@jbrowse/bandage-core 8.1.0 → 9.0.0

package/dist/chunks/{chunk-DYYIHN3P.js → chunk-TLQ7F2ZT.js}

@@ -8,12 +8,12 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-O2ANJQVH.js";
+} from "./chunk-WDTXW7T2.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-V3MD3IZB.js";
+} from "./chunk-MIW3HYPE.js";
 import {
   Canvas2DRenderer
 } from "./chunk-2WNBVB55.js";
@@ -42,14 +42,14 @@ import {
 } from "./chunk-HBEKUQO4.js";
 import {
   version
-} from "./chunk-T4SQ5QGM.js";
+} from "./chunk-AMS3MAFP.js";
 import {
   axisScaleOf
 } from "./chunk-TL4B342F.js";
 import {
   walkRowLabels,
   walkRowsExtent
-} from "./chunk-MP7LXLWV.js";
+} from "./chunk-3C5UXR2U.js";
 import {
   nodeInk
 } from "./chunk-PBENCR5L.js";

package/dist/chunks/{chunk-O2ANJQVH.js → chunk-WDTXW7T2.js}

@@ -2,7 +2,7 @@ import {
   alongRow,
   boxesGenes,
   rowPitch
-} from "./chunk-V3MD3IZB.js";
+} from "./chunk-MIW3HYPE.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";

package/dist/chunks/{chunk-OWFPAIJI.js → chunk-WEDZ76AK.js}

@@ -1,6 +1,6 @@
 import {
   tubeSpan
-} from "./chunk-DRA7733Q.js";
+} from "./chunk-BPRXQ2SS.js";
 
 // src/tubeMap/genes.ts
 function tubeMapGenes(byRefName, genes) {

package/dist/chunks/{chunk-3PYY7OIP.js → chunk-WNUZP3WQ.js}

@@ -1,8 +1,9 @@
 import {
+  hasTubeMapBackbone,
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-W2I4DOL4.js";
+} from "./chunk-INJ2UVOT.js";
 import {
   sampleRowLayout
 } from "./chunk-LOEA5IHZ.js";
@@ -14,7 +15,7 @@ import {
 } from "./chunk-HNQPEMYE.js";
 import {
   walkRowLayout
-} from "./chunk-MP7LXLWV.js";
+} from "./chunk-3C5UXR2U.js";
 import {
   isBackbone,
   isOffReference
@@ -24,7 +25,6 @@ import {
 var FORCE_LAYOUT_LABEL = "Force-directed layout";
 var hasBackbone = (graph) => graph.nodes.some(isBackbone);
 var hasWalks = (graph) => hasBackbone(graph) && (graph.paths?.length ?? 0) > 1;
-var hasTubeMapBackbone = (graph) => hasBackbone(graph) && hasTubeMapPaths(graph);
 var hasAlleles = (graph) => hasBackbone(graph) && graph.nodes.some(isOffReference);
 var LAYOUT_MODES = [
   {

package/dist/chunks/{chunk-733L2TS6.js → chunk-XXT2JCAC.js}

@@ -3,16 +3,13 @@ import { forward, getXCoordinateOfBaseWithinNode } from "@jbrowse/tubemap-core";
 function readMismatches(read, layout) {
   const marks = [];
   const entries = read.sequenceNew ?? [];
+  const visits = read.path.filter((segment) => segment.node !== null);
   entries.forEach((entry, i) => {
     const nodeIndex = layout.nodeMap.get(forward(entry.nodeName));
     const node = nodeIndex === void 0 ? void 0 : layout.nodes[nodeIndex];
-    let pathIndex = i;
-    while (pathIndex < read.path.length && read.path[pathIndex].node !== nodeIndex) {
-      pathIndex += 1;
-    }
-    const y = read.path[pathIndex]?.y;
+    const y = visits[i]?.y;
     if (node && y !== void 0) {
-      const base = { readId: read.id, y, height: read.width, nodeY: node.y };
+      const base = { readId: read.id, y, height: read.width };
       const at = (pos) => getXCoordinateOfBaseWithinNode(node, pos);
       for (const mm of entry.mismatches) {
         const x0 = at(mm.pos);
@@ -29,7 +26,13 @@ function readMismatches(read, layout) {
           } else if (mm.type === "deletion" && mm.length !== void 0) {
             const x1 = at(mm.pos + mm.length);
             if (x1 !== null) {
-              marks.push({ ...base, kind: "deletion", x0, x1 });
+              marks.push({
+                ...base,
+                kind: "deletion",
+                x0,
+                x1,
+                length: mm.length
+              });
             }
           } else if (mm.type === "substitution" && mm.seq !== void 0) {
             const x1 = at(mm.pos + mm.seq.length);

