@jbrowse/bandage-core 4.3.0 → 4.4.1

package/dist/chunks/{chunk-IFVLNU7X.js → chunk-JJU4D2SE.js}

@@ -5075,7 +5075,16 @@ function placeRowGenes(rows, byRow) {
 }
 var GENE_FONT_PX = 9;
 var GENE_CHAR_PX = 5.2;
-function rowGeneBoxes(genes, X, y) {
+var MIN_LETTERED_BAR_PX = 8;
+var genePad = (rowPx, barPx) => Math.min(2, (rowPx - barPx) / 2 - 1);
+function boxesGenes(rowPx, barPx) {
+  return genePad(rowPx, barPx) >= 1;
+}
+function rowGeneBoxes(genes, X, y, { rowPx = ROW_HEIGHT_PX, barPx = BAR_PX } = {}) {
+  if (!boxesGenes(rowPx, barPx)) {
+    return [];
+  }
+  const pad = genePad(rowPx, barPx);
   const boxes = genes.map((g) => {
     const x = X(g.start);
     return {
@@ -5086,7 +5095,7 @@ function rowGeneBoxes(genes, X, y) {
   });
   const taken = [];
   const named = new Set(
-    [...boxes].sort((a, b) => a.w - b.w).filter(({ g, x, w }) => {
+    (barPx >= MIN_LETTERED_BAR_PX ? [...boxes] : []).sort((a, b) => a.w - b.w).filter(({ g, x, w }) => {
       const half = g.name.length * GENE_CHAR_PX / 2;
       const at = [x + w / 2 - half, x + w / 2 + half];
       if (2 * half > w + 6 || taken.some(([a, b]) => at[0] < b + 2 && at[1] > a - 2)) {
@@ -5099,9 +5108,9 @@ function rowGeneBoxes(genes, X, y) {
   return boxes.map((box) => ({
     name: box.g.name,
     x: box.x,
-    y: y - BAR_PX / 2 - 2,
+    y: y - barPx / 2 - pad,
     w: box.w,
-    h: BAR_PX + 4,
+    h: barPx + 2 * pad,
     exons: box.g.exons.map((e) => ({
       x: X(e.start),
       w: Math.max(1, X(e.end) - X(e.start))
@@ -5133,7 +5142,13 @@ function walkRowsKey(bars, o = {}) {
       label: "walked outside the cut"
     });
   }
-  if (o.genes) {
+  if (o.genes?.crowded) {
+    entries.push({
+      swatch: { kind: "gene" },
+      label: "genes left out: too many rows to box them in",
+      note: true
+    });
+  } else if (o.genes) {
     entries.push({
       swatch: { kind: "gene" },
       label: "genes, each row's own annotation"
@@ -5260,7 +5275,7 @@ function coalesceRuns(runs, pxPerBp) {
   flush();
   return out;
 }
-function geneTree(box, y) {
+function geneTree(box, y, barPx) {
   return el(
     "g",
     { class: "row-gene", "data-testid": "graph-walk-gene" },
@@ -5268,9 +5283,9 @@ function geneTree(box, y) {
     ...box.exons.map(
       (e) => el("rect", {
         x: e.x,
-        y: y - BAR_PX / 2,
+        y: y - barPx / 2,
         width: e.w,
-        height: BAR_PX,
+        height: barPx,
         fill: GENE_INK,
         opacity: 0.35
       })
@@ -5366,9 +5381,10 @@ function walkRowsTree(bars, frame, o = {}) {
       },
       ...runs,
       ...ticks,
-      ...rowGeneBoxes(o.rowGenes?.get(row.name) ?? [], along, y).map(
-        (box) => geneTree(box, y)
-      ),
+      ...rowGeneBoxes(o.rowGenes?.get(row.name) ?? [], along, y, {
+        rowPx,
+        barPx
+      }).map((box) => geneTree(box, y, barPx)),
       call && el("rect", {
         "data-testid": "graph-walk-call",
         x: along(call.bp) - 1,
@@ -5397,6 +5413,183 @@ function walkRowsTree(bars, frame, o = {}) {
   return el("g", {}, ...[reference, ...rows].map(rowTree));
 }
 
