@jbrowse/bandage-core 8.0.2 → 8.2.0

package/README.md

@@ -8,7 +8,8 @@ and [BandageJS](https://github.com/cmdcolin/BandageJS).
 npm install @jbrowse/bandage-core
 ```
 
-- GFA and rGFA text in (`loadGraph`)
+- GFA and rGFA text in (`loadGraph`), or the same graph as typed arrays a worker
+  can transfer (`GraphTables`)
 - Layouts: Bandage's FMMM engine as WASM (`loadBandage`, `forceLayout`),
   ordered, anchored, sample rows, walk rows, tube map
 - A Canvas2D renderer (`buildGeometry`, `Canvas2DRenderer`), hit testing and

package/dist/chunks/{chunk-MP7LXLWV.js → chunk-3C5UXR2U.js}

@@ -1,6 +1,6 @@
 import {
   walkRows
-} from "./chunk-SZNZ2T6D.js";
+} from "./chunk-MAUEPAMG.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-XNE4UNSJ.js → chunk-3FXPFVKJ.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "8.0.2";
+var version = "8.2.0";
 
 export {
   version

package/dist/chunks/{chunk-XRPU24OP.js → chunk-5OIVTEF7.js}

@@ -1,15 +1,18 @@
-import {
-  seededNodes
-} from "./chunk-IGVV37VI.js";
 import {
   orientToReference
 } from "./chunk-PUG7LXDF.js";
+import {
+  seededNodes
+} from "./chunk-IGVV37VI.js";
 import {
   convertGFAToGraph
 } from "./chunk-OCMBULGN.js";
 import {
   parseGFA
 } from "./chunk-CDLPYR5O.js";
+import {
+  graphFromTables
+} from "./chunk-OA7RIMZ2.js";
 import {
   anchorGraph
 } from "./chunk-ST2IBUAN.js";
@@ -39,9 +42,9 @@ import {
 } from "./chunk-FYQWPEEY.js";
 
 // src/pipeline.ts
-function loadGraph(text, name, opts = {}) {
+function loadGraph(source, name, opts = {}) {
   const graph = anchorGraph(
-    convertGFAToGraph(parseGFA(text), name),
+    typeof source === "string" ? convertGFAToGraph(parseGFA(source), name) : graphFromTables(source, name),
     opts.referencePath
   );
   if (graph.nodes.length === 0) {

package/dist/chunks/{chunk-WC3Y3TD2.js → chunk-6VBDMZBZ.js}

@@ -1,6 +1,6 @@
 import {
   ENGINE_DEFAULTS
-} from "./chunk-XRPU24OP.js";
+} from "./chunk-5OIVTEF7.js";
 
 // src/figureSettings.ts
 var FIGURE_DEFAULTS = {

package/dist/chunks/{chunk-ZJQ6H3AR.js → chunk-CF62U3QS.js}

@@ -1,11 +1,11 @@
-import {
-  sampleRowLayout
-} from "./chunk-LOEA5IHZ.js";
 import {
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
 } from "./chunk-W2I4DOL4.js";
+import {
+  sampleRowLayout
+} from "./chunk-LOEA5IHZ.js";
 import {
   anchoredLayout
 } from "./chunk-L3O7AWLI.js";
@@ -14,7 +14,7 @@ import {
 } from "./chunk-HNQPEMYE.js";
 import {
   walkRowLayout
-} from "./chunk-MP7LXLWV.js";
+} from "./chunk-3C5UXR2U.js";
 import {
   isBackbone,
   isOffReference

package/dist/chunks/{chunk-H5ABLOPB.js → chunk-DE4UFDUZ.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-XNE4UNSJ.js";
+} from "./chunk-3FXPFVKJ.js";
 import {
   axisScaleOf
-} from "./chunk-AO2VAMA4.js";
+} from "./chunk-TL4B342F.js";
 import {
   walkRowLabels,
   walkRowsExtent
-} from "./chunk-MP7LXLWV.js";
+} from "./chunk-3C5UXR2U.js";
 import {
   nodeInk
 } from "./chunk-PBENCR5L.js";
@@ -91,7 +91,7 @@ import {
   FIT_PADDING,
   drawingBounds,
   fitTransform
-} from "./chunk-XRPU24OP.js";
+} from "./chunk-5OIVTEF7.js";
 import {
   deletionDrawing,
   deletionEdges

package/dist/chunks/{chunk-SZNZ2T6D.js → chunk-MAUEPAMG.js}

@@ -53,12 +53,16 @@ function sliceBetween(steps, span, region, flanked = true) {
   if (!region || !flanked) {
     return { ids: steps, complete: true, from: -1, to: -1 };
   }
+  const spanAt = (i) => {
+    const id = steps[i];
