arcs;
   }
   const arcs = [];
@@ -1900,7 +1931,8 @@ function arcPlacements(nodePositions, deletions, axis, version2, routes) {
       nodePositions,
       deletion,
       axis,
-      routes?.[deletion.edgeIndex]
+      routes?.[deletion.edgeIndex],
+      stranded
     );
     const apex = curves ? curveMidpoint(curves) : void 0;
     if (curves && apex) {
@@ -1917,6 +1949,7 @@ function arcPlacements(nodePositions, deletions, axis, version2, routes) {
   arcCache.set(nodePositions, {
     deletions,
     routes,
+    stranded,
     scaleX,
     scaleY,
     version: version2,
@@ -1929,6 +1962,7 @@ function sizeLabelCandidates({
   nodeLengths,
   deletions,
   deletionRoutes,
+  stranded = false,
   alleleDeletions,
   axis,
   translateX,
@@ -1945,7 +1979,8 @@ function sizeLabelCandidates({
     deletions,
     axis,
     version2,
-    deletionRoutes
+    deletionRoutes,
+    stranded
   )) {
     if (extent >= MIN_DELETION_LABEL_PX) {
       const text = deletionText(deletion.bp);
@@ -3374,7 +3409,7 @@ var COLOR_SCHEMES = [
   { value: "random", label: "Random" },
   { value: "rainbow", label: "Rainbow" },
   { value: "depth", label: "Depth" },
-  { value: "node-length", label: "Node Length" },
+  { value: "node-length", label: "Node length" },
   { value: "stable-rank", label: "Stable rank" },
   { value: "reference-position", label: "Reference position" },
   { value: "grey", label: "Grey" }
@@ -3465,10 +3500,10 @@ function brightenAbgr(c, factor) {
 
 // src/util/edgeCurves.ts
 var cache = /* @__PURE__ */ new WeakMap();
-function baseEdgeCurves(nodePositions, graph, axis, deletions, version2, routes) {
+function baseEdgeCurves(nodePositions, graph, axis, deletions, version2, routes, stranded = false) {
   const { scaleX, scaleY } = axis;
   const cached2 = cache.get(nodePositions);
-  if (cached2?.graph === graph && cached2.scaleX === scaleX && cached2.scaleY === scaleY && cached2.deletions === deletions && cached2.routes === routes && cached2.version === version2) {
+  if (cached2?.graph === graph && cached2.scaleX === scaleX && cached2.scaleY === scaleY && cached2.deletions === deletions && cached2.routes === routes && cached2.stranded === stranded && cached2.version === version2) {
     return cached2.curves;
   }
   const curves = /* @__PURE__ */ new Map();
@@ -3481,10 +3516,15 @@ function baseEdgeCurves(nodePositions, graph, axis, deletions, version2, routes)
       const route = bypassed && routes?.[ei];
       curves.set(
         ei,
-        route ? routedEdgeCurves(from, to, route) : computeEdgeCurves(
+        route ? routedEdgeCurves(
           from,
           to,
-          selfLinkOf(edge),
+          route,
+          stranded ? strandSides(edge) : void 0
+        ) : computeEdgeCurves(
+          from,
+          to,
+          edgeJoinOf(edge, stranded),
           0,
           0,
           axis,
@@ -3499,6 +3539,7 @@ function baseEdgeCurves(nodePositions, graph, axis, deletions, version2, routes)
     scaleY,
     deletions,
     routes,
+    stranded,
     version: version2,
     curves
   });
@@ -3523,6 +3564,7 @@ var ARROW_LENGTH_BASE_PX = 7;
 var ARROW_LENGTH_PER_EDGE_PX = 3;
 var ARROW_HALF_WIDTH_BASE_PX = 3;
 var ARROW_HALF_WIDTH_PER_EDGE_PX = 1.5;