+// src/layout/walkStrip.ts
+var PAD_PX = 6;
+var WALK_STRIP_CEILING_PX = 260;
+var LABEL_FONT_PX = 11;
+var MIN_ROW_PX = 3;
+var LABELLED_ROW_PX = 12;
+var READOUT_ROOM2 = 1.3;
+var MARK_INK = "#111";
+var TICK_PX = 3;
+function stripMarks(graph, rows, node) {
+  const visits = graph.pathVisits?.get(node.name) ?? [];
+  const marks = [];
+  for (const row of rows) {
+    const axis = row.axis;
+    if (!axis) {
+      continue;
+    }
+    const path = pathOrigin(row.name).name;
+    for (const v of visits) {
+      if (v.path !== path) {
+        continue;
+      }
+      const { start, end } = alongRow(axis, v.start, v.start + node.length);
+      if (end > 0 && start < row.bp) {
+        marks.push({ row: row.name, start, bp: end - start });
+      }
+    }
+  }
+  return marks;
+}
+var spanCache = /* @__PURE__ */ new WeakMap();
+function spansOf(graph, name) {
+  let byName = spanCache.get(graph);
+  if (!byName) {
+    byName = /* @__PURE__ */ new Map();
+    spanCache.set(graph, byName);
+  }
+  if (byName.has(name)) {
+    return byName.get(name);
+  }
+  const lengthOf = new Map(graph.nodes.map((n2) => [n2.id, n2.length]));
+  const pieces = (graph.paths ?? []).filter((p) => p.name === name);
+  let spans;
+  if (pieces.every((p) => p.start !== void 0)) {
+    spans = { ids: [], starts: [], ends: [] };
+    for (const piece of [...pieces].sort((a, b) => a.start - b.start)) {
+      let pos = piece.start;
+      for (const id of piece.nodeIds) {
+        const len = lengthOf.get(id) ?? 0;
+        spans.ids.push(id);
+        spans.starts.push(pos);
+        spans.ends.push(pos + len);
+        pos += len;
+      }
+    }
+  }
+  byName.set(name, spans);
+  return spans;
+}
+function segmentAt(graph, row, offset, pxPerBp) {
+  const axis = row.axis;
+  const spans = axis && spansOf(graph, row.name);
+  if (!axis || !spans || offset < 0 || offset > row.bp) {
+    return void 0;
+  }
+  const at = axis.reversed ? axis.start - offset : axis.start + offset;
+  const tol = 0.5 / pxPerBp;
+  const bar = axis.reversed ? { start: axis.start - row.bp, end: axis.start } : { start: axis.start, end: axis.start + row.bp };
+  const from = Math.max(at - tol, bar.start);
+  const to = Math.min(at + tol, bar.end);
+  let lo = 0;
+  let hi = spans.starts.length;
+  while (lo < hi) {
+    const mid = lo + hi >> 1;
+    if (spans.ends[mid] <= from) {
+      lo = mid + 1;
+    } else {
+      hi = mid;
+    }
+  }
+  let best;
+  let bestLen = -1;
+  let bestHolds = false;
+  for (let i = lo; i < spans.starts.length && spans.starts[i] < to; i++) {
+    const len = spans.ends[i] - spans.starts[i];
+    const holds = spans.starts[i] <= at && at < spans.ends[i];
+    if (len > bestLen || len === bestLen && holds && !bestHolds) {
+      bestLen = len;
+      best = spans.ids[i];
+      bestHolds = holds;
+    }
+  }
+  return best;
+}
+function walkStripFrame(bars, o) {
+  const maxHeight = o.maxHeight ?? WALK_STRIP_CEILING_PX;