+    return typeof id === "string" ? span.get(id) : void 0;
+  };
   let i0 = -1;
   let i1 = -1;
   let bestEnd = -Infinity;
   let bestStart = Infinity;
-  steps.forEach((id, i) => {
-    const s = typeof id === "string" ? span.get(id) : void 0;
+  steps.forEach((_, i) => {
+    const s = spanAt(i);
     if (s) {
       if (s.end <= region.start && s.end > bestEnd) {
         bestEnd = s.end;
@@ -70,15 +74,38 @@ function sliceBetween(steps, span, region, flanked = true) {
       }
     }
   });
-  if (i0 < 0 || i1 < 0) {
+  if (i0 >= 0 && i1 >= 0) {
+    const ids2 = steps.slice(Math.min(i0, i1) + 1, Math.max(i0, i1));
+    return {
+      ids: i0 < i1 ? ids2 : ids2.reverse(),
+      complete: true,
+      from: i0,
+      to: i1
+    };
+  }
+  const flank = i0 >= 0 ? i0 : i1;
+  let near = -1;
+  for (let d = 1; flank >= 0 && near < 0 && d < steps.length; d++) {
+    near = [flank - d, flank + d].find((j) => spanAt(j) !== void 0) ?? -1;
+  }
+  if (near < 0) {
     return { ids: steps, complete: false, from: -1, to: -1 };
   }
-  const ids = steps.slice(Math.min(i0, i1) + 1, Math.max(i0, i1));
+  const forward = near > flank === spanAt(near).start > spanAt(flank).start;
+  const after = forward === (flank === i0);
+  const ids = after ? steps.slice(flank + 1) : steps.slice(0, flank).reverse();
+  const last = ids.length > 0 ? ids.length - 1 : -1;
+  const end = last < 0 ? spanAt(flank) : spanAt(after ? flank + 1 + last : 0);
+  const stop = {
+    contigEnds: end !== void 0,
+    shortBp: !end ? 0 : Math.max(0, region.start - end.end, end.start - region.end)
+  };
   return {
-    ids: i0 < i1 ? ids : ids.reverse(),
-    complete: true,
-    from: i0,
-    to: i1
+    ids,
+    complete: false,
+    from: flank,
+    to: after ? steps.length : -1,
+    stop
   };
 }
 function filterSamples(rows, samples) {
@@ -117,7 +144,7 @@ function walkRows(graph, region, unit) {
   const rowOf = (pieces) => {
     const path = pieces[0];
     const ordered = [...pieces].sort((a, b) => (a.start ?? 0) - (b.start ?? 0));
-    const { ids, complete, from, to } = sliceBetween(
+    const { ids, complete, from, to, stop } = sliceBetween(
       stepsOf(ordered, lengthOf),
       span,
       cut,
@@ -177,6 +204,7 @@ function walkRows(graph, region, unit) {
       offReferenceBp,
       gapBp,
       complete,
+      stop,
       runs,
       axis
     };

package/dist/chunks/{chunk-V3MD3IZB.js → chunk-MIW3HYPE.js}

@@ -34,15 +34,24 @@ function units(bp, unit) {
   return unit ? ` \u2248 ${Math.round(bp / unit)} units` : "";
 }
 function walkRowReadout(row, reference, unit, call) {
-  const { bp, gapBp, complete } = row;
+  const { bp, gapBp, complete, stop } = row;
   if (!reference) {
     return `${kb(bp)}${units(bp, unit)}`;
   }
-  const delta = bp - reference.bp;
-  const against = delta === 0 ? "" : ` (${delta > 0 ? "+" : "\u2212"}${kb(Math.abs(delta))})`;
   const outside = gapBp > 0 ? ` \xB7 ${kb(gapBp)} outside the cut` : "";
   const called = call ? ` \xB7 called ${kb(call.bp)}${call.spanningReads === 0 ? " \xB7 no spanning read" : ""}` : "";
-  return `${kb(bp)}${units(bp, unit)}${against}${outside}${complete ? "" : " \xB7 partial walk"}${called}`;
+  if (complete) {
+    const delta = bp - reference.bp;
+    const against = delta === 0 ? "" : ` (${delta > 0 ? "+" : "\u2212"}${kb(Math.abs(delta))})`;
+    return `${kb(bp)}${units(bp, unit)}${against}${outside}${called}`;