package/dist/chunks/{chunk-GQ2AOHU4.js → chunk-YOYLCLIG.js}

@@ -1,35 +1,14 @@
-import {
-  isBackbone
-} from "./chunk-FYQWPEEY.js";
-
 // src/tubeMap/connectors.ts
-function referenceNodes(graph, layout) {
-  const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));
-  const out = [];
-  layout.nodes.forEach((node) => {
-    const graphNode = nodeById.get(node.name);
-    if (node.order >= 0 && graphNode && isBackbone(graphNode)) {
-      out.push({
-        node: node.name,
-        bp0: graphNode.stable.start,
-        bp1: graphNode.stable.start + node.sequenceLength,
-        x0: node.x,
-        x1: node.x + node.pixelWidth
-      });
-    }
-  });
-  return out;
-}
-function tubeMapConnectors(nodes, bpToScreen, tubeToScreen, width) {
+function tubeMapConnectors(boxes, bpToScreen, tubeToScreen, width) {
   const out = [];
-  for (const n of nodes) {
-    const bottom0 = tubeToScreen(n.x0);
-    const bottom1 = tubeToScreen(n.x1);
+  for (const box of boxes) {
+    const bottom0 = tubeToScreen(box.x0);
+    const bottom1 = tubeToScreen(box.x1);
     if (bottom1 >= 0 && bottom0 <= width) {
       out.push({
-        node: n.node,
-        top0: bpToScreen(n.bp0),
-        top1: bpToScreen(n.bp1),
+        node: box.name,
+        top0: bpToScreen(box.bp0),
+        top1: bpToScreen(box.bp1),
         bottom0,
         bottom1
       });
@@ -105,7 +84,6 @@ function drawTubeMapConnectors(ctx, connectors, bottom, {
 }
 
 export {
-  referenceNodes,
   tubeMapConnectors,
   connectorAt,
   drawTubeMapConnectors

package/dist/cli/figure.js

@@ -7,9 +7,9 @@ import {
 import {
   LAYOUT_MODES,
   layoutModeByValue
-} from "../chunks/chunk-3PYY7OIP.js";
-import "../chunks/chunk-W2I4DOL4.js";
-import "../chunks/chunk-TEDQJPMI.js";
+} from "../chunks/chunk-WNUZP3WQ.js";
+import "../chunks/chunk-INJ2UVOT.js";
+import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-LOEA5IHZ.js";
 import "../chunks/chunk-L3O7AWLI.js";
 import "../chunks/chunk-TZFWUT2C.js";
@@ -35,14 +35,14 @@ import "../chunks/chunk-LYJ4US66.js";
 import "../chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "../chunks/chunk-DYYIHN3P.js";
+} from "../chunks/chunk-TLQ7F2ZT.js";
 import "../chunks/chunk-LOCJN3BZ.js";
 import "../chunks/chunk-47DYCZOK.js";
-import "../chunks/chunk-O2ANJQVH.js";
+import "../chunks/chunk-WDTXW7T2.js";
 import {
   genesOnRow,
   placeRowGenes
-} from "../chunks/chunk-V3MD3IZB.js";
+} from "../chunks/chunk-MIW3HYPE.js";
 import "../chunks/chunk-2WNBVB55.js";
 import "../chunks/chunk-4BYTEJGW.js";
 import "../chunks/chunk-3S3YVOJ7.js";
@@ -53,13 +53,13 @@ import "../chunks/chunk-2LQ5BWT7.js";
 import "../chunks/chunk-6ZNQJ5ZD.js";
 import "../chunks/chunk-HBEKUQO4.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-T4SQ5QGM.js";
+import "../chunks/chunk-AMS3MAFP.js";
 import "../chunks/chunk-TL4B342F.js";
-import "../chunks/chunk-MP7LXLWV.js";
+import "../chunks/chunk-3C5UXR2U.js";
 import {
   filterSamples,
   walkRows
-} from "../chunks/chunk-SZNZ2T6D.js";
+} from "../chunks/chunk-MAUEPAMG.js";
 import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-7GBL7SJY.js";
 import {

