@jbrowse/bandage-core 9.10.0 → 10.0.1

package/README.md

@@ -57,6 +57,26 @@ Release with `pnpm version patch`: it lints, tests, stamps `src/version.ts`,
 writes the changelog with git-cliff and pushes the `v*` tag, and `publish.yml`
 publishes to npm with trusted publishing.
 
+## See also
+
+- [jbrowse-plugin-graphgenomeviewer](https://github.com/GMOD/jbrowse-plugin-graphgenomeviewer) -
+  JBrowse 2 plugin that browses these graphs by locus
+- [BandageJS](https://github.com/cmdcolin/BandageJS) - standalone page for GFA
+  and gbz-base graphs
+- [@jbrowse/graph-stress-layout](https://github.com/GMOD/graph-stress-layout) -
+  stress layout that keeps the reference straight
+- [@gmod/gbz-base](https://github.com/GMOD/gbz-base-js) - range-request reader
+  for `.gbz.db` databases
+- [ggbandage](https://github.com/GMOD/ggbandage) - Bandage-style graph figures
+  as ggplot2 layers
+- [@jbrowse/tubemap-core](https://github.com/GMOD/tubemap-core) -
+  sequenceTubeMap's layout, without the DOM
+
+Tutorials on [jbrowse.org](https://jbrowse.org/jb2/docs/tutorials/)
+
+- [HPRC part 1: graph alleles and haplotypes](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc/)
+- [HPRC part 3: repeat lengths](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc_repeats/)
+
 ## License
 
 Both Bandage and OGDF are GPL, which is why this package is GPL-3.0-or-later.

package/dist/bubbles/popBubble.js

@@ -1,7 +1,8 @@
 import {
   bubbleSubgraph
-} from "../chunks/chunk-A6PSWTLX.js";
-import "../chunks/chunk-IGJCTPFB.js";
+} from "../chunks/chunk-4QTNXTGW.js";
+import "../chunks/chunk-EMUUNWRU.js";
+import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {

package/dist/bubbles/superbubbles.js

@@ -1,14 +1,15 @@
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "../chunks/chunk-5GZEPPEW.js";
+} from "../chunks/chunk-BEWLQADP.js";
 import "../chunks/chunk-CLOP7UVD.js";
-import "../chunks/chunk-A6PSWTLX.js";
+import "../chunks/chunk-4QTNXTGW.js";
 import "../chunks/chunk-EHUBJDDB.js";
 import "../chunks/chunk-XKWD2RY3.js";
 import "../chunks/chunk-FX4RDMDN.js";
 import "../chunks/chunk-HNQPEMYE.js";
-import "../chunks/chunk-IGJCTPFB.js";
+import "../chunks/chunk-EMUUNWRU.js";
+import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-2CVHXFK7.js";
 import "../chunks/chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-TOVOJNT7.js → chunk-3XE3OUEN.js}

@@ -1,6 +1,6 @@
 import {
   walkRows
-} from "./chunk-6PYZYBBF.js";
+} from "./chunk-A647OH7N.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-A6PSWTLX.js → chunk-4QTNXTGW.js}

@@ -1,6 +1,6 @@
 import {
   trimOrigins
-} from "./chunk-IGJCTPFB.js";
+} from "./chunk-EMUUNWRU.js";
 