+  }
+  const region = unit ? "repeat" : "window";
+  if (stop?.contigEnds && bp === 0) {
+    const where = stop.shortBp > 0 ? `${kb(stop.shortBp)} before` : "at";
+    return `contig ends ${where} the ${region}${called}`;
+  }
+  const why = !stop ? "partial walk" : stop.contigEnds ? `contig ends inside the ${region}` : "does not rejoin the reference within the cut";
+  return `\u2265 ${kb(bp)}${units(bp, unit)} \xB7 ${why}${outside}${called}`;
 }
 function readoutPlacement(text, endX, width) {
   const x = endX + 6;

package/dist/chunks/chunk-OA7RIMZ2.js

@@ -0,0 +1,211 @@
+import {
+  panSNSample
+} from "./chunk-BPLIXMH7.js";
+
+// src/gfa/graphTables.ts
+function walkFields(panSN) {
+  const [sample = "", haplotype = "", ...contig] = panSN.split("#");
+  return { sample, haplotype, contig: contig.join("#") };
+}
+function graphFromTables({ nodes: n, links: l, walks: w }, name = "Imported GFA") {
+  const count = n.names.length;
+  const declared = n.lengths.length;
+  const canonical = new Uint8Array(count);
+  const claim = (node, reversed) => {
+    if (canonical[node] === 0) {
+      canonical[node] = reversed ? 2 : 1;
+    }
+  };
+  for (let i = 0; i < l.from.length; i++) {
+    claim(l.from[i], l.strands[i] & 1);
+    claim(l.to[i], l.strands[i] & 2);
+  }
+  const drawnWalks = [];
+  for (let p = 0; p < w.names.length; p++) {
+    if (w.offsets[p + 1] > w.offsets[p]) {
+      drawnWalks.push(p);
+    }
+  }
+  const traversals = new Int32Array(count);
+  for (const p of drawnWalks) {
+    for (let s = w.offsets[p]; s < w.offsets[p + 1]; s++) {
+      const node = w.steps[s];
+      if (traversals[node] === 0) {
+        claim(node, w.reversed[s]);
+      }
+      traversals[node]++;
+    }
+  }
+  const ids = n.names.map(
+    (segment, i) => `${segment}${canonical[i] === 2 ? "-" : "+"}`
+  );
+  const nodes = [];
+  for (let i = 0; i < declared; i++) {
+    const ref = n.refs[i];
+    nodes.push({
+      id: ids[i],
+      name: n.names[i],
+      length: n.lengths[i],
+      depth: Math.max(traversals[i], 1),
+      stable: ref < 0 ? void 0 : {
+        refName: n.refNames[ref],
+        start: n.starts[i],
+        rank: n.ranks[i]
+      },
+      samples: void 0
+    });
+  }
+  const edges = [];
+  const neighbours = new Array(count);
+  const pairList = (a, b) => {
+    const near = neighbours[a];
+    if (near) {
+      for (let j = 0; j < near.length; j += 2) {
+        if (near[j] === b) {
+          return near[j + 1];
+        }
+      }
+    }
+    return void 0;
+  };
+  const addPair = (a, b, list) => {
+    const near = neighbours[a];
+    if (near) {
+      near.push(b, list);
+    } else {
+      neighbours[a] = [b, list];
+    }
+  };
+  const edgeLists = [];
+  let lists = 0;
+  for (let i = 0; i < l.from.length; i++) {
+    const a = l.from[i];
+    const b = l.to[i];
+    edges.push({
+      from: ids[a],
+      to: ids[b],
+      fromStrand: l.strands[i] & 1 ? "-" : "+",
+      toStrand: l.strands[i] & 2 ? "-" : "+"
+    });
+    let list = pairList(a, b);
+    if (list === void 0) {
+      list = lists++;
+      addPair(a, b, list);
+      addPair(b, a, list);
+    }
+    edgeLists.push(list);
+  }
+  const nameIndex = /* @__PURE__ */ new Map();
+  const pathNames = [];
+  const crossing = Array.from({ length: lists }, () => []);
+  const lastWalk = new Int32Array(lists).fill(-1);
+  const paths = [];