package/dist/figure.js

@@ -1,10 +1,10 @@
 import {
   figureSvg
-} from "./chunks/chunk-DYYIHN3P.js";
+} from "./chunks/chunk-TLQ7F2ZT.js";
 import "./chunks/chunk-LOCJN3BZ.js";
 import "./chunks/chunk-47DYCZOK.js";
-import "./chunks/chunk-O2ANJQVH.js";
-import "./chunks/chunk-V3MD3IZB.js";
+import "./chunks/chunk-WDTXW7T2.js";
+import "./chunks/chunk-MIW3HYPE.js";
 import "./chunks/chunk-2WNBVB55.js";
 import "./chunks/chunk-4BYTEJGW.js";
 import "./chunks/chunk-3S3YVOJ7.js";
@@ -15,10 +15,10 @@ import "./chunks/chunk-2LQ5BWT7.js";
 import "./chunks/chunk-6ZNQJ5ZD.js";
 import "./chunks/chunk-HBEKUQO4.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-T4SQ5QGM.js";
+import "./chunks/chunk-AMS3MAFP.js";
 import "./chunks/chunk-TL4B342F.js";
-import "./chunks/chunk-MP7LXLWV.js";
-import "./chunks/chunk-SZNZ2T6D.js";
+import "./chunks/chunk-3C5UXR2U.js";
+import "./chunks/chunk-MAUEPAMG.js";
 import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-7GBL7SJY.js";
 import "./chunks/chunk-RAKOB6IV.js";

package/dist/index.js

@@ -3,8 +3,10 @@ import {
 } from "./chunks/chunk-TDQLINVI.js";
 import {
   drawTubeMap,
-  tubeMapPicture
-} from "./chunks/chunk-KCRL5JB2.js";
+  tubeMapMismatchAt,
+  tubeMapPicture,
+  tubeMapTrackAt
+} from "./chunks/chunk-LLP3FXPM.js";
 import {
   tubeMapFrame,
   tubeMapNodeAt
@@ -12,8 +14,8 @@ import {
 import {
   drawTubeMapGenes,
   tubeMapGenes
-} from "./chunks/chunk-OWFPAIJI.js";
-import "./chunks/chunk-733L2TS6.js";
+} from "./chunks/chunk-WEDZ76AK.js";
+import "./chunks/chunk-XXT2JCAC.js";
 import {
   tubeMapNodeColors
 } from "./chunks/chunk-FFFQNQUI.js";
@@ -26,13 +28,12 @@ import {
   referenceBoxes,
   rulerBoxes,
   tubeX
-} from "./chunks/chunk-DRA7733Q.js";
+} from "./chunks/chunk-BPRXQ2SS.js";
 import {
   connectorAt,
   drawTubeMapConnectors,
-  referenceNodes,
   tubeMapConnectors
-} from "./chunks/chunk-GQ2AOHU4.js";
+} from "./chunks/chunk-YOYLCLIG.js";
 import {
   createForceLayoutCache
 } from "./chunks/chunk-SKKYLBRA.js";
@@ -69,9 +70,9 @@ import {
   LAYOUT_MODES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-3PYY7OIP.js";
-import "./chunks/chunk-W2I4DOL4.js";
-import "./chunks/chunk-TEDQJPMI.js";
+} from "./chunks/chunk-WNUZP3WQ.js";
+import "./chunks/chunk-INJ2UVOT.js";
+import "./chunks/chunk-CWFNEKST.js";
 import "./chunks/chunk-LOEA5IHZ.js";
 import "./chunks/chunk-L3O7AWLI.js";
 import "./chunks/chunk-TZFWUT2C.js";
@@ -112,7 +113,7 @@ import {
 } from "./chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "./chunks/chunk-DYYIHN3P.js";
+} from "./chunks/chunk-TLQ7F2ZT.js";
 import {
   layoutGeometryInputs
 } from "./chunks/chunk-LOCJN3BZ.js";
@@ -130,7 +131,7 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunks/chunk-O2ANJQVH.js";
+} from "./chunks/chunk-WDTXW7T2.js";
 import {
   BAR_PX,
   CALL_TICK,
@@ -157,7 +158,7 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunks/chunk-V3MD3IZB.js";
+} from "./chunks/chunk-MIW3HYPE.js";
 import {
   Canvas2DRenderer
 } from "./chunks/chunk-2WNBVB55.js";
@@ -204,7 +205,7 @@ import {
 import "./chunks/chunk-G2FD7S3C.js";
 import {
   version
-} from "./chunks/chunk-T4SQ5QGM.js";
+} from "./chunks/chunk-AMS3MAFP.js";
 import {
   axisScaleOf,
   contains,
@@ -216,11 +217,11 @@ import {
 import {
   walkRowLabels,
   walkRowsExtent
-} from "./chunks/chunk-MP7LXLWV.js";
+} from "./chunks/chunk-3C5UXR2U.js";
 import {
   filterSamples,
   walkRows
-} from "./chunks/chunk-SZNZ2T6D.js";
+} from "./chunks/chunk-MAUEPAMG.js";
 import {
   NODE_WIDTHS,
   maxNodeWidthPx,
@@ -463,7 +464,6 @@ export {
   referenceBoxes,
   referenceKnots,
   referenceLabel,
-  referenceNodes,
   referencePathQuery,
   referenceSamplesOf,
   referenceStripBlocks,
@@ -489,9 +489,11 @@ export {
   tubeMapConnectors,
   tubeMapFrame,
   tubeMapGenes,
+  tubeMapMismatchAt,
   tubeMapNodeAt,
   tubeMapNodeColors,
   tubeMapPicture,
+  tubeMapTrackAt,
   tubeX,
   unitTicks,
   version,

