@jbrowse/bandage-core 4.0.24 → 4.0.25

package/dist/cli/figure.js

@@ -1,38 +1,27 @@
 #!/usr/bin/env node
 import {
-  cutWindowGFA,
+  HPRC_GBZ,
+  cutGbzRegion,
+  featuresOnBackbone,
   figureSvg,
   forceLayout,
-  haplotypeWanted,
+  genesFromBed,
+  genesFromGff3Lines,
+  genesFromText,
+  graphBackbone,
   layoutModeByValue,
   loadBandage,
   loadGraph,
-  referencePathQuery,
-  referenceSamplesOf,
-  resolveReferenceSample
-} from "../chunks/chunk-4AOHEU76.js";
+  openGbz,
+  parseRegion
+} from "../chunks/chunk-B5ZHLU4N.js";
 
 // src/cli/figure.ts
 import { open, readFile, writeFile } from "node:fs/promises";
 import path from "node:path";
 import { parseArgs } from "node:util";
 import { gunzipSync } from "node:zlib";
-import { GBZBase } from "@gmod/gbz-base";
-var HPRC = {
-  db: "https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.gbz.db",
-  index: "https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.haplotype-index.anchored.db"
-};
-var WALK_LIMIT = 1e5;
-function parseRegion(text) {
-  const m = /^\s*([^:\s]+):([\d,]+)-([\d,]+)\s*$/.exec(text);
-  if (!m) {
-    throw new Error(
-      `"${text}" is not a region like chr6:160,614,798-160,647,758`
-    );
-  }
-  const n = (s) => Number(s.replaceAll(",", ""));
-  return { refName: m[1], start: n(m[2]), end: n(m[3]) };
-}
+import { TabixIndexedFile } from "@gmod/tabix";
 var isUrl = (s) => /^https?:\/\//.test(s);
 function byteSource(location) {
   if (isUrl(location)) {
@@ -64,36 +53,40 @@ function byteSource(location) {
     }
   };
 }
-async function gfaText(location) {
+async function text(location) {
   const bytes = isUrl(location) ? new Uint8Array(await (await fetch(location)).arrayBuffer()) : await readFile(location);
   const gzipped = bytes[0] === 31 && bytes[1] === 139;
   return new TextDecoder().decode(gzipped ? gunzipSync(bytes) : bytes);
 }
-async function cutGbz(gbz) {
-  const { db, index } = gbz.db === "hprc" ? HPRC : gbz;
-  const base = await GBZBase.open(
-    byteSource(db),
-    index ? { haplotypeIndex: byteSource(index) } : {}
+async function readGenes(genes, graph, resolve) {
+  const backbone = graphBackbone(graph);
+  if (!backbone) {
+    return [];
+  }
+  const file = resolve(genes.file);
+  const format = genes.format ?? (/\.bed(\.gz)?$/i.test(genes.file) ? "bed" : "gff3");
+  if (!genes.index) {
+    return featuresOnBackbone(genesFromText(await text(file)), backbone);
+  }
+  const index = resolve(genes.index);
+  const csi = index.endsWith(".csi");
+  const tabix = new TabixIndexedFile(
+    isUrl(file) ? { url: file, ...csi ? { csiUrl: index } : { tbiUrl: index } } : { path: file, ...csi ? { csiPath: index } : { tbiPath: index } }
   );
-  const samples = await referenceSamplesOf(base);
-  const sample = resolveReferenceSample({
-    configured: "",
-    anchorPrefix: gbz.referenceSample ?? samples[0] ?? "",
-    referenceSamples: samples
-  });
-  const region = parseRegion(gbz.region);
-  const query = await referencePathQuery(base, sample, region.refName);
-  if (!query) {
-    throw new Error(`${sample} has no indexed path named ${region.refName}`);
+  const indexed = new Set(await tabix.getReferenceSequenceNames());
+  const lines = [];
+  for (const contig of backbone.contigs) {
+    const refName = [contig.contig, contig.refName].find((n) => indexed.has(n));
+    if (refName !== void 0) {
+      await tabix.getLines(refName, contig.start, contig.end, {
+        lineCallback: (line) => lines.push(line)
+      });
+    }
   }
-  const wanted = gbz.haplotypes?.length ? gbz.haplotypes : void 0;