+  const labelPx = o.labelPx ?? Math.max(...[bars.reference, ...bars.rows].map((r) => r.label.length)) * LABEL_CHAR_PX + 16;
+  const count = bars.rows.length + 1;
+  const rowPx = Math.max(
+    MIN_ROW_PX,
+    Math.min(ROW_HEIGHT_PX, Math.floor((maxHeight - 2 * PAD_PX) / count))
+  );
+  const labelled = rowPx >= LABELLED_ROW_PX;
+  const readouts = rowPx >= 14;
+  const barPx = Math.max(2, Math.round(rowPx * 0.6));
+  const longest = Math.max(bars.reference.bp, ...bars.rows.map((r) => r.bp), 1);
+  const left = labelled ? labelPx : PAD_PX;
+  const usable = Math.max(1, o.width - left - PAD_PX);
+  const scaleX = usable / (longest * (readouts ? READOUT_ROOM2 : 1));
+  return {
+    scaleX,
+    scaleY: 1,
+    translateX: left - bars.origin * scaleX,
+    translateY: PAD_PX + rowPx / 2,
+    width: o.width,
+    height: count * rowPx + 2 * PAD_PX,
+    rowPx,
+    barPx,
+    readouts,
+    labelled,
+    boxesGenes: boxesGenes(rowPx, barPx)
+  };
+}
+function stripRowAt(bars, frame, x, y) {
+  const i = Math.round((y - frame.translateY) / frame.rowPx);
+  const row = [bars.reference, ...bars.rows][i];
+  const offset = (x - frame.translateX) / frame.scaleX - bars.origin;
+  return row && i >= 0 && offset >= 0 && offset <= row.bp ? { index: i, row, offset } : void 0;
+}
+function walkMarksTree(bars, frame, marks) {
+  const index = new Map(
+    [bars.reference, ...bars.rows].map((row, i) => [row.name, i])
+  );
+  const X = (offset) => (bars.origin + offset) * frame.scaleX + frame.translateX;
+  return el(
+    "g",
+    { "data-testid": "graph-walk-marks" },
+    ...marks.flatMap((m) => {
+      const i = index.get(m.row);
+      if (i === void 0) {
+        return [];
+      }
+      const y = i * frame.rowPx + frame.translateY;
+      const x = X(m.start);
+      const w = Math.max(2, m.bp * frame.scaleX);
+      const tick = (top) => el("rect", { x, y: top, width: w, height: TICK_PX, fill: MARK_INK });
+      return [
+        tick(y - frame.barPx / 2 - TICK_PX - 1),
+        tick(y + frame.barPx / 2 + 1)
+      ];
+    })
+  );
+}
+function walkStripLabelsTree(bars, frame, bold = /* @__PURE__ */ new Set()) {
+  return el(
+    "g",
+    { "font-family": "sans-serif", "font-size": LABEL_FONT_PX, fill: "#333" },
+    ...(frame.labelled ? [bars.reference, ...bars.rows] : []).map(
+      (row, i) => el(
+        "text",
+        {
+          x: 6,
+          y: i * frame.rowPx + frame.translateY + 4,
+          "font-weight": bold.has(row.name) ? 600 : void 0
+        },
+        row.label
+      )
+    )
+  );
+}
+function stripGeneGaps(frame, gaps, rowGenes) {
+  if (rowGenes ? !rowGenes.size : !gaps) {
+    return void 0;
+  }
+  return frame.boxesGenes ? gaps : { untracked: 0, unread: 0, ...gaps, crowded: true };
+}
+
 // src/renderer/svgCanvas.ts
 var n = (v) => +v.toFixed(1);
 function paint(css) {
@@ -5510,7 +5703,7 @@ function svgCanvas(width, height) {
 }
 