 // src/bubbles/popBubble.ts
 function bubbleSubgraph(graph, segmentIds) {

package/dist/chunks/chunk-A647OH7N.js

@@ -0,0 +1,284 @@
+import {
+  pathOrigin
+} from "./chunk-EMUUNWRU.js";
+import {
+  panSNContig,
+  panSNSample
+} from "./chunk-BPLIXMH7.js";
+
+// src/layout/walkRows.ts
+function sampleOf(path) {
+  return path.sample ?? panSNSample(path.name);
+}
+function labelOf(path) {
+  return path.haplotype !== void 0 && path.sample !== void 0 ? `${path.sample}#${path.haplotype}` : sampleOf(path);
+}
+var NodeTable = class {
+  constructor(graph) {
+    this.index = /* @__PURE__ */ new Map();
+    this.lengths = [];
+    this.onReference = new Uint8Array(0);
+    this.referenceStart = new Float64Array(0);
+    this.referenceEnd = new Float64Array(0);
+    for (const node of graph.nodes) {
+      this.lengths[this.indexOf(node.id)] = node.length;
+    }
+  }
+  indexOf(id) {
+    let i = this.index.get(id);
+    if (i === void 0) {
+      i = this.lengths.length;
+      this.index.set(id, i);
+      this.lengths.push(0);
+    }
+    return i;
+  }
+  nodesOf(path) {
+    const nodes = new Int32Array(path.nodeIds.length);
+    path.nodeIds.forEach((id, k) => {
+      nodes[k] = this.indexOf(id);
+    });
+    return nodes;
+  }
+  spanAt(steps, k) {
+    const node = k >= 0 && k < steps.length ? steps[k] : -1;
+    return node >= 0 && this.onReference[node] ? { start: this.referenceStart[node], end: this.referenceEnd[node] } : void 0;
+  }
+};
+function stepsOf(pieces, table) {
+  const out = [];
+  let end;
+  for (const piece of pieces) {
+    if (end !== void 0 && piece.start !== void 0 && piece.start > end) {
+      out.push(end - piece.start);
+    }
+    let bp = 0;
+    for (const node of piece.nodes) {
+      out.push(node);
+      bp += table.lengths[node];
+    }
+    end = piece.start === void 0 ? void 0 : piece.start + bp;
+  }
+  return Float64Array.from(out);
+}
+function stepSpan(pieces, table, k) {
+  let end;
+  let at = 0;
+  let found;
+  for (const piece of pieces) {
+    if (piece.start === void 0 || end !== void 0 && piece.start < end) {
+      return void 0;
+    }
+    if (end !== void 0 && piece.start > end) {
+      if (at++ === k) {
+        found = { start: end, end: piece.start };
+      }
+    }
+    let pos = piece.start;
+    for (const node of piece.nodes) {
+      const len = table.lengths[node];
+      if (at++ === k) {
+        found = { start: pos, end: pos + len };
+      }
+      pos += len;
+    }
+    end = pos;
+  }
+  return found;
+}
+function sliceBetween(steps, table, region, flanked = true) {
+  if (!region || !flanked) {
+    return { ids: steps, complete: true, from: -1, to: -1 };
+  }
+  const { onReference, referenceStart, referenceEnd } = table;
+  let i0 = -1;
+  let i1 = -1;
+  let bestEnd = -Infinity;
+  let bestStart = Infinity;
+  for (let i = 0; i < steps.length; i++) {
+    const node = steps[i];
+    if (node >= 0 && onReference[node]) {
+      const end2 = referenceEnd[node];
+      const start = referenceStart[node];
+      if (end2 <= region.start && end2 > bestEnd) {
+        bestEnd = end2;
+        i0 = i;
+      }
+      if (start >= region.end && start < bestStart) {
+        bestStart = start;
+        i1 = i;
+      }
+    }
+  }
+  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 spanAt = (k) => table.spanAt(steps, k);
+  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 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,
+    complete: false,
+    from: flank,
+    to: after ? steps.length : -1,
+    stop
+  };
+}
+function filterSamples(rows, samples) {
+  return samples ? rows.filter((r) => samples.includes(r.sample)).sort(
+    (a, b) => samples.indexOf(a.sample) - samples.indexOf(b.sample) || a.label.localeCompare(b.label)
+  ) : rows;
+}
+function walkRows(graph, region, unit) {
+  const paths = graph.paths ?? [];
+  const isReference = (p) => pathOrigin(p.name).name === graph.referencePath;
+  const referencePieces = paths.some(isReference) ? paths.filter(isReference).sort((a, b) => (a.start ?? 0) - (b.start ?? 0)) : paths.slice(0, 1);
+  const first = referencePieces[0];