+var MIN_LINK_HEADS = 3;
 var MIN_ARROW_FIT = 0.5;
 var MIN_ARROW_SCALE = 0.45;
 var ARROW_CURVE_STEPS = 12;
@@ -3587,12 +3629,17 @@ function arrowheadFor({
   toSegments
 }) {
   const length = ARROW_LENGTH_BASE_PX + ARROW_LENGTH_PER_EDGE_PX * edgeHalfWidth;
-  const n2 = backFromEnd(curves, scale, yToX, nodeHalfWidth + length);
+  const n2 = backFromEnd(
+    curves,
+    scale,
+    yToX,
+    nodeHalfWidth + MIN_LINK_HEADS * length
+  );
   const lengthPx = walkPx[n2 - 1];
+  const abutting = lengthPx < ABUTTING_PX;
   const inset = Math.min(nodeHalfWidth, lengthPx);
-  const room = lengthPx < ABUTTING_PX ? polylinePx(fromSegments, scale, yToX) : lengthPx - inset;
-  const fit = Math.min(1, room / length);
-  if (fit < MIN_ARROW_FIT) {
+  const fit = abutting ? Math.min(1, polylinePx(fromSegments, scale, yToX) / length) : 1;
+  if (abutting ? fit < MIN_ARROW_FIT : lengthPx < MIN_LINK_HEADS * length) {
     return void 0;
   }
   const tip = walkPointAt(n2, inset);
@@ -3619,6 +3666,13 @@ function polylinePx(segments, scale, yToX) {
   }
   return length * scale;
 }
+function leavesStart(edge, segments, first, stranded, yToX) {
+  if (stranded) {
+    return strandSides(edge).from === "start";
+  }
+  const gap = (p) => Math.hypot(p.x - first.x0, (p.y - first.y0) * yToX);
+  return gap(segments[0]) < gap(segments.at(-1));
+}
 function intoDirection(last, toSegments) {
   if (toSegments.length < 2) {
     return void 0;
@@ -3964,6 +4018,7 @@ function buildGeometry(options) {
     referenceRamp,
     deletions,
     deletionRoutes,
+    stranded,
     hiddenEdges,
     version: version2 = 0
   } = options;
@@ -3976,7 +4031,8 @@ function buildGeometry(options) {
     axis,
     deletions,
     version2,
-    deletionRoutes
+    deletionRoutes,
+    stranded
   );
   const nodeStrokes = [];
   const nodeStrokeRuns = /* @__PURE__ */ new Map();
@@ -4028,7 +4084,7 @@ function buildGeometry(options) {
       }
       const head = showArrows && arrowColor !== void 0 ? arrowheadFor({
         curves,
-        edgeHalfWidth: edgeThickness,
+        edgeHalfWidth: connectorThickness / 2,
         nodeHalfWidth: intoHalfWidth,
         scale,
         yToX,
@@ -4048,7 +4104,13 @@ function buildGeometry(options) {
       const width = fromNode ? nodeWidthPx(fromNode, contigThickness, nodeWidth2, depthNorm) : contigThickness;
       const laneWidth = Math.max(width / laneWalks.length, MIN_WALK_LANE_PX);
       const normals = pointNormalsOf(fromSegments, yToX);
-      const { nx, ny } = (edge.fromStrand === "-" ? normals[0] : normals.at(-1)) ?? {
+      const { nx, ny } = (leavesStart(
+        edge,
+        fromSegments,
+        baseCurves[0],
+        stranded,
+        yToX
+      ) ? normals[0] : normals.at(-1)) ?? {
         nx: 0,
         ny: 0
       };
@@ -4932,6 +4994,7 @@ function layoutLabels(m) {
     nodeLengths: m.nodeLengths,
     deletions: m.showDeletionEdges ? m.deletions : [],
     deletionRoutes: m.deletionRoutes,
+    stranded: m.stranded,
     alleleDeletions: m.alleleDeletions,
     axis: m.axisScale,
     translateX,
@@ -5609,6 +5672,154 @@ function stripGeneGaps(frame, rowGenes, gaps) {
   return frame.boxesGenes ? gaps : { untracked: 0, unread: 0, ...gaps, crowded: true };
 }
 