 // src/version.ts
-var version = "4.3.0";
+var version = "4.4.1";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {
@@ -5558,6 +5751,7 @@ var FONT = 'font-family="Helvetica, Arial, sans-serif" font-size="11"';
 var BAR_PX2 = 48;
 var SWATCH_PX = 18;
 var KEY_GAP_PX = 16;
+var STRIP_KEY_PX = 22;
 var FADED = "rgb(160,160,160)";
 var EXON_COLOR = "#daa520";
 var GENE_INK2 = "#1c1c22";
@@ -5615,6 +5809,10 @@ function figureSvg(graph, layout, o = {}) {
   const nodeById = new Map(graph.nodes.map((node) => [node.id, node]));
   const colorScheme = resolveColorScheme(o.colorScheme ?? "auto", graph);
   const referenceRamp = colorScheme === "reference-position" && !layout.tubeMap ? computeReferenceRamp(graph, rampDomain) : void 0;
+  const rampInterval = referenceRamp && {
+    start: referenceRamp.start,
+    end: referenceRamp.start + referenceRamp.span
+  };
   const deletions = layout.tubeMap ? [] : deletionEdges(graph);
   const layers = o.walks ?? [];
   const walkRamp = layers.some((l) => l.color?.field === "reference") ? referenceRamp ?? computeReferenceRamp(graph, rampDomain) : void 0;
@@ -5681,10 +5879,7 @@ function figureSvg(graph, layout, o = {}) {
             rows,
             { ...t, width: w, height: h },
             {
-              ramp: referenceRamp && {
-                start: referenceRamp.start,
-                end: referenceRamp.start + referenceRamp.span
-              },
+              ramp: rampInterval,
               rowGenes: o.rowGenes
             }
           )
@@ -5807,10 +6002,7 @@ function figureSvg(graph, layout, o = {}) {
     if (rows) {
       const key = walkRowsKeyTree(
         walkRowsKey(rows, {
-          ramp: referenceRamp && {
-            start: referenceRamp.start,
-            end: referenceRamp.start + referenceRamp.span
-          },
+          ramp: rampInterval,
           genes: o.rowGenes?.size ? o.rowGeneGaps : void 0
         }),
         x,
@@ -5846,6 +6038,36 @@ function figureSvg(graph, layout, o = {}) {
     );
     height = header + h;
   }
+  const strip = o.walkStrip;
+  if (strip && !rows && !layout.tubeMap) {
+    const frame = walkStripFrame(strip.rows, { width });
+    const key = walkRowsKeyTree(
+      walkRowsKey(strip.rows, {
+        ramp: rampInterval,
+        genes: stripGeneGaps(frame, strip.rowGeneGaps, strip.rowGenes)
+      }),
+      6,
+      height + frame.height
+    );
+    parts.push(
+      `<line x1="0" x2="${width}" y1="${height + 0.5}" y2="${height + 0.5}" stroke="#ddd"/>`,
+      `<svg y="${height}" width="${width}" height="${frame.height}">${serializeEl(
+        walkRowsTree(strip.rows, frame, {
+          ramp: rampInterval,
+          rowGenes: strip.rowGenes,
+          idPrefix: "strip"
+        })
+      )}${serializeEl(
+        walkStripLabelsTree(
+          strip.rows,
+          frame,
+          new Set(layers.map((l) => l.walk))
+        )
+      )}</svg>`,
+      serializeEl(key.tree)
+    );
+    height += frame.height + STRIP_KEY_PX;
+  }
   const metadata = JSON.stringify({
     generator: `@jbrowse/bandage-core@${version}`,
     ...o.spec === void 0 ? {} : { spec: o.spec }
@@ -6456,7 +6678,6 @@ export {
   panSNSample,
   panSNHaplotype,
   panSNContig,
-  pathOrigin,
   trimOrigins,
   loadGraph,
   engineRequest,
@@ -6543,6 +6764,15 @@ export {
   walkRowsKeyTree,
   coalesceRuns,
   walkRowsTree,
+  WALK_STRIP_CEILING_PX,
+  LABELLED_ROW_PX,
+  stripMarks,
+  segmentAt,
+  walkStripFrame,
+  stripRowAt,
+  walkMarksTree,
+  walkStripLabelsTree,
+  stripGeneGaps,
   svgCanvas,
   version,
   axisScaleOf,