-  const text = await cutWindowGFA(base, query, region.start, region.end, {
-    context: 1e3,
-    snarls: "contained",
-    limit: WALK_LIMIT,
-    ...wanted ? { keep: (name) => haplotypeWanted(name, wanted) } : {}
-  });
-  return { text, region, name: `${sample} ${gbz.region}` };
+  return featuresOnBackbone(
+    format === "gff3" ? genesFromGff3Lines(lines) : genesFromBed(lines.join("\n")),
+    backbone
+  );
 }
 var engine = async (request) => {
   const bandage = await loadBandage();
@@ -101,15 +94,26 @@ var engine = async (request) => {
   const result = bandage.computeLayout(request.graph, request.options);
   return { result, duration: performance.now() - start };
 };
-async function renderSpec(spec, base = ".") {
-  const source = spec.gbz ? await cutGbz(spec.gbz) : spec.gfa ? {
-    text: await gfaText(
-      isUrl(spec.gfa) ? spec.gfa : path.resolve(base, spec.gfa)
-    ),
-    region: spec.region ? parseRegion(spec.region) : void 0,
-    name: path.basename(spec.gfa)
-  } : void 0;
-  if (!source) {
+async function renderSpec(spec, base) {
+  const resolve = (location) => isUrl(location) ? location : path.resolve(base, location);
+  let source;
+  if (spec.gbz) {
+    const { db, index } = spec.gbz.db === "hprc" ? HPRC_GBZ : spec.gbz;
+    const cut = await cutGbzRegion(
+      await openGbz(
+        byteSource(resolve(db)),
+        index ? byteSource(resolve(index)) : void 0
+      ),
+      spec.gbz
+    );
+    source = { ...cut, name: `${cut.sample} ${spec.gbz.region}` };
+  } else if (spec.gfa) {
+    source = {
+      text: await text(resolve(spec.gfa)),
+      name: path.basename(spec.gfa),
+      region: spec.region ? parseRegion(spec.region) : void 0
+    };
+  } else {
     throw new Error("a spec names its graph as `gfa` or `gbz`");
   }
   const graph = loadGraph(source.text, source.name, {
@@ -128,7 +132,8 @@ async function renderSpec(spec, base = ".") {
     ...spec,
     walks: spec.walks?.map((w) => typeof w === "string" ? { walk: w } : w),
     region: source.region,
-    metadata: JSON.stringify(spec)
+    genes: spec.genes ? await readGenes(spec.genes, graph, resolve) : void 0,
+    spec
   });
 }
 async function main() {

package/dist/index.js

@@ -8,10 +8,13 @@ import {
   FADED_ALPHA,
   FIT_PADDING,
   FORCE_LAYOUT_LABEL,
+  HALO_FACTOR,
+  HPRC_GBZ,
   LABEL_CHAR_PX,
   LABEL_PAD,
   LABEL_PX,
   LAYOUT_MODES,
+  LEGEND_INSET_PX,
   LIFT_BACKDROP_COLOR,
   NODE_WIDTHS,
   REFERENCE_RAMP_MAX_HUE,
@@ -29,6 +32,7 @@ import {
   computeReferenceRamp,
   contains,
   curveBounds,
+  cutGbzRegion,
   cutWindowGFA,
   deletionEdges,
   drawingBounds,
@@ -42,15 +46,20 @@ import {
   fadeAbgr,
   featuresOnBackbone,
   figureSvg,
-  firstNodeAtOrAfter,
   fitTransform,
   forceLayout,
   formatBp,
+  geneCoverageNote,
+  genePins,
+  genesFromBed,
+  genesFromGff3Lines,
+  genesFromText,
   getNodeColor,
   graphBackbone,
   haplotypeWanted,
   isBackbone,
   layoutExtent,
+  layoutLabels,
   layoutModeByValue,
   loadBandage,
   loadGraph,
@@ -58,19 +67,16 @@ import {
   meanDepth,
   modeUsesLayoutEngine,
   nodeInk,
-  nodeLabelBudget,
   nodeWidthPx,
-  occupancy,
+  openGbz,
   padded,
   panSNContig,
   panSNHaplotype,
   panSNSample,
+  parseRegion,
   pathColorsLegible,
   pathLegend,
   pathRibbonOffsets,
-  placeLabels,
-  placeSizeLabels,
-  polylineSlice,
   rangeText,
   refNameBinding,
   referenceOrder,
@@ -79,23 +85,23 @@ import {
   resolveColorScheme,
   resolveEncoding,
   resolveReferenceSample,
-  rowLabelBox,
   schemeCss,
   screenToLayout,