+  const others = paths.filter((p) => !referencePieces.includes(p));
+  if (!first || others.length === 0) {
+    return void 0;
+  }
+  const walks = /* @__PURE__ */ new Map();
+  for (const path of others) {
+    const pieces = walks.get(path.name);
+    if (pieces) {
+      pieces.push(path);
+    } else {
+      walks.set(path.name, [path]);
+    }
+  }
+  const table = new NodeTable(graph);
+  const referenceStart = first.start ?? 0;
+  const cut = region && region.end > region.start ? region : void 0;
+  const referenceNodes = referencePieces.map((piece) => table.nodesOf(piece));
+  const nodeCount = table.lengths.length;
+  table.onReference = new Uint8Array(nodeCount);
+  table.referenceStart = new Float64Array(nodeCount);
+  table.referenceEnd = new Float64Array(nodeCount);
+  let reachesBefore = false;
+  let reachesAfter = false;
+  for (const [p, piece] of referencePieces.entries()) {
+    let pos = piece.start ?? 0;
+    for (const node of referenceNodes[p]) {
+      const len = table.lengths[node];
+      if (!table.onReference[node]) {
+        table.onReference[node] = 1;
+        table.referenceStart[node] = pos;
+        table.referenceEnd[node] = pos + len;
+        reachesBefore ||= cut !== void 0 && pos + len <= cut.start;
+        reachesAfter ||= cut !== void 0 && pos >= cut.end;
+      }
+      pos += len;
+    }
+  }
+  const flanked = cut === void 0 || reachesBefore && reachesAfter;
+  const rowOf = (paths2, nodes) => {
+    const path = paths2[0];
+    const pieces = paths2.map((piece, p) => ({
+      start: piece.start,
+      nodes: nodes?.[p] ?? table.nodesOf(piece)
+    })).sort((a, b) => (a.start ?? 0) - (b.start ?? 0));
+    const { ids, complete, from, to, stop } = sliceBetween(
+      stepsOf(pieces, table),
+      table,
+      cut,
+      flanked
+    );
+    const contig = path.contig ?? panSNContig(pathOrigin(path.name).name);
+    const axisSpan = stepSpan(pieces, table, from < 0 ? 0 : from);
+    const axis = !axisSpan ? void 0 : from < 0 ? { contig, start: axisSpan.start, reversed: false } : from < to ? { contig, start: axisSpan.end, reversed: false } : { contig, start: axisSpan.start, reversed: true };
+    const { lengths, onReference, referenceStart: referenceStart2, referenceEnd } = table;
+    const runs = [];
+    let last;
+    let bp = 0;
+    let offReferenceBp = 0;
+    let gapBp = 0;
+    let step = 0;
+    for (const node of ids) {
+      if (node < 0) {
+        last = { start: bp, bp: -node, onReference: false, gap: true };
+        runs.push(last);
+        bp -= node;
+        gapBp -= node;
+        step = 0;
+        continue;
+      }
+      const len = lengths[node];
+      const on = onReference[node] === 1;
+      const at = last?.referenceStart;
+      const forward = on && at !== void 0 && step >= 0 && at + last.bp === referenceStart2[node];
+      const backward = on && at !== void 0 && step <= 0 && referenceEnd[node] === at;
+      if (!on && last && !last.onReference && !last.gap) {
+        last.bp += len;
+      } else if (forward || backward) {
+        last.bp += len;
+        if (!forward) {
+          last.referenceStart = referenceStart2[node];
+          last.reversed = true;
+        }
+        step = forward ? 1 : -1;
+      } else {
+        last = {
+          start: bp,
+          bp: len,
+          onReference: on,
+          referenceStart: on ? referenceStart2[node] : void 0
+        };
+        runs.push(last);
+        step = 0;
+      }
+      bp += len;
+      if (!on) {
+        offReferenceBp += len;
+      }
+    }
+    return {
+      name: path.name,
+      label: labelOf(path),
+      sample: sampleOf(path),
+      haplotype: path.haplotype,
+      bp,
+      offReferenceBp,
+      gapBp,
+      complete,
+      stop,
+      runs,
+      axis
+    };
+  };
+  const origin = cut ? cut.start : referenceStart;
+  return {
+    origin,
+    unit,
+    reference: rowOf(referencePieces, referenceNodes),
+    rows: [...walks.values()].map((paths2) => rowOf(paths2)).sort(
+      (a, b) => Number(b.complete) - Number(a.complete) || b.bp - a.bp || a.label.localeCompare(b.label)
+    )
+  };
+}
+
+export {
+  filterSamples,
+  walkRows
+};