package/dist/layout/tubeMapLayout.js

@@ -1,12 +1,15 @@
 import {
+  boxGraph,
+  hasTubeMapBackbone,
   hasTubeMapPaths,
+  mergedRuns,
+  pathSteps,
   tubeMapLayout,
   tubeMapReferenceLayout,
   tubeMapTracks,
-  tubeWidth,
-  visitStrands
-} from "../chunks/chunk-W2I4DOL4.js";
-import "../chunks/chunk-TEDQJPMI.js";
+  tubeWidth
+} from "../chunks/chunk-INJ2UVOT.js";
+import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
 import "../chunks/chunk-7GBL7SJY.js";
 import "../chunks/chunk-3ZZSX5HN.js";
@@ -19,10 +22,13 @@ import "../chunks/chunk-2CVHXFK7.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {
+  boxGraph,
+  hasTubeMapBackbone,
   hasTubeMapPaths,
+  mergedRuns,
+  pathSteps,
   tubeMapLayout,
   tubeMapReferenceLayout,
   tubeMapTracks,
-  tubeWidth,
-  visitStrands
+  tubeWidth
 };

package/dist/layout/walkRowDraw.js

@@ -26,7 +26,7 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "../chunks/chunk-V3MD3IZB.js";
+} from "../chunks/chunk-MIW3HYPE.js";
 import "../chunks/chunk-6ZNQJ5ZD.js";
 import "../chunks/chunk-HBEKUQO4.js";
 import "../chunks/chunk-G2FD7S3C.js";

package/dist/layout/walkRowLayout.js

@@ -2,8 +2,8 @@ import {
   walkRowLabels,
   walkRowLayout,
   walkRowsExtent
-} from "../chunks/chunk-MP7LXLWV.js";
-import "../chunks/chunk-SZNZ2T6D.js";
+} from "../chunks/chunk-3C5UXR2U.js";
+import "../chunks/chunk-MAUEPAMG.js";
 import "../chunks/chunk-ST2IBUAN.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-CPMHA4W5.js";

package/dist/layout/walkRows.js

@@ -1,7 +1,7 @@
 import {
   filterSamples,
   walkRows
-} from "../chunks/chunk-SZNZ2T6D.js";
+} from "../chunks/chunk-MAUEPAMG.js";
 import "../chunks/chunk-ST2IBUAN.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-FYQWPEEY.js";

package/dist/layout/walkStrip.js

@@ -9,10 +9,10 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "../chunks/chunk-O2ANJQVH.js";
+} from "../chunks/chunk-WDTXW7T2.js";
 import {
   LABELLED_ROW_PX
-} from "../chunks/chunk-V3MD3IZB.js";
+} from "../chunks/chunk-MIW3HYPE.js";
 import "../chunks/chunk-6ZNQJ5ZD.js";
 import "../chunks/chunk-HBEKUQO4.js";
 import "../chunks/chunk-G2FD7S3C.js";