+  const anchorPaths = [];
+  const visits = new Array(count);
+  const filled = new Int32Array(count);
+  const visitOrder = [];
+  for (const p of drawnWalks) {
+    const { sample, haplotype, contig } = walkFields(w.names[p]);
+    const pathName = `${sample}#${+haplotype}#${contig}`;
+    let named = nameIndex.get(pathName);
+    const repeat = named !== void 0;
+    if (named === void 0) {
+      named = pathNames.length;
+      nameIndex.set(pathName, named);
+      pathNames.push(pathName);
+    }
+    const start = w.starts[p];
+    const visitSample = panSNSample(pathName);
+    const first = w.offsets[p];
+    const nodeIds = new Array(w.offsets[p + 1] - first);
+    let pos = start;
+    let prev = -1;
+    for (let s = first; s < w.offsets[p + 1]; s++) {
+      const node = w.steps[s];
+      nodeIds[s - first] = ids[node];
+      if (filled[node] === 0) {
+        visits[node] = new Array(traversals[node]);
+        visitOrder.push(node);
+      }
+      visits[node][filled[node]++] = {
+        path: pathName,
+        sample: visitSample,
+        start: pos,
+        strand: w.reversed[s] ? "-" : "+"
+      };
+      pos += node < declared ? n.lengths[node] : 0;
+      if (prev >= 0) {
+        const list = pairList(prev, node);
+        if (list !== void 0 && lastWalk[list] !== p) {
+          lastWalk[list] = p;
+          const names = crossing[list];
+          if (!repeat || !names.includes(named)) {
+            names.push(named);
+          }
+        }
+      }
+      prev = node;
+    }
+    paths.push({
+      name: pathName,
+      nodeIds,
+      start,
+      sample,
+      haplotype: +haplotype,
+      contig
+    });
+    anchorPaths.push({
+      name: pathName,
+      sample: visitSample,
+      start,
+      length: pos - start
+    });
+  }
+  edges.forEach((edge, i) => {
+    const names = crossing[edgeLists[i]];
+    if (names.length > 0) {
+      edge.pathIds = names.map((k) => pathNames[k]);
+    }
+  });
+  const walked = drawnWalks.length > 0;
+  return {
+    name,
+    nodes,
+    edges,
+    paths: walked ? paths : void 0,
+    anchorPaths: walked ? anchorPaths : void 0,
+    pathVisits: walked ? new Map(visitOrder.map((node) => [n.names[node], visits[node]])) : void 0,
+    anchoredBy: nodes.some((node) => node.stable) ? "tags" : void 0
+  };
+}
+function graphTablesGFA({ nodes, links, walks }) {
+  const { names } = nodes;
+  const lines = ["H	VN:Z:1.1"];
+  for (let i = 0; i < nodes.lengths.length; i++) {
+    const ref = nodes.refs[i];
+    const stable = ref < 0 ? "" : `	SN:Z:${nodes.refNames[ref]}	SO:i:${nodes.starts[i]}	SR:i:${nodes.ranks[i]}`;
+    lines.push(`S	${names[i]}	*	LN:i:${nodes.lengths[i]}${stable}`);
+  }
+  for (let i = 0; i < links.from.length; i++) {
+    const strands = links.strands[i];
+    lines.push(
+      `L	${names[links.from[i]]}	${strands & 1 ? "-" : "+"}	${names[links.to[i]]}	${strands & 2 ? "-" : "+"}	0M`
+    );
+  }
+  for (let p = 0; p < walks.names.length; p++) {
+    const { sample, haplotype, contig } = walkFields(walks.names[p]);
+    let body = "";
+    for (let s = walks.offsets[p]; s < walks.offsets[p + 1]; s++) {
+      body += (walks.reversed[s] ? "<" : ">") + names[walks.steps[s]];
+    }
+    lines.push(
+      `W	${sample}	${haplotype}	${contig}	${walks.starts[p]}	${walks.ends[p]}	${body}`
+    );
+  }
+  return lines.join("\n");
+}
+
+export {
+  graphFromTables,