package/dist/chunks/{chunk-NGODVSCA.js → chunk-AZJF2PZE.js}

@@ -1,32 +1,32 @@
 import {
   layoutEngine
-} from "./chunk-VK6XMP6B.js";
+} from "./chunk-FLUQODT2.js";
 import {
   layoutModeByValue
-} from "./chunk-FUUJ76KD.js";
+} from "./chunk-IFOZFVZK.js";
 import {
   parseRegion
-} from "./chunk-73RSLGZT.js";
+} from "./chunk-FLFBYSJO.js";
 import {
   layoutGeometryInputs
 } from "./chunk-LOCJN3BZ.js";
 import {
   version
-} from "./chunk-2VTM3DHG.js";
+} from "./chunk-KY4LV2Z6.js";
 import {
   axisScaleOf
-} from "./chunk-PT37VS5B.js";
+} from "./chunk-QORSYW7J.js";
 import {
   facetLifts,
   walkLift
-} from "./chunk-MVMP6AGI.js";
+} from "./chunk-QIVPRZ4H.js";
 import {
   walkKey
 } from "./chunk-2LQ5BWT7.js";
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-4IYP43W6.js";
+} from "./chunk-NP356MC2.js";
 import {
   abgrAlpha,
   abgrBlue,
@@ -36,14 +36,14 @@ import {
 import {
   pathLegend,
   walkLabelsOf
-} from "./chunk-XZ2BLAA6.js";
+} from "./chunk-REE4GUDM.js";
 import {
   drawingBounds,
   engineSettingsOf,
   fitTransform,
   forceLayout,
   loadGraph
-} from "./chunk-HRAU4VTB.js";
+} from "./chunk-MSX3BDO4.js";
 import {
   referenceLabel
 } from "./chunk-RAKOB6IV.js";

package/dist/chunks/{chunk-5GZEPPEW.js → chunk-BEWLQADP.js}

@@ -5,7 +5,7 @@ import {
 } from "./chunk-CLOP7UVD.js";
 import {
   bubbleSubgraph
-} from "./chunk-A6PSWTLX.js";
+} from "./chunk-4QTNXTGW.js";
 import {
   coversGraph
 } from "./chunk-EHUBJDDB.js";

package/dist/chunks/{chunk-Q6UIUY6X.js → chunk-CFNFT4RA.js}

@@ -1,7 +1,7 @@
 import {
   engineKey,
   forceLayout
-} from "./chunk-HRAU4VTB.js";
+} from "./chunk-MSX3BDO4.js";
 
 // src/layout/forceCache.ts
 var DEFAULT_SIZE = 4;

package/dist/chunks/{chunk-K5NYTPLC.js → chunk-DCJC32QW.js}

@@ -1,6 +1,6 @@
 import {
   REFERENCE_RAMP_MAX_HUE
-} from "./chunk-4IYP43W6.js";
+} from "./chunk-NP356MC2.js";
 