package/dist/cli/figure.js

@@ -16,8 +16,9 @@ import {
   loadGraph,
   openGbz,
   parseRegion,
-  refNameBinding
-} from "../chunks/chunk-IFVLNU7X.js";
+  refNameBinding,
+  walkRows
+} from "../chunks/chunk-JJU4D2SE.js";
 
 // src/cli/figure.ts
 import { access, open, readFile, writeFile } from "node:fs/promises";
@@ -146,7 +147,8 @@ async function renderSpec(spec, base) {
         byteSource(resolve(db)),
         indexLocation ? byteSource(indexLocation) : void 0
       ),
-      spec.gbz
+      // the strip measures whole walks, which a cut only follows when asked
+      spec.walkStrip ? { snarls: "overlapping", ...spec.gbz } : spec.gbz
     );
     source = { ...cut, name: `${cut.sample} ${spec.gbz.region}` };
   } else if (spec.gfa) {
@@ -170,8 +172,10 @@ async function renderSpec(spec, base) {
     },
     engine
   )).result;
+  const stripRows = spec.walkStrip ? walkRows(graph, source.region) : void 0;
   return figureSvg(graph, layout, {
     ...spec,
+    walkStrip: stripRows && { rows: stripRows },
     walks: spec.walks?.map((w) => typeof w === "string" ? { walk: w } : w),
     region: source.region,
     genes: spec.genes ? await readGenes(spec.genes, graph, resolve) : void 0,

package/dist/index.js

@@ -13,6 +13,7 @@ import {
   GENE_INK,
   HALO_FACTOR,
   HPRC_GBZ,
+  LABELLED_ROW_PX,
   LABEL_CHAR_PX,
   LABEL_PAD,
   LABEL_PX,
@@ -28,6 +29,7 @@ import {
   ROW_HEIGHT_PX,
   WALK_FIELDS,
   WALK_SCHEMES,
+  WALK_STRIP_CEILING_PX,
   WELL_KNOWN_SAMPLES,
   alongRow,
   assemblyWalk,
@@ -87,7 +89,6 @@ import {
   parseRegion,
   pathColorsLegible,
   pathLegend,
-  pathOrigin,
   pathRibbonOffsets,
   placeRowGenes,
   rampHue,
@@ -107,7 +108,11 @@ import {
   runPaint,
   schemeCss,
   screenToLayout,
+  segmentAt,
   serializeEl,
+  stripGeneGaps,
+  stripMarks,
+  stripRowAt,
   svgCanvas,
   svgPath,
   translateCurves,
@@ -118,6 +123,7 @@ import {
   walkHighlight,
   walkKey,
   walkLift,
+  walkMarksTree,
   walkPosition,
   walkRowReadout,
   walkRows,
@@ -125,10 +131,12 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree,
+  walkStripFrame,
+  walkStripLabelsTree,
   wellKnownSample,
   yToXOf,
   zoomAbout
-} from "./chunks/chunk-IFVLNU7X.js";
+} from "./chunks/chunk-JJU4D2SE.js";
 