+// src/reference.ts
+var WELL_KNOWN_SAMPLES = /* @__PURE__ */ new Map([
+  ["hg38", "GRCh38"],
+  ["hg19", "GRCh37"],
+  ["hs1", "CHM13"],
+  ["t2t-chm13", "CHM13"],
+  ["chm13v2", "CHM13"]
+]);
+function wellKnownSample(assemblyName) {
+  return WELL_KNOWN_SAMPLES.get(assemblyName.toLowerCase());
+}
+function sampleOf2(refName) {
+  const sample = refName.includes("#") ? panSNSample(refName) : void 0;
+  return sample === void 0 || isGenericSample(sample) ? void 0 : sample;
+}
+function haplotypeOf(refName) {
+  return panSNHaplotype(refName) ?? panSNSample(refName);
+}
+function graphHaplotypes(graph) {
+  const refNames = new Set((graph.anchorPaths ?? []).map((p) => p.name));
+  for (const node of graph.nodes) {
+    if (node.stable) {
+      refNames.add(node.stable.refName);
+    }
+  }
+  const bySample = /* @__PURE__ */ new Map();
+  for (const refName of refNames) {
+    const sample = sampleOf2(refName);
+    if (sample !== void 0) {
+      const haplotypes = bySample.get(sample) ?? bySample.set(sample, /* @__PURE__ */ new Set()).get(sample);
+      haplotypes.add(haplotypeOf(refName));
+    }
+  }
+  return bySample;
+}
+function backboneFrom(contigs, haplotypes) {
+  const samples = new Set(contigs.map((c) => sampleOf2(c.refName)));
+  const [sample] = samples;
+  if (samples.size !== 1 || sample === void 0) {
+    return { contigs, prefixes: [], named: false };
+  }
+  const own = new Set(contigs.map((c) => haplotypeOf(c.refName)));
+  const unique = [...haplotypes.get(sample) ?? []].every((h) => own.has(h));
+  const shared = new Set(contigs.map((c) => panSNHaplotype(c.refName)));
+  const [haplotype] = shared;
+  return {
+    contigs,
+    prefixes: [
+      ...unique ? [sample] : [],
+      ...shared.size === 1 && haplotype ? [haplotype] : []
+    ],
+    named: true
+  };
+}
+function graphBackbone(graph) {
+  const spans = /* @__PURE__ */ new Map();
+  for (const node of graph.nodes) {
+    if (isBackbone(node)) {
+      const { refName, start } = node.stable;
+      const end = start + node.length;
+      const span = spans.get(refName);
+      if (span) {
+        span.start = Math.min(span.start, start);
+        span.end = Math.max(span.end, end);
+      } else {
+        spans.set(refName, {
+          refName,
+          contig: panSNContig(refName),
+          start,
+          end
+        });
+      }
+    }
+  }
+  const contigs = [...spans.values()];
+  return contigs.length ? backboneFrom(contigs, graphHaplotypes(graph)) : void 0;
+}
+function referenceLabel(graph, region) {
+  const backbone = graphBackbone(graph);
+  const contig = region ? panSNContig(region.refName) : backbone?.contigs.length === 1 ? backbone.contigs[0].contig : void 0;
+  const sample = backbone?.named ? panSNSample(backbone.contigs[0].refName) : void 0;
+  return contig && (sample ? `${sample} ${contig}` : contig);
+}
+function backboneAssembly(backbone, assemblies) {
+  const names = (a) => [a.name, ...a.aliases ?? []];
+  const naming = (prefix) => (a) => names(a).some((n2) => n2.toLowerCase() === prefix.toLowerCase());
+  const prefixes = [...backbone?.prefixes ?? []].reverse();
+  const sample = backbone?.prefixes.find((p) => !p.includes("#"))?.toLowerCase();
+  for (const prefix of prefixes) {
+    const assembly = assemblies.find(naming(prefix));
+    if (assembly) {
+      return assembly;
+    }
+  }
+  return sample === void 0 ? void 0 : assemblies.find(
+    (a) => names(a).some((n2) => wellKnownSample(n2)?.toLowerCase() === sample)
+  );
+}
+function assemblyWalk(graph, assembly) {
+  const haplotypes = graphHaplotypes(graph);
+  return graph.anchorPaths?.find(
+    (walk) => backboneAssembly(
+      backboneFrom(
+        [
+          {
+            refName: walk.name,
+            contig: panSNContig(walk.name),
+            start: walk.start,
+            end: walk.start + walk.length
+          }
+        ],
+        haplotypes
+      ),
+      [assembly]
+    )
+  );
+}
+function contigNames(contig) {
+  const bare = contig.replace(/^chr/i, "");
+  const forms = !bare ? [] : /^(M|MT)$/i.test(bare) ? ["M", "MT"] : [bare];
+  return [.../* @__PURE__ */ new Set([contig, ...forms.flatMap((f) => [f, `chr${f}`])])];
+}
+function refNameBinding(refNames, aliases = {}) {
+  const exact = new Set(refNames);
+  const byName = /* @__PURE__ */ new Map();
+  for (const refName of exact) {
+    const contig = panSNContig(refName);
+    const alias = aliases[contig];
+    for (const name of /* @__PURE__ */ new Set([
+      ...contigNames(contig),
+      ...alias ? [alias] : []
+    ])) {
+      byName.set(name, byName.has(name) ? void 0 : refName);
+    }
+  }
+  return (name) => exact.has(name) ? name : byName.get(name);
+}
+function featuresOnBackbone(features, backbone, aliases) {
+  const bind = refNameBinding(
+    backbone.contigs.map((c) => c.refName),
+    aliases
+  );
+  return features.flatMap((f) => {
+    const refName = bind(f.refName);
+    return refName === void 0 ? [] : [refName === f.refName ? f : { ...f, refName }];
+  });
+}
+
 // src/renderer/svgCanvas.ts
 var n = (v) => +v.toFixed(1);
 function paint(css) {
@@ -5722,7 +5933,7 @@ function svgCanvas(width, height) {
 }
 