package/dist/layoutModes.js

@@ -4,17 +4,17 @@ import {
   LAYOUT_MODE_VALUES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-3PYY7OIP.js";
-import "./chunks/chunk-W2I4DOL4.js";
-import "./chunks/chunk-TEDQJPMI.js";
+} from "./chunks/chunk-WNUZP3WQ.js";
+import "./chunks/chunk-INJ2UVOT.js";
+import "./chunks/chunk-CWFNEKST.js";
 import "./chunks/chunk-LOEA5IHZ.js";
 import "./chunks/chunk-L3O7AWLI.js";
 import "./chunks/chunk-TZFWUT2C.js";
 import "./chunks/chunk-C44YRP5F.js";
 import "./chunks/chunk-RVS2QCOX.js";
 import "./chunks/chunk-HNQPEMYE.js";
-import "./chunks/chunk-MP7LXLWV.js";
-import "./chunks/chunk-SZNZ2T6D.js";
+import "./chunks/chunk-3C5UXR2U.js";
+import "./chunks/chunk-MAUEPAMG.js";
 import "./chunks/chunk-7GBL7SJY.js";
 import "./chunks/chunk-3ZZSX5HN.js";
 import "./chunks/chunk-AB35TJST.js";

package/dist/tubeMap/axis.js

@@ -6,7 +6,7 @@ import {
   rulerMarks,
   tubeSpan,
   tubeX
-} from "../chunks/chunk-DRA7733Q.js";
+} from "../chunks/chunk-BPRXQ2SS.js";
 import "../chunks/chunk-3ZZSX5HN.js";
 import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-TAMCZHLW.js";

package/dist/tubeMap/coarsen.js

@@ -1,9 +1,7 @@
 import {
-  visitStrands
-} from "../chunks/chunk-W2I4DOL4.js";
-import {
-  canonicalStrand
-} from "../chunks/chunk-TEDQJPMI.js";
+  pathSteps
+} from "../chunks/chunk-INJ2UVOT.js";
+import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
 import "../chunks/chunk-7GBL7SJY.js";
 import "../chunks/chunk-3ZZSX5HN.js";
@@ -21,20 +19,11 @@ import {
 } from "../chunks/chunk-FYQWPEEY.js";
 
 // src/tubeMap/coarsen.ts
-function readWalk(path, nodeById, strands) {
-  const visitName = pathOrigin(path.name).name;
-  const seen = /* @__PURE__ */ new Map();
+function readWalk(path, steps) {
   const runs = [];
   const open = () => ({ a: -Infinity, b: Infinity, detour: [], bp: 0 });
   const gaps = [open()];
-  for (const id of path.nodeIds) {
-    const node = nodeById.get(id);
-    if (!node) {
-      continue;
-    }
-    const k = seen.get(node.name) ?? 0;
-    seen.set(node.name, k + 1);
-    const strand = strands.get(`${visitName}	${node.name}`)?.[k] ?? canonicalStrand(node);
+  for (const { node, strand } of steps) {
     const gap = gaps.at(-1);
     const last = runs.at(-1);
     if (isBackbone(node)) {
@@ -119,13 +108,13 @@ function findCuts(walks, sigma, cuts) {
       }
     }
   }
+  const spans = walks.flatMap(({ runs, gaps }) => [
+    ...gaps.filter((g) => isSmall(g, sigma)).map((g) => [g.a, g.b]),
+    ...runs.filter((r) => r.inverted && r.end - r.start < sigma).map((r) => [r.start, r.end])
+  ]);
   for (let changed = true; changed; ) {
     changed = false;
     const sorted = [...cuts.keys()].sort((x, y) => x - y);
-    const spans = walks.flatMap(({ runs, gaps }) => [
-      ...gaps.filter((g) => isSmall(g, sigma)).map((g) => [g.a, g.b]),
-      ...runs.filter((r) => r.inverted && r.end - r.start < sigma).map((r) => [r.start, r.end])
-    ]);
     for (const [a, b] of spans) {
       if (strictlyInside(sorted, a, b)) {
         changed ||= !cuts.has(a) || !cuts.has(b);
@@ -179,9 +168,8 @@ function coarsenTubeMap(graph, sigma) {
   if (backbone.length === 0 || paths.length === 0) {
     return void 0;
   }
-  const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));
-  const strands = visitStrands(graph);
-  const walks = paths.map((p) => readWalk(p, nodeById, strands));
+  const stepsOf = pathSteps(graph);
+  const walks = paths.map((p, i) => readWalk(p, stepsOf[i]));
   const cuts = findCuts(walks, sigma, referenceGaps(backbone));
   const sortedCuts = [...cuts.keys()].sort((x, y) => x - y);
   const merged = mergeReference(backbone, cuts);