 // src/index.ts
 import { getDpr } from "@jbrowse/render-core/canvas2dUtils";
@@ -1776,155 +1784,6 @@ function bubbleSubgraph(graph, segmentIds) {
     referencePath: graph.referencePath
   };
 }
-
-// src/layout/walkStrip.ts
-var PAD_PX = 6;
-var MIN_ROW_PX = 3;
-var LABELLED_ROW_PX = 12;
-var READOUT_ROOM = 1.3;
-var MARK_INK = "#111";
-var TICK_PX2 = 3;
-function stripMarks(graph, rows, node) {
-  const visits = graph.pathVisits?.get(node.name) ?? [];
-  const marks = [];
-  for (const row of rows) {
-    const axis = row.axis;
-    if (!axis) {
-      continue;
-    }
-    const path = pathOrigin(row.name).name;
-    for (const v of visits) {
-      if (v.path !== path) {
-        continue;
-      }
-      const { start, end } = alongRow(axis, v.start, v.start + node.length);
-      if (end > 0 && start < row.bp) {
-        marks.push({ row: row.name, start, bp: end - start });
-      }
-    }
-  }
-  return marks;
-}
-var spanCache = /* @__PURE__ */ new WeakMap();
-function spansOf(graph, name) {
-  let byName = spanCache.get(graph);
-  if (!byName) {
-    byName = /* @__PURE__ */ new Map();
-    spanCache.set(graph, byName);
-  }
-  if (byName.has(name)) {
-    return byName.get(name);
-  }
-  const lengthOf = new Map(graph.nodes.map((n) => [n.id, n.length]));
-  const pieces = (graph.paths ?? []).filter((p) => p.name === name);
-  let spans;
-  if (pieces.every((p) => p.start !== void 0)) {
-    spans = { ids: [], starts: [], ends: [] };
-    for (const piece of [...pieces].sort((a, b) => a.start - b.start)) {
-      let pos = piece.start;
-      for (const id of piece.nodeIds) {
-        const len = lengthOf.get(id) ?? 0;
-        spans.ids.push(id);
-        spans.starts.push(pos);
-        spans.ends.push(pos + len);
-        pos += len;
-      }
-    }
-  }
-  byName.set(name, spans);
-  return spans;
-}
-function segmentAt(graph, row, offset, pxPerBp) {
-  const axis = row.axis;
-  const spans = axis && spansOf(graph, row.name);
-  if (!axis || !spans || offset < 0 || offset > row.bp) {
-    return void 0;
-  }
-  const at = axis.reversed ? axis.start - offset : axis.start + offset;
-  const tol = 0.5 / pxPerBp;
-  const bar = axis.reversed ? { start: axis.start - row.bp, end: axis.start } : { start: axis.start, end: axis.start + row.bp };
-  const from = Math.max(at - tol, bar.start);
-  const to = Math.min(at + tol, bar.end);
-  let lo = 0;
-  let hi = spans.starts.length;
-  while (lo < hi) {
-    const mid = lo + hi >> 1;
-    if (spans.ends[mid] <= from) {
-      lo = mid + 1;
-    } else {
-      hi = mid;
-    }
-  }
-  let best;
-  let bestLen = -1;
-  let bestHolds = false;
-  for (let i = lo; i < spans.starts.length && spans.starts[i] < to; i++) {
-    const len = spans.ends[i] - spans.starts[i];
-    const holds = spans.starts[i] <= at && at < spans.ends[i];
-    if (len > bestLen || len === bestLen && holds && !bestHolds) {
-      bestLen = len;
-      best = spans.ids[i];
-      bestHolds = holds;
-    }
-  }
-  return best;
-}
-function walkStripFrame(bars, o) {
-  const count = bars.rows.length + 1;
-  const rowPx = Math.max(
-    MIN_ROW_PX,
-    Math.min(ROW_HEIGHT_PX, Math.floor((o.maxHeight - 2 * PAD_PX) / count))
-  );
-  const labelled = rowPx >= LABELLED_ROW_PX;
-  const readouts = rowPx >= 14;
-  const barPx = Math.max(2, Math.round(rowPx * 0.6));
-  const longest = Math.max(bars.reference.bp, ...bars.rows.map((r) => r.bp), 1);
-  const left = labelled ? o.labelPx : PAD_PX;
-  const usable = Math.max(1, o.width - left - PAD_PX);
-  const scaleX = usable / (longest * (readouts ? READOUT_ROOM : 1));
-  return {
-    scaleX,
-    scaleY: 1,
-    translateX: left - bars.origin * scaleX,
-    translateY: PAD_PX + rowPx / 2,
-    width: o.width,
-    height: count * rowPx + 2 * PAD_PX,
-    rowPx,
-    barPx,
-    readouts,
-    labelled
-  };
-}
-function stripRowAt(bars, frame, x, y) {
-  const i = Math.round((y - frame.translateY) / frame.rowPx);
-  const row = [bars.reference, ...bars.rows][i];
-  const offset = (x - frame.translateX) / frame.scaleX - bars.origin;
-  return row && i >= 0 && offset >= 0 && offset <= row.bp ? { index: i, row, offset } : void 0;
-}
-function walkMarksTree(bars, frame, marks) {
-  const index = new Map(
-    [bars.reference, ...bars.rows].map((row, i) => [row.name, i])
-  );
-  const X = (offset) => (bars.origin + offset) * frame.scaleX + frame.translateX;
-  return el(
-    "g",
-    { "data-testid": "graph-walk-marks" },
-    ...marks.flatMap((m) => {
-      const i = index.get(m.row);
-      if (i === void 0) {
-        return [];
-      }
-      const y = i * frame.rowPx + frame.translateY;
-      const x = X(m.start);
-      const w = Math.max(2, m.bp * frame.scaleX);
-      const tick = (top) => el("rect", { x, y: top, width: w, height: TICK_PX2, fill: MARK_INK });
-      return [
-        tick(y - frame.barPx / 2 - TICK_PX2 - 1),
-        tick(y + frame.barPx / 2 + 1)
-      ];
-    })
-  );
-}
 export {
   BUBBLE_KIND_COLORS,
   BUBBLE_KIND_NAMES,
@@ -1958,6 +1817,7 @@ export {
   ON_REFERENCE as WALK_ON_REFERENCE,
   OUTSIDE_CUT as WALK_OUTSIDE_CUT,
   WALK_SCHEMES,
+  WALK_STRIP_CEILING_PX,
   WELL_KNOWN_SAMPLES,
   alongRow,
   assemblyWalk,
@@ -2051,6 +1911,7 @@ export {
   segmentAt,
   serializeEl,
   stripBlockAt,
+  stripGeneGaps,
   stripMarks,
   stripRowAt,
   svgCanvas,
@@ -2076,6 +1937,7 @@ export {
   walkRowsKeyTree,
   walkRowsTree,
   walkStripFrame,
+  walkStripLabelsTree,
   warpX,
   wellKnownSample,
   wheelZoomFactor,