+  graphTablesGFA
+};

package/dist/chunks/{chunk-WBFYKGXL.js → chunk-SKKYLBRA.js}

@@ -1,7 +1,7 @@
 import {
   engineKey,
   forceLayout
-} from "./chunk-XRPU24OP.js";
+} from "./chunk-5OIVTEF7.js";
 
 // src/layout/forceCache.ts
 var DEFAULT_SIZE = 4;

package/dist/chunks/{chunk-AO2VAMA4.js → chunk-TL4B342F.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-XRPU24OP.js";
+} from "./chunk-5OIVTEF7.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {

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/cli/figure.js

@@ -7,10 +7,10 @@ import {
 import {
   LAYOUT_MODES,
   layoutModeByValue
-} from "../chunks/chunk-ZJQ6H3AR.js";
-import "../chunks/chunk-LOEA5IHZ.js";
+} from "../chunks/chunk-CF62U3QS.js";
 import "../chunks/chunk-W2I4DOL4.js";
 import "../chunks/chunk-TEDQJPMI.js";
+import "../chunks/chunk-LOEA5IHZ.js";
 import "../chunks/chunk-L3O7AWLI.js";
 import "../chunks/chunk-TZFWUT2C.js";
 import "../chunks/chunk-C44YRP5F.js";
@@ -35,14 +35,14 @@ import "../chunks/chunk-LYJ4US66.js";
 import "../chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "../chunks/chunk-H5ABLOPB.js";
+} from "../chunks/chunk-DE4UFDUZ.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-XNE4UNSJ.js";
-import "../chunks/chunk-AO2VAMA4.js";
-import "../chunks/chunk-MP7LXLWV.js";
+import "../chunks/chunk-3FXPFVKJ.js";
+import "../chunks/chunk-TL4B342F.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 {
@@ -80,12 +80,13 @@ import {
   engineSettingsOf,
   forceLayout,
   loadGraph
-} from "../chunks/chunk-XRPU24OP.js";
-import "../chunks/chunk-IGVV37VI.js";
+} from "../chunks/chunk-5OIVTEF7.js";
 import "../chunks/chunk-PUG7LXDF.js";
+import "../chunks/chunk-IGVV37VI.js";
 import "../chunks/chunk-OCMBULGN.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-CDLPYR5O.js";
+import "../chunks/chunk-OA7RIMZ2.js";
 import "../chunks/chunk-ES2N6V56.js";
 import "../chunks/chunk-ST2IBUAN.js";
 import "../chunks/chunk-BPLIXMH7.js";

package/dist/figure.js

@@ -1,10 +1,10 @@
 import {
   figureSvg
-} from "./chunks/chunk-H5ABLOPB.js";
+} from "./chunks/chunk-DE4UFDUZ.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-XNE4UNSJ.js";
-import "./chunks/chunk-AO2VAMA4.js";
-import "./chunks/chunk-MP7LXLWV.js";
-import "./chunks/chunk-SZNZ2T6D.js";
+import "./chunks/chunk-3FXPFVKJ.js";
+import "./chunks/chunk-TL4B342F.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";
@@ -31,12 +31,13 @@ import "./chunks/chunk-AB35TJST.js";
 import "./chunks/chunk-JKJWSY4V.js";
 import "./chunks/chunk-NNODIW4U.js";
 import "./chunks/chunk-XV4P5KEQ.js";
-import "./chunks/chunk-XRPU24OP.js";
-import "./chunks/chunk-IGVV37VI.js";
+import "./chunks/chunk-5OIVTEF7.js";
 import "./chunks/chunk-PUG7LXDF.js";
+import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-OCMBULGN.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
+import "./chunks/chunk-OA7RIMZ2.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-BPLIXMH7.js";

package/dist/figureSettings.js

@@ -1,13 +1,14 @@
 import {
   FIGURE_DEFAULTS,
   figureSpecSettings
-} from "./chunks/chunk-WC3Y3TD2.js";
-import "./chunks/chunk-XRPU24OP.js";
-import "./chunks/chunk-IGVV37VI.js";
+} from "./chunks/chunk-6VBDMZBZ.js";
+import "./chunks/chunk-5OIVTEF7.js";
 import "./chunks/chunk-PUG7LXDF.js";
+import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-OCMBULGN.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