 // src/version.ts
-var version = "5.0.0";
+var version = "5.1.0";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {
@@ -5845,9 +6056,10 @@ function figureSvg(graph, layout, o = {}) {
     ])
   );
   const labelOf2 = (name) => labels.get(name) ?? name;
+  const referenceName = o.referenceName ?? referenceLabel(graph, region);
   const reference = lift?.referenceDomain && {
     ...lift.referenceDomain,
-    name: region?.refName
+    name: referenceName
   };
   const contigThickness = o.contigThickness ?? 6;
   const nodeWidth2 = o.nodeWidth ?? "depth";
@@ -5953,6 +6165,7 @@ function figureSvg(graph, layout, o = {}) {
         referenceRamp,
         deletions: new Map(deletions.map((d) => [d.edgeIndex, d.bypassed])),
         deletionRoutes: layout.deletionRoutes,
+        stranded: layout.stranded,
         hiddenEdges: new Set(
           o.showDeletionEdges ? [] : deletions.map((d) => d.edgeIndex)
         )
@@ -6036,10 +6249,10 @@ function figureSvg(graph, layout, o = {}) {
           x,
           2,
           encodingStops({ field: "reference", scheme: "rainbow" }),
-          "Reference position",
+          referenceName ? `${referenceName} position` : "Reference position",
           "",
           rangeText(
-            region?.refName,
+            referenceName,
             referenceRamp.start,
             referenceRamp.start + referenceRamp.span
           )
@@ -6198,14 +6411,22 @@ function genesFromGff3Lines(lines) {
     const start = top?.start ?? Math.min(...rows2.map((r) => r.start));
     const end = top?.end ?? Math.max(...rows2.map((r) => r.end));
     const a = first.attrs;
-    const exons = rows2.filter((r) => r.type === "exon").map((r) => ({ start: r.start, end: r.end }));
+    const spans = (type) => rows2.filter((r) => r.type === type).map((r) => ({ start: r.start, end: r.end }));
+    const exons = spans("exon");
+    const coding = spans("CDS");
+    const transcribed = rows2.some(
+      (r) => r !== top && r.type !== "exon" && r.type !== "CDS"
+    );
     genes.push({
       name: a.get("Name") ?? a.get("gene_name") ?? a.get("gene") ?? a.get("gene_id") ?? key.split("	")[1],
       refName: first.refName,
       start,
       end,
       strand: first.strand,
-      exons: exons.length ? mergedIntervals(exons) : [{ start, end }]
+      // A range read holds only the rows over its window, so a gene with
+      // transcripts but no exon or CDS there is intronic in it. Only a gene
+      // with no transcripts, as a bacterium's gene and CDS, is one exon.
+      exons: exons.length ? mergedIntervals(exons) : transcribed ? mergedIntervals(coding) : [{ start, end }]
     });
   }
   return genes;
@@ -6261,148 +6482,6 @@ function genesFromText(text) {
   return /^\d+$/.test(cols[1] ?? "") && /^\d+$/.test(cols[2] ?? "") ? genesFromBed(text) : genesFromGff3Lines(text.split(/\r?\n/));
 }
 