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

@@ -3,7 +3,7 @@ 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' | 'genes' | 'spec'> {
+export interface FigureSpec extends Omit<FigureOptions, 'walks' | 'region' | 'genes' | 'spec' | 'walkStrip'> {
     gfa?: string;
     gbz?: GbzSource;
     region?: string;
@@ -12,6 +12,7 @@ export interface FigureSpec extends Omit<FigureOptions, 'walks' | 'region' | 'ge
     quality?: number;
     bubbleSpread?: BubbleSpread;
     walks?: (string | WalkLayer)[];
+    walkStrip?: boolean;
     genes?: {
         file: string;
         index?: string;

package/dist/types/figure.d.ts

@@ -2,6 +2,7 @@ import type { ColorScheme } from './colorSchemes.js';
 import type { FacetInput } from './facetGrid.js';
 import type { GeneModel } from './genes/genePins.js';
 import type { GeneGaps, RowGene, WalkRowsWithCalls } from './layout/walkRowDraw.js';
+import type { WalkRows } from './layout/walkRows.js';
 import type { NodeWidth } from './nodeWidths.js';
 import type { Graph, LayoutResult } from './types.js';
 import type { WalkLayer } from './walkEncoding.js';
@@ -30,5 +31,10 @@ export interface FigureOptions {
     walkRows?: WalkRowsWithCalls;
     rowGenes?: Map<string, RowGene[]>;
     rowGeneGaps?: GeneGaps;
+    walkStrip?: {
+        rows: WalkRows;
+        rowGenes?: Map<string, RowGene[]>;
+        rowGeneGaps?: GeneGaps;
+    };
 }
 export declare function figureSvg(graph: Graph, layout: LayoutResult, o?: FigureOptions): string;