package/dist/tubeMap/connectors.js

@@ -1,13 +1,10 @@
 import {
   connectorAt,
   drawTubeMapConnectors,
-  referenceNodes,
   tubeMapConnectors
-} from "../chunks/chunk-GQ2AOHU4.js";
-import "../chunks/chunk-FYQWPEEY.js";
+} from "../chunks/chunk-YOYLCLIG.js";
 export {
   connectorAt,
   drawTubeMapConnectors,
-  referenceNodes,
   tubeMapConnectors
 };

package/dist/tubeMap/deviations.js

@@ -1,20 +1,15 @@
 import {
-  isBackbone
-} from "../chunks/chunk-FYQWPEEY.js";
+  referenceBoxes
+} from "../chunks/chunk-BPRXQ2SS.js";
+import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-TAMCZHLW.js";
+import "../chunks/chunk-N6FECAXP.js";
+import "../chunks/chunk-2CVHXFK7.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-FYQWPEEY.js";
 
 // src/tubeMap/deviations.ts
-function boxesOf(graph, layout) {
-  const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));
-  const boxes = [];
-  layout.nodes.forEach((node, index) => {
-    const g = nodeById.get(node.name);
-    if (node.order >= 0 && g && isBackbone(g)) {
-      const bp0 = g.stable.start;
-      boxes.push({ bp0, bp1: bp0 + node.sequenceLength, index, node });
-    }
-  });
-  return boxes.sort((a, b) => a.bp0 - b.bp0);
-}
 function boxAt(boxes, bp, visited) {
   let lo = 0;
   let hi = boxes.length - 1;
@@ -30,8 +25,9 @@ function boxAt(boxes, bp, visited) {
     (box) => box && visited.has(box.index) && box.bp0 <= bp && bp <= box.bp1
   );
 }
-function deviationMarks(graph, layout, deviations) {
-  const boxes = boxesOf(graph, layout);
+function deviationMarks(drawing, deviations) {
+  const { layout } = drawing;
+  const boxes = [...referenceBoxes(drawing).values()].flat().sort((a, b) => a.bp0 - b.bp0);
   const marks = [];
   for (const track of layout.tracks) {
     const devs = track.name ? deviations.get(track.name) : void 0;
@@ -45,12 +41,12 @@ function deviationMarks(graph, layout, deviations) {
       for (const d of devs) {
         const box = boxAt(boxes, d.start, visited);
         if (box) {
-          const { node, bp0, bp1 } = box;
-          const at = (bp) => node.x + (Math.min(bp, bp1) - bp0) / (bp1 - bp0) * node.pixelWidth;
+          const { bp0, bp1, x0, x1, index } = box;
+          const at = (bp) => x0 + (Math.min(bp, bp1) - bp0) / (bp1 - bp0) * (x1 - x0);
           marks.push({
             x0: at(d.start),
             x1: at(d.end),
-            y: visited.get(box.index),
+            y: visited.get(index),
             height: track.width
           });
         }

package/dist/tubeMap/draw.js

@@ -4,10 +4,12 @@ import {
   mismatchesLegible,
   parsePath,
   trackColors,
-  tubeMapPicture
-} from "../chunks/chunk-KCRL5JB2.js";
-import "../chunks/chunk-733L2TS6.js";
-import "../chunks/chunk-TEDQJPMI.js";
+  tubeMapMismatchAt,
+  tubeMapPicture,
+  tubeMapTrackAt
+} from "../chunks/chunk-LLP3FXPM.js";
+import "../chunks/chunk-XXT2JCAC.js";
+import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
 export {
   drawTubeMap,
@@ -15,5 +17,7 @@ export {
   mismatchesLegible,
   parsePath,
   trackColors,
-  tubeMapPicture
+  tubeMapMismatchAt,
+  tubeMapPicture,
+  tubeMapTrackAt
 };

package/dist/tubeMap/genes.js

@@ -3,8 +3,8 @@ import {
   drawTubeMapGenes,
   tubeMapGeneRows,
   tubeMapGenes
-} from "../chunks/chunk-OWFPAIJI.js";
-import "../chunks/chunk-DRA7733Q.js";
+} from "../chunks/chunk-WEDZ76AK.js";
+import "../chunks/chunk-BPRXQ2SS.js";
 import "../chunks/chunk-3ZZSX5HN.js";
 import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-TAMCZHLW.js";

package/dist/tubeMap/mismatches.js

@@ -1,6 +1,6 @@
 import {
   tubeMapMismatches
-} from "../chunks/chunk-733L2TS6.js";
+} from "../chunks/chunk-XXT2JCAC.js";
 export {
   tubeMapMismatches
 };