-// src/reference.ts
-var WELL_KNOWN_SAMPLES = /* @__PURE__ */ new Map([
-  ["hg38", "GRCh38"],
-  ["hg19", "GRCh37"],
-  ["hs1", "CHM13"],
-  ["t2t-chm13", "CHM13"],
-  ["chm13v2", "CHM13"]
-]);
-function wellKnownSample(assemblyName) {
-  return WELL_KNOWN_SAMPLES.get(assemblyName.toLowerCase());
-}
-function sampleOf2(refName) {
-  const sample = refName.includes("#") ? panSNSample(refName) : void 0;
-  return sample === void 0 || isGenericSample(sample) ? void 0 : sample;
-}
-function haplotypeOf(refName) {
-  return panSNHaplotype(refName) ?? panSNSample(refName);
-}
-function graphHaplotypes(graph) {
-  const refNames = new Set((graph.anchorPaths ?? []).map((p) => p.name));
-  for (const node of graph.nodes) {
-    if (node.stable) {
-      refNames.add(node.stable.refName);
-    }
-  }
-  const bySample = /* @__PURE__ */ new Map();
-  for (const refName of refNames) {
-    const sample = sampleOf2(refName);
-    if (sample !== void 0) {
-      const haplotypes = bySample.get(sample) ?? bySample.set(sample, /* @__PURE__ */ new Set()).get(sample);
-      haplotypes.add(haplotypeOf(refName));
-    }
-  }
-  return bySample;
-}
-function backboneFrom(contigs, haplotypes) {
-  const samples = new Set(contigs.map((c) => sampleOf2(c.refName)));
-  const [sample] = samples;
-  if (samples.size !== 1 || sample === void 0) {
-    return { contigs, prefixes: [], named: false };
-  }
-  const own = new Set(contigs.map((c) => haplotypeOf(c.refName)));
-  const unique = [...haplotypes.get(sample) ?? []].every((h) => own.has(h));
-  const shared = new Set(contigs.map((c) => panSNHaplotype(c.refName)));
-  const [haplotype] = shared;
-  return {
-    contigs,
-    prefixes: [
-      ...unique ? [sample] : [],
-      ...shared.size === 1 && haplotype ? [haplotype] : []
-    ],
-    named: true
-  };
-}
-function graphBackbone(graph) {
-  const spans = /* @__PURE__ */ new Map();
-  for (const node of graph.nodes) {
-    if (isBackbone(node)) {
-      const { refName, start } = node.stable;
-      const end = start + node.length;
-      const span = spans.get(refName);
-      if (span) {
-        span.start = Math.min(span.start, start);
-        span.end = Math.max(span.end, end);
-      } else {
-        spans.set(refName, {
-          refName,
-          contig: panSNContig(refName),
-          start,
-          end
-        });
-      }
-    }
-  }
-  const contigs = [...spans.values()];
-  return contigs.length ? backboneFrom(contigs, graphHaplotypes(graph)) : void 0;
-}
-function backboneAssembly(backbone, assemblies) {
-  const names = (a) => [a.name, ...a.aliases ?? []];
-  const naming = (prefix) => (a) => names(a).some((n2) => n2.toLowerCase() === prefix.toLowerCase());
-  const prefixes = [...backbone?.prefixes ?? []].reverse();
-  const sample = backbone?.prefixes.find((p) => !p.includes("#"))?.toLowerCase();
-  for (const prefix of prefixes) {
-    const assembly = assemblies.find(naming(prefix));
-    if (assembly) {
-      return assembly;
-    }
-  }
-  return sample === void 0 ? void 0 : assemblies.find(
-    (a) => names(a).some((n2) => wellKnownSample(n2)?.toLowerCase() === sample)
-  );
-}
-function assemblyWalk(graph, assembly) {
-  const haplotypes = graphHaplotypes(graph);
-  return graph.anchorPaths?.find(
-    (walk) => backboneAssembly(
-      backboneFrom(
-        [
-          {
-            refName: walk.name,
-            contig: panSNContig(walk.name),
-            start: walk.start,
-            end: walk.start + walk.length
-          }
-        ],
-        haplotypes
-      ),
-      [assembly]
-    )
-  );
-}
-function contigNames(contig) {
-  const bare = contig.replace(/^chr/i, "");
-  const forms = !bare ? [] : /^(M|MT)$/i.test(bare) ? ["M", "MT"] : [bare];
-  return [.../* @__PURE__ */ new Set([contig, ...forms.flatMap((f) => [f, `chr${f}`])])];
-}
-function refNameBinding(refNames, aliases = {}) {
-  const exact = new Set(refNames);
-  const byName = /* @__PURE__ */ new Map();
-  for (const refName of exact) {
-    const contig = panSNContig(refName);
-    const alias = aliases[contig];
-    for (const name of /* @__PURE__ */ new Set([
-      ...contigNames(contig),
-      ...alias ? [alias] : []
-    ])) {
-      byName.set(name, byName.has(name) ? void 0 : refName);
-    }
-  }
-  return (name) => exact.has(name) ? name : byName.get(name);
-}
-function featuresOnBackbone(features, backbone, aliases) {
-  const bind = refNameBinding(
-    backbone.contigs.map((c) => c.refName),
-    aliases
-  );
-  return features.flatMap((f) => {
-    const refName = bind(f.refName);
-    return refName === void 0 ? [] : [refName === f.refName ? f : { ...f, refName }];
-  });
-}
-
 // src/gbzJoin.ts
 var UNKNOWN_SAMPLE = "unknown";
 function parseWalk(line) {
@@ -6796,6 +6875,14 @@ export {
   walkMarksTree,
   walkStripLabelsTree,
   stripGeneGaps,
+  WELL_KNOWN_SAMPLES,
+  wellKnownSample,
+  graphBackbone,
+  referenceLabel,
+  backboneAssembly,
+  assemblyWalk,
+  refNameBinding,
+  featuresOnBackbone,
   svgCanvas,
   version,
   axisScaleOf,
@@ -6809,13 +6896,6 @@ export {
   mergeOverlappingByName,
   genesFromBed,
   genesFromText,
-  WELL_KNOWN_SAMPLES,
-  wellKnownSample,
-  graphBackbone,
-  backboneAssembly,
-  assemblyWalk,
-  refNameBinding,
-  featuresOnBackbone,
   haplotypeWanted,
   referenceSamplesOf,
   resolveReferenceSample,