-  sizeLabelCandidates,
   svgCanvas,
   svgPath,
   translateCurves,
+  version,
   viewportOf,
   walkHighlight,
   walkKey,
   walkLift,
+  walkPosition,
   walkRows,
   walkRowsExtent,
   wellKnownSample,
   yToXOf,
   zoomAbout
-} from "./chunks/chunk-4AOHEU76.js";
+} from "./chunks/chunk-B5ZHLU4N.js";
 
 // src/index.ts
 import { getDpr } from "@jbrowse/render-core/canvas2dUtils";
@@ -212,14 +218,14 @@ var SpatialIndex = class {
   }
 };
 var EdgeSpatialIndex = class {
-  constructor(nodePositions, graph, drawPaths, axis, cellSize, deletions, version = 0) {
+  constructor(nodePositions, graph, drawPaths, axis, cellSize, deletions, version2 = 0) {
     this.cells = /* @__PURE__ */ new Map();
     this.edgeCurves = baseEdgeCurves(
       nodePositions,
       graph,
       axis,
       deletions,
-      version
+      version2
     );
     const boxes = [];
     let extentX = 0;
@@ -332,19 +338,19 @@ function distanceToEdgeCurves(px, py, curves, yToX = 1) {
   return minDist;
 }
 var nodeCache = /* @__PURE__ */ new WeakMap();
-function getSpatialIndex(nodePositions, version) {
+function getSpatialIndex(nodePositions, version2) {
   const cached = nodeCache.get(nodePositions);
-  if (cached?.version === version) {
+  if (cached?.version === version2) {
     return cached.index;
   }
   const index = new SpatialIndex(nodePositions);
-  nodeCache.set(nodePositions, { version, index });
+  nodeCache.set(nodePositions, { version: version2, index });
   return index;
 }
 var edgeCache = /* @__PURE__ */ new WeakMap();
-function getEdgeSpatialIndex(nodePositions, graph, drawPaths, axis, version, deletions) {
+function getEdgeSpatialIndex(nodePositions, graph, drawPaths, axis, version2, deletions) {
   const cached = edgeCache.get(nodePositions);
-  if (cached?.graph === graph && cached.drawPaths === drawPaths && cached.scaleX === axis.scaleX && cached.scaleY === axis.scaleY && cached.version === version && cached.deletions === deletions) {
+  if (cached?.graph === graph && cached.drawPaths === drawPaths && cached.scaleX === axis.scaleX && cached.scaleY === axis.scaleY && cached.version === version2 && cached.deletions === deletions) {
     return cached.index;
   }
   const index = new EdgeSpatialIndex(
@@ -354,23 +360,23 @@ function getEdgeSpatialIndex(nodePositions, graph, drawPaths, axis, version, del
     axis,
     void 0,
     deletions,
-    version
+    version2
   );
   edgeCache.set(nodePositions, {
     graph,
     drawPaths,
     scaleX: axis.scaleX,
     scaleY: axis.scaleY,
-    version,
+    version: version2,
     index,
     deletions
   });
   return index;
 }
 var MIN_NODE_REACH_PX = 5;
-function findHoveredNode(nodePositions, graphX, graphY, axis, version = 0, ink) {
+function findHoveredNode(nodePositions, graphX, graphY, axis, version2 = 0, ink) {
   const yToX = yToXOf(axis);
-  const index = getSpatialIndex(nodePositions, version);
+  const index = getSpatialIndex(nodePositions, version2);
   const reach = (px) => Math.max(MIN_NODE_REACH_PX, px) / axis.scaleX;
   const queryReach = reach(ink?.maxHalfWidthPx ?? 0);
   const candidates = index.query(graphX, graphY, queryReach, queryReach / yToX);
@@ -393,7 +399,7 @@ function findHoveredNode(nodePositions, graphX, graphY, axis, version = 0, ink)
   }
   return hovered;
 }
-function findHoveredEdge(nodePositions, graph, graphX, graphY, axis, drawPaths, version = 0, deletions, hiddenEdges) {
+function findHoveredEdge(nodePositions, graph, graphX, graphY, axis, drawPaths, version2 = 0, deletions, hiddenEdges) {
   const yToX = yToXOf(axis);