+import "./chunks/chunk-OA7RIMZ2.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-BPLIXMH7.js";

package/dist/gfa/graphTables.js

@@ -0,0 +1,9 @@
+import {
+  graphFromTables,
+  graphTablesGFA
+} from "../chunks/chunk-OA7RIMZ2.js";
+import "../chunks/chunk-BPLIXMH7.js";
+export {
+  graphFromTables,
+  graphTablesGFA
+};

package/dist/index.js

@@ -35,7 +35,7 @@ import {
 } from "./chunks/chunk-GQ2AOHU4.js";
 import {
   createForceLayoutCache
-} from "./chunks/chunk-WBFYKGXL.js";
+} from "./chunks/chunk-SKKYLBRA.js";
 import {
   bubbleSubgraph
 } from "./chunks/chunk-VHW7FDHU.js";
@@ -69,10 +69,10 @@ import {
   LAYOUT_MODES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-ZJQ6H3AR.js";
-import "./chunks/chunk-LOEA5IHZ.js";
+} from "./chunks/chunk-CF62U3QS.js";
 import "./chunks/chunk-W2I4DOL4.js";
 import "./chunks/chunk-TEDQJPMI.js";
+import "./chunks/chunk-LOEA5IHZ.js";
 import "./chunks/chunk-L3O7AWLI.js";
 import "./chunks/chunk-TZFWUT2C.js";
 import "./chunks/chunk-C44YRP5F.js";
@@ -112,7 +112,7 @@ import {
 } from "./chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "./chunks/chunk-H5ABLOPB.js";
+} from "./chunks/chunk-DE4UFDUZ.js";
 import {
   layoutGeometryInputs
 } from "./chunks/chunk-LOCJN3BZ.js";
@@ -130,7 +130,7 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunks/chunk-O2ANJQVH.js";
+} from "./chunks/chunk-WDTXW7T2.js";
 import {
   BAR_PX,
   CALL_TICK,
@@ -157,7 +157,7 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunks/chunk-V3MD3IZB.js";
+} from "./chunks/chunk-MIW3HYPE.js";
 import {
   Canvas2DRenderer
 } from "./chunks/chunk-2WNBVB55.js";
@@ -204,7 +204,7 @@ import {
 import "./chunks/chunk-G2FD7S3C.js";
 import {
   version
-} from "./chunks/chunk-XNE4UNSJ.js";
+} from "./chunks/chunk-3FXPFVKJ.js";
 import {
   axisScaleOf,
   contains,
@@ -212,15 +212,15 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-AO2VAMA4.js";
+} from "./chunks/chunk-TL4B342F.js";
 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,
@@ -283,7 +283,7 @@ import {
 import {
   FIGURE_DEFAULTS,
   figureSpecSettings
-} from "./chunks/chunk-WC3Y3TD2.js";
+} from "./chunks/chunk-6VBDMZBZ.js";
 import {
   ENGINE_DEFAULTS,
   FIT_PADDING,
@@ -296,12 +296,16 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-XRPU24OP.js";
-import "./chunks/chunk-IGVV37VI.js";
+} from "./chunks/chunk-5OIVTEF7.js";
 import "./chunks/chunk-PUG7LXDF.js";
+import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-OCMBULGN.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
+import {
+  graphFromTables,
+  graphTablesGFA
+} from "./chunks/chunk-OA7RIMZ2.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import {
@@ -425,6 +429,8 @@ export {
   genesOnRow,
   getDpr,
   graphBackbone,
+  graphFromTables,
+  graphTablesGFA,
   haplotypeWanted,
   layoutEngine,
   layoutExtent,

package/dist/layout/forceCache.js

@@ -1,12 +1,13 @@
 import {
   createForceLayoutCache
-} from "../chunks/chunk-WBFYKGXL.js";
-import "../chunks/chunk-XRPU24OP.js";
-import "../chunks/chunk-IGVV37VI.js";
+} from "../chunks/chunk-SKKYLBRA.js";
+import "../chunks/chunk-5OIVTEF7.js";
 import "../chunks/chunk-PUG7LXDF.js";
+import "../chunks/chunk-IGVV37VI.js";
 import "../chunks/chunk-OCMBULGN.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-CDLPYR5O.js";
+import "../chunks/chunk-OA7RIMZ2.js";
 import "../chunks/chunk-ES2N6V56.js";
 import "../chunks/chunk-ST2IBUAN.js";