package/dist/types/index.d.ts

@@ -58,7 +58,7 @@ export { walkRows } from './layout/walkRows.js';
 export type { WalkAxis, WalkRow, WalkRows, WalkRun } from './layout/walkRows.js';
 export { BAR_PX as WALK_BAR_PX, DISAGREES as WALK_DISAGREES, GAP_PX as WALK_GAP_PX, GENE_INK as WALK_GENE_INK, OFF_REFERENCE as WALK_OFF_REFERENCE, ON_REFERENCE as WALK_ON_REFERENCE, OUTSIDE_CUT as WALK_OUTSIDE_CUT, alongRow, coalesceRuns, placeRowGenes, readoutPlacement, rowGeneBoxes, rowSpan, runPaint, unitTicks, walkRowReadout, walkRowsKey, walkRowsKeyTree, walkRowsTree, } from './layout/walkRowDraw.js';
 export type { GeneBox, GeneGaps, KeyEntry, KeySwatch, ReadoutCall, RowGene, WalkRowsFrame, WalkRowsWithCalls, } from './layout/walkRowDraw.js';
-export { LABELLED_ROW_PX, segmentAt, stripMarks, stripRowAt, walkMarksTree, walkStripFrame, } from './layout/walkStrip.js';
+export { LABELLED_ROW_PX, WALK_STRIP_CEILING_PX, segmentAt, stripGeneGaps, stripMarks, stripRowAt, walkMarksTree, walkStripFrame, walkStripLabelsTree, } from './layout/walkStrip.js';
 export type { StripFrame, StripMark } from './layout/walkStrip.js';
 export { el, serializeEl } from './el.js';
 export type { El, ElAttrs } from './el.js';

package/dist/types/layout/walkRowDraw.d.ts

@@ -50,6 +50,7 @@ export interface RowGene {
     }[];
 }
 export declare function placeRowGenes(rows: WalkRow[], byRow: Map<string, GeneModel[]>): Map<string, RowGene[]>;
+export declare function boxesGenes(rowPx: number, barPx: number): boolean;
 export interface GeneBox {
     name: string;
     x: number;
@@ -66,7 +67,10 @@ export interface GeneBox {
         size: number;
     };
 }
-export declare function rowGeneBoxes(genes: RowGene[], X: (offset: number) => number, y: number): GeneBox[];
+export declare function rowGeneBoxes(genes: RowGene[], X: (offset: number) => number, y: number, { rowPx, barPx }?: {
+    rowPx?: number | undefined;
+    barPx?: number | undefined;
+}): GeneBox[];
 export type KeySwatch = {
     kind: 'bar';
     fill: string;
@@ -82,6 +86,7 @@ export interface KeyEntry {
     note?: true;
 }
 export interface GeneGaps {
+    crowded?: boolean;
     untracked: number;
     unplaced?: number;
     unread: number;

package/dist/types/layout/walkStrip.d.ts

@@ -1,6 +1,7 @@
-import type { WalkRowsFrame } from './walkRowDraw.js';
+import type { GeneGaps, RowGene, WalkRowsFrame } from './walkRowDraw.js';
 import type { WalkRow, WalkRows } from './walkRows.js';
 import type { Graph, GraphNode } from '../types.js';
+export declare const WALK_STRIP_CEILING_PX = 260;
 export declare const LABELLED_ROW_PX = 12;
 export interface StripMark {
     row: string;
@@ -14,11 +15,12 @@ export interface StripFrame extends WalkRowsFrame {
     barPx: number;
     readouts: boolean;
     labelled: boolean;
+    boxesGenes: boolean;
 }
 export declare function walkStripFrame(bars: WalkRows, o: {
     width: number;
-    maxHeight: number;
-    labelPx: number;
+    maxHeight?: number;
+    labelPx?: number;
 }): StripFrame;
 export declare function stripRowAt(bars: WalkRows, frame: StripFrame, x: number, y: number): {
     index: number;
@@ -26,3 +28,5 @@ export declare function stripRowAt(bars: WalkRows, frame: StripFrame, x: number,
     offset: number;
 } | undefined;
 export declare function walkMarksTree(bars: WalkRows, frame: StripFrame, marks: StripMark[]): import("../index.js").El;
+export declare function walkStripLabelsTree(bars: WalkRows, frame: StripFrame, bold?: ReadonlySet<string>): import("../index.js").El;
+export declare function stripGeneGaps(frame: StripFrame, gaps: GeneGaps | undefined, rowGenes?: Map<string, RowGene[]>): GeneGaps | undefined;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "4.3.0";
+export declare const version = "4.4.1";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "4.3.0",
+  "version": "4.4.1",
   "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": {