   const edgeThreshold = 10 / axis.scaleX;
   const edgeIndex = getEdgeSpatialIndex(
@@ -401,7 +407,7 @@ function findHoveredEdge(nodePositions, graph, graphX, graphY, axis, drawPaths,
     graph,
     drawPaths,
     axis,
-    version,
+    version2,
     deletions
   );
   const candidates = edgeIndex.query(
@@ -470,6 +476,7 @@ var REFERENCE_STRIP_PX = 12;
 var REFERENCE_STRIP_ZONE_PX = REFERENCE_STRIP_PX + 8;
 var OVERHANG_PX = 8;
 var OVERHANG_CAP_PX = OVERHANG_PX + 3;
+var MIN_STAGGER_PX = 12;
 var PALE = abgrToCssRgba(fadeAbgr(LIFT_BACKDROP_COLOR, FADED_ALPHA));
 function referenceStripBlocks(graph, {
   colorScheme,
@@ -553,7 +560,8 @@ function stripPixels(blocks, frame, width, dpr) {
       claimed = px1;
     }
   }
-  return out;
+  const covered = out.length > 0 ? out.at(-1).x1 - out[0].x0 : 0;
+  return covered >= out.length * MIN_STAGGER_PX ? out : out.map(({ tier: _, ...b }) => b);
 }
 function drawOverhang(ctx, edgeX, inward, ink) {
   const capX = inward > 0 ? edgeX : edgeX - OVERHANG_CAP_PX;
@@ -580,9 +588,11 @@ function drawReferenceStrip(ctx, blocks, frame, {
   const ink = darkMode ? "#ffffff" : "#18181c";
   ctx.clearRect(0, 0, width, REFERENCE_STRIP_ZONE_PX);
   for (const b of stripPixels(blocks, frame, width, dpr)) {
-    const rows = b.colors.length > 1 ? b.colors.length : 2;
+    const { tier } = b;
+    const staggered = tier !== void 0 && b.colors.length === 1;
+    const rows = staggered ? 2 : b.colors.length;
     b.colors.forEach((color, i) => {
-      const row = b.colors.length > 1 ? i : b.tier;
+      const row = staggered ? tier : i;
       const y0 = rowEdge(row, rows, dpr);
       ctx.fillStyle = color;
       ctx.fillRect(b.x0, y0, b.x1 - b.x0, rowEdge(row + 1, rows, dpr) - y0);
@@ -1052,7 +1062,7 @@ function niceStep(raw) {
   const m = raw / pow;
   return (m <= 1 ? 1 : m <= 2 ? 2 : m <= 5 ? 5 : 10) * pow;
 }
-function placeLabels2(candidates) {
+function placeLabels(candidates) {
   const placed = [];
   for (const a of candidates) {
     if (placed.every(
@@ -1089,7 +1099,7 @@ function scaleMarks(boxes, x, width, measure) {
   return {
     spans: [{ x0: from, x1: to }],
     ticks,
-    labels: placeLabels2(positions)
+    labels: placeLabels(positions)
   };
 }
 function boxMarks(boxes, x, width, measure) {
@@ -1130,7 +1140,7 @@ function boxMarks(boxes, x, width, measure) {
   return {
     spans,
     ticks,
-    labels: placeLabels2([...ends, ...lengths, ...boundaries])
+    labels: placeLabels([...ends, ...lengths, ...boundaries])
   };
 }
 function rulerMarks(boxes, x, width, measure, referenceAxis = false) {
@@ -1698,220 +1708,6 @@ function bubbleSubgraph(graph, segmentIds) {
     referencePath: graph.referencePath
   };
 }
-
-// src/labelLayout.ts
-var HALO_FACTOR = 3.4;
-var LEGEND_INSET_PX = 6;
-var ROUTE_STACK = 8;
-var GENE_PIN_DROP_PX = 18;
-var GENE_STACK = 2;
-var TOPMOST_BASELINE = LABEL_PX + LABEL_PAD;
-function geneCoverageNote(pin) {
-  const length = pin.gene.end - pin.gene.start;
-  if (pin.covered >= 0.98) {
-    return void 0;
-  }
-  const [per, unit] = length >= 1e6 ? [1e6, "Mb"] : length >= 1e3 ? [1e3, "kb"] : [1, "bp"];
-  const amount = (bp) => +(bp / per).toFixed(per === 1 ? 0 : 1);
-  return `${amount(pin.covered * length)} of ${amount(length)} ${unit}`;
-}
-function byExtent(items, extent) {
-  return [...items].sort((a, b) => extent(b) - extent(a));
-}
-function layoutLabels(m) {
-  const { paneWidth: width, canvasHeight: height, translateX, translateY } = m;
-  const { scaleX, scaleY } = m.axisScale;
-  const frame = { width, height };