 import "../chunks/chunk-BPLIXMH7.js";

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-ZJQ6H3AR.js";
-import "./chunks/chunk-LOEA5IHZ.js";
+} from "./chunks/chunk-CF62U3QS.js";
 import "./chunks/chunk-W2I4DOL4.js";
 import "./chunks/chunk-TEDQJPMI.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/pipeline.js

@@ -11,12 +11,13 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-XRPU24OP.js";
-import "./chunks/chunk-IGVV37VI.js";
+} from "./chunks/chunk-5OIVTEF7.js";
 import "./chunks/chunk-PUG7LXDF.js";
+import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-OCMBULGN.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
+import "./chunks/chunk-OA7RIMZ2.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-BPLIXMH7.js";

package/dist/types/gfa/graphTables.d.ts

@@ -0,0 +1,41 @@
+import type { Graph } from '../types.js';
+/**
+ * A graph as typed arrays, the shape a worker can hand across postMessage
+ * without copying: what a GFA of S lines tagged LN/SN/SO/SR, L lines and W
+ * lines states, with every link end and walk step an index into the node
+ * table. `graphFromTables` builds the Graph that converting that GFA builds,
+ * and `graphTablesGFA` writes the GFA.
+ */
+export interface GraphTables {
+    nodes: {
+        names: string[];
+        lengths: Int32Array;
+        refs: Int32Array;
+        starts: Float64Array;
+        ranks: Int32Array;
+        refNames: string[];
+    };
+    links: {
+        from: Int32Array;
+        to: Int32Array;
+        strands: Uint8Array;
+    };
+    walks: {
+        names: string[];
+        starts: Float64Array;
+        ends: Float64Array;
+        offsets: Int32Array;
+        steps: Int32Array;
+        reversed: Uint8Array;
+    };
+}
+/**
+ * The Graph `convertGFAToGraph` builds from `graphTablesGFA(tables)`, deep
+ * equal, built by index: a step costs a few array reads and its visit, where
+ * the text costs a string and several map lookups.
+ */
+export declare function graphFromTables({ nodes: n, links: l, walks: w }: GraphTables, name?: string): Graph;
+/**
+ * The tables as GFA text: S lines in table order, then L lines, then W lines
+ */
+export declare function graphTablesGFA({ nodes, links, walks }: GraphTables): string;

package/dist/types/index.d.ts

@@ -68,7 +68,7 @@ export { BUBBLE_KIND_COLORS, BUBBLE_KIND_NAMES, bubbleSegmentIds, classifyBubble
 export { bubbleSubgraph } from './bubbles/popBubble.js';
 export type { MinigraphBubble } from './bubbles/bubbleLine.js';
 export { filterSamples, walkRows } from './layout/walkRows.js';
-export type { WalkAxis, WalkRow, WalkRows, WalkRun } from './layout/walkRows.js';
+export type { WalkAxis, WalkRow, WalkRows, WalkRun, WalkStop, } from './layout/walkRows.js';
 export { BAR_PX as WALK_BAR_PX, CALL_TICK as WALK_CALL_TICK, 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, UNBACKED_TICK as WALK_UNBACKED_TICK, alongRow, callTickInk, coalesceRuns, genesOnRow, placeRowGenes, readoutPlacement, rowGeneBoxes, rowPitch, rowSpan, runPaint, unitTicks, walkRowReadout, walkRowsKey, walkRowsKeyTree, walkRowsTree, } from './layout/walkRowDraw.js';
 export type { GeneBox, GeneGaps, KeyEntry, KeySwatch, ReadoutCall, RowGene, RowPitch, WalkRowsFrame, WalkRowsWithCalls, } from './layout/walkRowDraw.js';
 export { LABELLED_ROW_PX, WALK_STRIP_CEILING_PX, segmentAt, stripGeneGaps, stripMarks, stripRowAt, walkMarksTree, walkStripFrame, walkStripLabelsTree, } from './layout/walkStrip.js';