 // src/referenceRampCss.ts
 function rampHueCss(hue) {

package/dist/chunks/{chunk-IGJCTPFB.js → chunk-EMUUNWRU.js}

@@ -1,3 +1,6 @@
+import {
+  PathVisitsBuilder
+} from "./chunk-RAEABQNW.js";
 import {
   panSNSample
 } from "./chunk-BPLIXMH7.js";
@@ -13,23 +16,13 @@ function pathOrigin(pathName) {
 }
 function surveyPaths(paths, lengthOf) {
   const anchorPaths = [];
-  const pathVisits = /* @__PURE__ */ new Map();
+  const visits = new PathVisitsBuilder();
   for (const path of paths) {
     const sample = panSNSample(path.name);
+    const p = visits.pathOf(path.name, sample);
     let pos = path.start;
     for (const step of path.steps) {
-      const visit = {
-        path: path.name,
-        sample,
-        start: pos,
-        strand: step.strand
-      };
-      const existing = pathVisits.get(step.id);
-      if (existing) {
-        existing.push(visit);
-      } else {
-        pathVisits.set(step.id, [visit]);
-      }
+      visits.addAt(visits.declare(step.id), p, pos, step.strand === "-");
       pos += lengthOf(step.id);
     }
     anchorPaths.push({
@@ -39,7 +32,7 @@ function surveyPaths(paths, lengthOf) {
       length: pos - path.start
     });
   }
-  return { anchorPaths, pathVisits };
+  return { anchorPaths, pathVisits: visits.build() };
 }
 function chooseReferencePath(anchorPaths, preferred) {
   const named = anchorPaths.find(
@@ -49,41 +42,56 @@ function chooseReferencePath(anchorPaths, preferred) {
 }
 var OFF_REFERENCE_RANK = 1;
 function anchorNode(node, visits, reference, samplesOf) {
-  let anchored = node;
-  if (visits && visits.length > 0) {
-    const anchor = visits.find((v) => v.path === reference) ?? visits[0];
-    anchored = {
-      ...node,
-      stable: {
-        refName: anchor.path,
-        start: anchor.start,
-        rank: anchor.path === reference ? REFERENCE_RANK : OFF_REFERENCE_RANK,
-        strand: anchor.strand
-      },
-      samples: samplesOf(visits)
-    };
+  const slot = visits.slot(node.name);
+  if (slot < 0 || visits.offsets[slot] === visits.offsets[slot + 1]) {
+    return node;
   }
-  return anchored;
+  const own = visits.firstBy(slot, reference);
+  const anchor = own >= 0 ? own : visits.offsets[slot];
+  return {
+    ...node,
+    stable: {
+      refName: visits.paths[visits.path[anchor]],
+      start: visits.start[anchor],
+      rank: own >= 0 ? REFERENCE_RANK : OFF_REFERENCE_RANK,
+      strand: visits.strand(anchor)
+    },
+    samples: samplesOf(slot)
+  };
 }
-function sampleSorter(paths) {
-  const sorted = [...new Set(paths.map((p) => p.sample))].sort();
+function sampleSorter(visits) {
+  const sorted = [...new Set(visits.samples)].sort();
   const rank = new Map(sorted.map((sample, i) => [sample, i]));
+  const pathRank = Int32Array.from(visits.samples, (s) => rank.get(s));
   const seen = new Uint8Array(sorted.length);
-  return (visits) => {
-    const ranks = [];
-    for (const { sample } of visits) {
-      const r = rank.get(sample);
-      if (r === void 0) {
-        ranks.forEach((r2) => seen[r2] = 0);
-        return [...new Set(visits.map((v) => v.sample))].sort();
-      }
+  const ranks = new Int32Array(sorted.length);
+  return (slot) => {
+    let n = 0;
+    for (let i = visits.offsets[slot]; i < visits.offsets[slot + 1]; i++) {
+      const r = pathRank[visits.path[i]];
       if (seen[r] === 0) {
         seen[r] = 1;
-        ranks.push(r);
+        ranks[n++] = r;
+      }
+    }
+    let out;
+    if (n === sorted.length) {
+      out = sorted;
+      seen.fill(0);
+    } else if (n * 8 < sorted.length) {
+      const found = ranks.subarray(0, n);
+      found.forEach((r) => seen[r] = 0);
+      out = Array.from(found.sort(), (r) => sorted[r]);
+    } else {
+      out = [];
+      for (let r = 0; r < sorted.length; r++) {
+        if (seen[r] === 1) {
+          seen[r] = 0;
+          out.push(sorted[r]);
+        }
       }
     }
-    ranks.forEach((r) => seen[r] = 0);
-    return Array.from(Int32Array.from(ranks).sort(), (r) => sorted[r]);
+    return out;
   };
 }
 function anchorFromPaths(graph, preferred) {
@@ -92,11 +100,12 @@ function anchorFromPaths(graph, preferred) {
   if (!reference || !anchorPaths || !pathVisits) {
     return graph;
   }
-  const samplesOf = sampleSorter(anchorPaths);
+  const samplesOf = sampleSorter(pathVisits);
+  const referenceIndex = pathVisits.pathIndex(reference.name);
   return {
     ...graph,
     nodes: graph.nodes.map(
-      (node) => anchorNode(node, pathVisits.get(node.name), reference.name, samplesOf)
+      (node) => anchorNode(node, pathVisits, referenceIndex, samplesOf)
     ),
     anchoredBy: "paths",
     referencePath: reference.name