-  const screen = (p) => ({
-    x: p.x * scaleX + translateX,
-    y: p.y * scaleY + translateY
-  });
-  const reserved = m.drawnRowLabels.map(
-    ({ label, y }) => rowLabelBox(label, y * scaleY + translateY)
-  );
-  const stripPx = m.referenceStripZonePx ?? 0;
-  if (stripPx > 0) {
-    reserved.push({ x0: 0, x1: width, y0: 0, y1: stripPx });
-  }
-  if (m.legendSize.width > 0) {
-    reserved.push({
-      x0: width - LEGEND_INSET_PX - m.legendSize.width,
-      x1: width,
-      y0: 0,
-      y1: stripPx + LEGEND_INSET_PX + m.legendSize.height
-    });
-  }
-  if (m.poppedFrom) {
-    reserved.push({
-      x0: 0,
-      x1: 60 + m.poppedFrom.label.length * LABEL_CHAR_PX * 1.2,
-      y0: 0,
-      y1: 44
-    });
-  }
-  const take = occupancy(frame, reserved);
-  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 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
-      };
-    }),
-    frame,
-    take
-  );
-  const genes = placeLabels(
-    byExtent(m.genePins, (pin) => pin.gene.end - pin.gene.start).map((pin) => {
-      const { x, y } = screen(pin.at);
-      const note = geneCoverageNote(pin);
-      return {
-        item: pin,
-        x,
-        y: y + m.contigThickness + GENE_PIN_DROP_PX,
-        text: note ? `${pin.gene.name} \xB7 ${note}` : pin.gene.name,
-        fallback: note ? `${pin.gene.name} \u2026` : void 0,
-        stack: GENE_STACK
-      };
-    }),
-    frame,
-    take
-  );
-  const sizeCandidates = m.nodePositions && m.labelsNodeSizes ? sizeLabelCandidates({
-    nodePositions: m.nodePositions,
-    nodeLengths: m.nodeLengths,
-    deletions: m.showDeletionEdges ? m.deletions : [],
-    alleleDeletions: m.alleleDeletions,
-    axis: m.axisScale,
-    translateX,
-    translateY,
-    width,
-    height,
-    version: m.positionsVersion
-  }) : { deletions: [], nodes: [] };
-  const deletionLabels = placeSizeLabels(sizeCandidates.deletions, take);
-  const routes2 = placeLabels(
-    byBubble.flatMap(
-      (h) => h.routes.map((route) => {
-        const { x, y } = screen(route.at);
-        return {
-          item: { halo: h, route },
-          x,
-          y: y + 4,
-          text: route.text,
-          stack: ROUTE_STACK
-        };
-      })
-    ),
-    frame,
-    take
-  );
-  const nodeLabels = placeSizeLabels(
-    sizeCandidates.nodes,
-    take,
-    nodeLabelBudget(width, height)
-  );
-  return {
-    bubbles,
-    genes,
-    routes: routes2,
-    sizes: [...deletionLabels, ...nodeLabels]
-  };
-}
-
-// src/genes/genePins.ts
-function genePins(graph, genes, positions) {
-  const byRefName = /* @__PURE__ */ new Map();
-  for (const node of graph.nodes) {
-    if (isBackbone(node)) {
-      const { refName } = node.stable;
-      if (positions[node.id]?.length) {
-        const entry = byRefName.get(refName) ?? byRefName.set(refName, { nodes: [], reach: 0 }).get(refName);
-        entry.nodes.push(node);
-        entry.reach = Math.max(entry.reach, node.length);
-      }
-    }
-  }
-  for (const { nodes } of byRefName.values()) {
-    nodes.sort((a, b) => a.stable.start - b.stable.start);
-  }
-  const pins = [];
-  for (const gene of genes) {
-    const backbone = byRefName.get(gene.refName);
-    if (!backbone) {
-      continue;
-    }
-    const parts = [];
-    const exonsByNode = [];
-    let at;
-    let atDistance = Infinity;
-    let covered = 0;
-    const mid = (gene.start + gene.end) / 2;
-    const { nodes, reach } = backbone;
-    for (let i = firstNodeAtOrAfter(nodes, gene.start - reach); i < nodes.length && nodes[i].stable.start < gene.end; i++) {