package/dist/cli/figure.js

@@ -21,7 +21,7 @@ import {
   placeRowGenes,
   refNameBinding,
   walkRows
-} from "../chunks/chunk-WWH65AAB.js";
+} from "../chunks/chunk-Y2MDXT4O.js";
 
 // src/cli/figure.ts
 import { access, open, readFile, writeFile } from "node:fs/promises";
@@ -171,7 +171,9 @@ async function renderSpec(spec, base) {
     {
       quality: spec.quality ?? 2,
       linearLayout: false,
-      bubbleSpread: spec.bubbleSpread ?? "auto"
+      bubbleSpread: spec.bubbleSpread ?? "auto",
+      spacing: spec.spacing,
+      componentSeparation: spec.componentSeparation
     },
     engine
   )).result;

package/dist/index.js

@@ -99,6 +99,7 @@ import {
   rangeText,
   readoutPlacement,
   refNameBinding,
+  referenceLabel,
   referenceOrder,
   referencePathQuery,
   referenceSamplesOf,
@@ -138,7 +139,7 @@ import {
   wellKnownSample,
   yToXOf,
   zoomAbout
-} from "./chunks/chunk-WWH65AAB.js";
+} from "./chunks/chunk-Y2MDXT4O.js";
 
 // src/index.ts
 import { getDpr } from "@jbrowse/render-core/canvas2dUtils";
@@ -255,7 +256,7 @@ var SpatialIndex = class {
   }
 };
 var EdgeSpatialIndex = class {
-  constructor(nodePositions, graph, drawPaths, axis, cellSize, deletions, version2 = 0, routes2) {
+  constructor(nodePositions, graph, drawPaths, axis, cellSize, deletions, version2 = 0, routes2, stranded = false) {
     this.cells = /* @__PURE__ */ new Map();
     this.edgeCurves = baseEdgeCurves(
       nodePositions,
@@ -263,7 +264,8 @@ var EdgeSpatialIndex = class {
       axis,
       deletions,
       version2,
-      routes2
+      routes2,
+      stranded
     );
     const boxes = [];
     let extentX = 0;
@@ -386,9 +388,9 @@ function getSpatialIndex(nodePositions, version2) {
   return index;
 }
 var edgeCache = /* @__PURE__ */ new WeakMap();
-function getEdgeSpatialIndex(nodePositions, graph, drawPaths, axis, version2, deletions, routes2) {
+function getEdgeSpatialIndex(nodePositions, graph, drawPaths, axis, version2, deletions, routes2, stranded = false) {
   const cached = edgeCache.get(nodePositions);
-  if (cached?.graph === graph && cached.drawPaths === drawPaths && cached.scaleX === axis.scaleX && cached.scaleY === axis.scaleY && cached.version === version2 && cached.deletions === deletions && cached.routes === routes2) {
+  if (cached?.graph === graph && cached.drawPaths === drawPaths && cached.scaleX === axis.scaleX && cached.scaleY === axis.scaleY && cached.version === version2 && cached.deletions === deletions && cached.routes === routes2 && cached.stranded === stranded) {
     return cached.index;
   }
   const index = new EdgeSpatialIndex(
@@ -399,7 +401,8 @@ function getEdgeSpatialIndex(nodePositions, graph, drawPaths, axis, version2, de
     void 0,
     deletions,
     version2,
-    routes2
+    routes2,
+    stranded
   );
   edgeCache.set(nodePositions, {
     graph,
@@ -409,7 +412,8 @@ function getEdgeSpatialIndex(nodePositions, graph, drawPaths, axis, version2, de
     version: version2,
     index,
     deletions,
-    routes: routes2
+    routes: routes2,
+    stranded
   });
   return index;
 }
@@ -439,7 +443,7 @@ function findHoveredNode(nodePositions, graphX, graphY, axis, version2 = 0, ink)
   }
   return hovered;
 }
-function findHoveredEdge(nodePositions, graph, graphX, graphY, axis, drawPaths, version2 = 0, deletions, hiddenEdges, deletionRoutes) {
+function findHoveredEdge(nodePositions, graph, graphX, graphY, axis, drawPaths, version2 = 0, deletions, hiddenEdges, deletionRoutes, stranded = false) {
   const yToX = yToXOf(axis);
   const edgeThreshold = 10 / axis.scaleX;
   const edgeIndex = getEdgeSpatialIndex(
@@ -449,7 +453,8 @@ function findHoveredEdge(nodePositions, graph, graphX, graphY, axis, drawPaths,
     axis,
     version2,
     deletions,
-    deletionRoutes
+    deletionRoutes,
+    stranded
   );
   const candidates = edgeIndex.query(
     graphX,
@@ -1899,6 +1904,7 @@ export {
   refNameBinding,
   referenceBoxes,
   referenceKnots,
+  referenceLabel,
   referenceNodes,
   referencePathQuery,
   referenceSamplesOf,

package/dist/types/cli/figure.d.ts

@@ -11,6 +11,8 @@ export interface FigureSpec extends Omit<FigureOptions, 'walks' | 'region' | 'ge
     layout?: LayoutModeValue;
     quality?: number;
     bubbleSpread?: BubbleSpread;
+    spacing?: number;
+    componentSeparation?: number;
     walks?: (string | WalkLayer)[];
     walkStrip?: boolean;
     walkRowSamples?: string[];

package/dist/types/colorSchemes.d.ts

@@ -16,7 +16,7 @@ export declare const COLOR_SCHEMES: readonly [{
     readonly label: "Depth";
 }, {
     readonly value: "node-length";
-    readonly label: "Node Length";
+    readonly label: "Node length";
 }, {
     readonly value: "stable-rank";
     readonly label: "Stable rank";

package/dist/types/deletionEdges.d.ts

@@ -4,6 +4,8 @@ export interface DeletionEdge {
     edgeIndex: number;
     from: string;
     to: string;
+    fromStrand?: '+' | '-';
+    toStrand?: '+' | '-';
     refName: string;
     start: number;
     end: number;
@@ -20,5 +22,5 @@ export declare function bypassedPoints(nodePositions: Record<string, {
 export declare function deletionArcCurves(nodePositions: Record<string, {
     x: number;
     y: number;
-}[]>, deletion: DeletionEdge, axis: AxisScale, route?: NodeSegment[]): import("./util/geometry.js").BezierCurve[] | undefined;
+}[]>, deletion: DeletionEdge, axis: AxisScale, route?: NodeSegment[], stranded?: boolean): import("./util/geometry.js").BezierCurve[] | undefined;
 export declare function deletionEdges(graph: Graph): DeletionEdge[];