package/dist/chunks/{chunk-2FLBFVMO.js → chunk-FFFYXMOP.js}

@@ -5,23 +5,23 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-DMH4NL2M.js";
-import {
-  walkRowsKey,
-  walkRowsKeyTree,
-  walkRowsTree
-} from "./chunk-FJZ2TB46.js";
+} from "./chunk-WI7ZHJ27.js";
 import {
   Canvas2DRenderer
 } from "./chunk-WBCOREDZ.js";
 import {
-  genePins
-} from "./chunk-BUBZ32IC.js";
+  walkRowsKey,
+  walkRowsKeyTree,
+  walkRowsTree
+} from "./chunk-VZNKA3K2.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
   exonStretches
 } from "./chunk-3S3YVOJ7.js";
+import {
+  genePins
+} from "./chunk-BUBZ32IC.js";
 import {
   geneLabelCandidates
 } from "./chunk-DRG4236Y.js";
@@ -36,17 +36,17 @@ import {
 } from "./chunk-LOCJN3BZ.js";
 import {
   version
-} from "./chunk-2VTM3DHG.js";
+} from "./chunk-KY4LV2Z6.js";
 import {
   axisScaleOf
-} from "./chunk-PT37VS5B.js";
+} from "./chunk-QORSYW7J.js";
 import {
   facetLifts,
   walkLift
-} from "./chunk-MVMP6AGI.js";
+} from "./chunk-QIVPRZ4H.js";
 import {
   encodingStops
-} from "./chunk-KYY5363X.js";
+} from "./chunk-VOWI544A.js";
 import {
   rangeText,
   walkKey
@@ -54,15 +54,15 @@ import {
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-4IYP43W6.js";
+} from "./chunk-NP356MC2.js";
 import {
   walkRowLabels,
   walkRowsExtent
-} from "./chunk-TOVOJNT7.js";
+} from "./chunk-3XE3OUEN.js";
 import {
   pathLegend,
   walkLabelsOf
-} from "./chunk-XZ2BLAA6.js";
+} from "./chunk-REE4GUDM.js";
 import {
   nodeInk
 } from "./chunk-PBENCR5L.js";
@@ -70,7 +70,7 @@ import {
   FIT_PADDING,
   drawingBounds,
   fitTransform
-} from "./chunk-HRAU4VTB.js";
+} from "./chunk-MSX3BDO4.js";
 import {
   referenceLabel
 } from "./chunk-RAKOB6IV.js";