-      const node = nodes[i];
-      const nodeStart = node.stable.start;
-      const nodeEnd = nodeStart + node.length;
-      if (nodeEnd <= gene.start) {
-        continue;
-      }
-      const line = positions[node.id];
-      covered += Math.min(nodeEnd, gene.end) - Math.max(nodeStart, gene.start);
-      const nodeParts = [];
-      for (const exon of gene.exons) {
-        const a = Math.max(exon.start, nodeStart);
-        const b = Math.min(exon.end, nodeEnd);
-        if (b <= a) {
-          continue;
-        }
-        const stretch = polylineSlice(
-          line,
-          (a - nodeStart) / node.length,
-          (b - nodeStart) / node.length
-        );
-        if (stretch.length === 1) {
-          stretch.push({ ...stretch[0] });
-        }
-        nodeParts.push(svgPath(stretch));
-      }
-      if (nodeParts.length > 0) {
-        parts.push(...nodeParts);
-        exonsByNode.push({ nodeId: node.id, d: nodeParts.join("") });
-      }
-      const pinBp = Math.min(Math.max(mid, nodeStart), nodeEnd);
-      const distance = Math.abs(pinBp - mid);
-      if (distance < atDistance) {
-        atDistance = distance;
-        const [p] = polylineSlice(
-          line,
-          (pinBp - nodeStart) / node.length,
-          (pinBp - nodeStart) / node.length
-        );
-        at = p;
-      }
-    }
-    if (at) {
-      pins.push({
-        gene,
-        exons: parts.join(""),
-        exonsByNode,
-        at,
-        covered: covered / (gene.end - gene.start)
-      });
-    }
-  }
-  return pins;
-}
 export {
   BUBBLE_KIND_COLORS,
   BUBBLE_KIND_NAMES,
@@ -1924,6 +1720,7 @@ export {
   FIT_PADDING,
   FORCE_LAYOUT_LABEL,
   HALO_FACTOR,
+  HPRC_GBZ,
   LABEL_CHAR_PX,
   LABEL_PAD,
   LABEL_PX,
@@ -1949,6 +1746,7 @@ export {
   computeReferenceRamp,
   connectorAt,
   contains,
+  cutGbzRegion,
   cutWindowGFA,
   deletionEdges,
   drawReferenceStrip,
@@ -1973,6 +1771,9 @@ export {
   formatBp,
   geneCoverageNote,
   genePins,
+  genesFromBed,
+  genesFromGff3Lines,
+  genesFromText,
   getDpr,
   graphBackbone,
   haplotypeWanted,
@@ -1986,10 +1787,12 @@ export {
   modeUsesLayoutEngine,
   nodeInk,
   nodeWidthPx,
+  openGbz,
   padded,
   panSNContig,
   panSNHaplotype,
   panSNSample,
+  parseRegion,
   pathColorsLegible,
   pathLegend,
   rangeText,
@@ -2014,10 +1817,12 @@ export {
   tubeMapNodeAt,
   tubeMapPicture,
   tubeX,
+  version,
   viewportOf,
   walkHighlight,
   walkKey,
   walkLift,
+  walkPosition,
   walkRows,
   walkRowsExtent,
   warpX,

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

@@ -1,20 +1,20 @@
 import type { BubbleSpread } from '../bubbleSpreads.js';
 import type { FigureOptions } from '../figure.js';
+import type { GbzSource } from '../gbzCut.js';
 import type { LayoutModeValue } from '../layoutModes.js';
 import type { WalkLayer } from '../walkEncoding.js';
-export interface FigureSpec extends Omit<FigureOptions, 'walks' | 'region'> {
+export interface FigureSpec extends Omit<FigureOptions, 'walks' | 'region' | 'genes' | 'spec'> {
     gfa?: string;
-    gbz?: {
-        db: string;
-        index?: string;
-        region: string;
-        haplotypes?: string[];
-        referenceSample?: string;
-    };
+    gbz?: GbzSource;
     region?: string;
     referencePath?: string;
     layout?: LayoutModeValue;
     quality?: number;
     bubbleSpread?: BubbleSpread;
     walks?: (string | WalkLayer)[];
+    genes?: {
+        file: string;
+        index?: string;
+        format?: 'gff3' | 'bed';
+    };
 }