package/dist/types/figure.d.ts

@@ -21,6 +21,7 @@ export interface FigureOptions {
         start: number;
         end: number;
     };
+    referenceName?: string;
     colorDomain?: {
         start: number;
         end: number;

package/dist/types/graphLabels.d.ts

@@ -25,6 +25,7 @@ interface SizeLabelArgs {
     nodeLengths: Map<string, number>;
     deletions: DeletionEdge[];
     deletionRoutes?: DeletionRoutes;
+    stranded?: boolean;
     alleleDeletions?: AlleleDeletion[];
     axis: AxisScale;
     translateX: number;
@@ -37,7 +38,7 @@ export interface SizeLabelCandidate {
     label: GraphLabel;
     box: Box;
 }
-export declare function sizeLabelCandidates({ nodePositions, nodeLengths, deletions, deletionRoutes, alleleDeletions, axis, translateX, translateY, width, height, version, }: SizeLabelArgs): {
+export declare function sizeLabelCandidates({ nodePositions, nodeLengths, deletions, deletionRoutes, stranded, alleleDeletions, axis, translateX, translateY, width, height, version, }: SizeLabelArgs): {
     deletions: SizeLabelCandidate[];
     nodes: SizeLabelCandidate[];
 };

package/dist/types/index.d.ts

@@ -70,7 +70,7 @@ export type { LabelLayout, LabelLayoutSource } from './labelLayout.js';
 export { formatBp } from './graphLabels.js';
 export { genePins } from './genes/genePins.js';
 export type { GeneModel, GenePin } from './genes/genePins.js';
-export { WELL_KNOWN_SAMPLES, assemblyWalk, backboneAssembly, featuresOnBackbone, graphBackbone, refNameBinding, wellKnownSample, } from './reference.js';
+export { WELL_KNOWN_SAMPLES, assemblyWalk, backboneAssembly, featuresOnBackbone, graphBackbone, refNameBinding, referenceLabel, wellKnownSample, } from './reference.js';
 export type { AssemblyNames, Backbone, BackboneContig } from './reference.js';
 export { LABEL_CHAR_PX, LABEL_PAD, LABEL_PX } from './overlayLabels.js';
 export type { Graph, GraphEdge, GraphNode, LayoutResult, NodeSegment, } from './types.js';

package/dist/types/labelLayout.d.ts

@@ -35,6 +35,7 @@ export interface LabelLayoutSource {
     showDeletionEdges: boolean;
     deletions: DeletionEdge[];
     deletionRoutes?: DeletionRoutes;
+    stranded?: boolean;
     alleleDeletions: AlleleDeletion[];
     positionsVersion: number;
 }

package/dist/types/pipeline.d.ts

@@ -27,6 +27,8 @@ export interface EngineSettings {
     quality: number;
     linearLayout: boolean;
     bubbleSpread: BubbleSpread;
+    spacing?: number;
+    componentSeparation?: number;
 }
 export declare function engineRequest(graph: Graph, scaling: LayoutScaling, settings: EngineSettings): EngineRequest;
 export declare function engineKey(graph: Graph, settings: EngineSettings): string;
@@ -42,6 +44,7 @@ export declare function forceLayout(graph: Graph, settings: EngineSettings, engi
         nodePositions: {
             [x: string]: NodeSegment[];
         };
+        stranded: boolean;
         rowLabels?: import("./types.js").RowLabel[];
         sampleRows?: string[];
         alleleDeletions?: import("./types.js").AlleleDeletion[];

package/dist/types/reference.d.ts

@@ -17,6 +17,9 @@ export interface AssemblyNames {
 export declare const WELL_KNOWN_SAMPLES: ReadonlyMap<string, string>;
 export declare function wellKnownSample(assemblyName: string): string | undefined;
 export declare function graphBackbone(graph: Graph): Backbone | undefined;
+export declare function referenceLabel(graph: Graph, region?: {
+    refName: string;
+}): string | undefined;
 export declare function backboneAssembly<T extends AssemblyNames>(backbone: Backbone | undefined, assemblies: T[]): T | undefined;
 export declare function assemblyWalk(graph: Graph, assembly: AssemblyNames): PathOrigin | undefined;
 export declare function contigNames(contig: string): string[];

package/dist/types/renderer/GeometryBuilder.d.ts

@@ -29,6 +29,7 @@ export interface BuildOptions {
     referenceRamp?: ReferenceRamp;
     deletions?: Map<number, string[]>;
     deletionRoutes?: DeletionRoutes;
+    stranded?: boolean;
     hiddenEdges?: ReadonlySet<number>;
     version?: number;
 }

package/dist/types/types.d.ts

@@ -74,4 +74,5 @@ export interface LayoutResult {
     };
     tubeMap?: TubeMapDrawing;
     deletionRoutes?: Record<number, NodeSegment[]>;
+    stranded?: boolean;
 }