@@ -91,6 +91,8 @@ export { LABEL_CHAR_PX, LABEL_PAD, LABEL_PX } from './overlayLabels.js';
 export type { Graph, GraphEdge, GraphNode, LayoutResult, NodeSegment, } from './types.js';
 export { cutWindowGFA, haplotypeWanted, referencePathQuery, referenceSamplesOf, resolveReferenceSample, } from './gbzWindow.js';
 export type { GbzWindowOptions } from './gbzWindow.js';
+export { graphFromTables, graphTablesGFA } from './gfa/graphTables.js';
+export type { GraphTables } from './gfa/graphTables.js';
 export { engineKey } from './pipeline.js';
 export { axisScaleOf, contains, padded, screenToLayout, viewportOf, zoomAbout, } from './viewport.js';
 export type { PaneTransform } from './viewport.js';

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

@@ -14,7 +14,7 @@ export interface ReadoutCall {
     spanningReads?: number;
     agrees?: boolean;
 }
-export declare function walkRowReadout(row: Pick<WalkRow, 'bp' | 'gapBp' | 'complete'>, reference: Pick<WalkRow, 'bp'> | undefined, unit?: number, call?: ReadoutCall): string;
+export declare function walkRowReadout(row: Pick<WalkRow, 'bp' | 'gapBp' | 'complete' | 'stop'>, reference: Pick<WalkRow, 'bp'> | undefined, unit?: number, call?: ReadoutCall): string;
 export declare function readoutPlacement(text: string, endX: number, width: number): {
     x: number;
     anchor: "start";

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

@@ -12,6 +12,10 @@ export interface WalkAxis {
     start: number;
     reversed: boolean;
 }
+export interface WalkStop {
+    contigEnds: boolean;
+    shortBp: number;
+}
 export interface WalkRow {
     name: string;
     label: string;
@@ -21,6 +25,7 @@ export interface WalkRow {
     offReferenceBp: number;
     gapBp: number;
     complete: boolean;
+    stop?: WalkStop;
     runs: WalkRun[];
     axis?: WalkAxis;
 }

package/dist/types/pipeline.d.ts

@@ -1,4 +1,5 @@
 import type { BubbleSpread } from './bubbleSpreads.js';
+import type { GraphTables } from './gfa/graphTables.js';
 import type { LayoutScaling } from './layout/drawnScale.js';
 import type { LayoutNode } from './layout/referenceSeeds.js';
 import type { LayoutEngineKind } from './layoutEngines.js';
@@ -9,7 +10,7 @@ export interface Bounds {
     maxX: number;
     maxY: number;
 }
-export declare function loadGraph(text: string, name: string, opts?: {
+export declare function loadGraph(source: string | GraphTables, name: string, opts?: {
     referencePath?: string;
     maxNodes?: number;
 }): Graph;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "8.0.2";
+export declare const version = "8.2.0";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-XNE4UNSJ.js";
+} from "./chunks/chunk-3FXPFVKJ.js";
 export {
   version
 };

package/dist/viewport.js

@@ -5,13 +5,14 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-AO2VAMA4.js";
-import "./chunks/chunk-XRPU24OP.js";
-import "./chunks/chunk-IGVV37VI.js";
+} from "./chunks/chunk-TL4B342F.js";
+import "./chunks/chunk-5OIVTEF7.js";
 import "./chunks/chunk-PUG7LXDF.js";
+import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-OCMBULGN.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
+import "./chunks/chunk-OA7RIMZ2.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-BPLIXMH7.js";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "8.0.2",
+  "version": "8.2.0",
   "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": {