package/dist/types/util/SpatialIndex.d.ts

@@ -19,7 +19,7 @@ export declare class EdgeSpatialIndex {
     private cellSize;
     private cells;
     private edgeCurves;
-    constructor(nodePositions: Record<string, NodeSegment[]>, graph: Graph, drawPaths: boolean, axis: AxisScale, cellSize?: number | CellSize, deletions?: Map<number, string[]>, version?: number, routes?: DeletionRoutes);
+    constructor(nodePositions: Record<string, NodeSegment[]>, graph: Graph, drawPaths: boolean, axis: AxisScale, cellSize?: number | CellSize, deletions?: Map<number, string[]>, version?: number, routes?: DeletionRoutes, stranded?: boolean);
     getCurves(ei: number): import("./geometry.js").BezierCurve[] | undefined;
     query(x: number, y: number, radiusX: number, radiusY?: number): number[];
 }

package/dist/types/util/edgeCurves.d.ts

@@ -2,4 +2,4 @@ import type { DeletionRoutes } from '../layout/deletionRoutes.js';
 import type { Graph, NodeSegment } from '../types.js';
 import type { AxisScale, BezierCurve } from './geometry.js';
 export type EdgeCurves = Map<number, BezierCurve[]>;
-export declare function baseEdgeCurves(nodePositions: Record<string, NodeSegment[]>, graph: Graph, axis: AxisScale, deletions: Map<number, string[]> | undefined, version: number, routes?: DeletionRoutes): EdgeCurves;
+export declare function baseEdgeCurves(nodePositions: Record<string, NodeSegment[]>, graph: Graph, axis: AxisScale, deletions: Map<number, string[]> | undefined, version: number, routes?: DeletionRoutes, stranded?: boolean): EdgeCurves;

package/dist/types/util/geometry.d.ts

@@ -28,6 +28,12 @@ export declare function curveBounds(curves: BezierCurve[]): {
 export declare function dashCurves(curves: BezierCurve[], dashWorld: number): BezierCurve[][];
 export declare function translateCurves(curves: BezierCurve[], dx: number, dy: number): BezierCurve[];
 type Side = 'start' | 'end';
+export interface EdgeSides {
+    from: Side;
+    to: Side;
+}
+export declare function ownStrand(id: string): "+" | "-";
+export declare function strandSides(edge: GraphEdge): EdgeSides;
 export declare function bowAround(p1x: number, p1y: number, p2x: number, p2y: number, toward: NodeSegment[], maxBow?: number): number;
 export interface AxisScale {
     scaleX: number;
@@ -42,6 +48,8 @@ export declare function pathRibbonOffsets(fromSegments: NodeSegment[], toSegment
 }[];
 export type SelfLink = boolean | Side;
 export declare function selfLinkOf(edge: GraphEdge): SelfLink;
-export declare function computeEdgeCurves(fromSegments: NodeSegment[], toSegments: NodeSegment[], selfLink: SelfLink, offsetX: number, offsetY: number, axis: AxisScale, bypassed?: NodeSegment[], maxBowIn?: number): BezierCurve[];
-export declare function routedEdgeCurves(fromSegments: NodeSegment[], toSegments: NodeSegment[], route: NodeSegment[]): BezierCurve[];
+export type EdgeJoin = SelfLink | EdgeSides;
+export declare function edgeJoinOf(edge: GraphEdge, stranded?: boolean): EdgeJoin;
+export declare function computeEdgeCurves(fromSegments: NodeSegment[], toSegments: NodeSegment[], join: EdgeJoin, offsetX: number, offsetY: number, axis: AxisScale, bypassed?: NodeSegment[], maxBowIn?: number): BezierCurve[];
+export declare function routedEdgeCurves(fromSegments: NodeSegment[], toSegments: NodeSegment[], route: NodeSegment[], sides?: EdgeSides): BezierCurve[];
 export {};

package/dist/types/util/hitDetection.d.ts

@@ -8,4 +8,4 @@ export interface NodeInk {
     maxHalfWidthPx: number;
 }
 export declare function findHoveredNode(nodePositions: Record<string, NodeSegment[]>, graphX: number, graphY: number, axis: AxisScale, version?: number, ink?: NodeInk): string | null;
-export declare function findHoveredEdge(nodePositions: Record<string, NodeSegment[]>, graph: Graph, graphX: number, graphY: number, axis: AxisScale, drawPaths: boolean, version?: number, deletions?: Map<number, string[]>, hiddenEdges?: ReadonlySet<number>, deletionRoutes?: DeletionRoutes): number | null;
+export declare function findHoveredEdge(nodePositions: Record<string, NodeSegment[]>, graph: Graph, graphX: number, graphY: number, axis: AxisScale, drawPaths: boolean, version?: number, deletions?: Map<number, string[]>, hiddenEdges?: ReadonlySet<number>, deletionRoutes?: DeletionRoutes, stranded?: boolean): number | null;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "5.0.0";
+export declare const version = "5.1.0";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "5.0.0",
+  "version": "5.1.0",
   "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": {