@jbrowse/bandage-core 10.0.0 → 10.1.0

package/dist/viewport.js

@@ -5,17 +5,17 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-OOLNLCIO.js";
-import "./chunks/chunk-W4GZCVUK.js";
+} from "./chunks/chunk-L5WF4ZPS.js";
+import "./chunks/chunk-XTCNEKO5.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-OPPVSPEF.js";
+import "./chunks/chunk-VPE4AYP7.js";
 import "./chunks/chunk-PUG7LXDF.js";
-import "./chunks/chunk-QXAB2FLJ.js";
+import "./chunks/chunk-IW6CYVX2.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-PSMKPSO4.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-JVLURPFW.js";
-import "./chunks/chunk-EMUUNWRU.js";
+import "./chunks/chunk-M6LK4GII.js";
 import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-G45YY72K.js";

package/dist/walkEncoding.js

@@ -9,13 +9,13 @@ import {
   schemeColor,
   schemeCss,
   schemeRgb
-} from "./chunks/chunk-VOWI544A.js";
-import "./chunks/chunk-NP356MC2.js";
+} from "./chunks/chunk-ALDGONEI.js";
+import "./chunks/chunk-SBMJNRTV.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-REE4GUDM.js";
+import "./chunks/chunk-TWRLC3KK.js";
 import "./chunks/chunk-PBENCR5L.js";
-import "./chunks/chunk-EMUUNWRU.js";
+import "./chunks/chunk-M6LK4GII.js";
 import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-BPLIXMH7.js";

package/dist/walkHighlight.js

@@ -2,14 +2,14 @@ import {
   facetLifts,
   walkHighlight,
   walkLift
-} from "./chunks/chunk-QIVPRZ4H.js";
-import "./chunks/chunk-VOWI544A.js";
-import "./chunks/chunk-NP356MC2.js";
+} from "./chunks/chunk-R456ME6J.js";
+import "./chunks/chunk-ALDGONEI.js";
+import "./chunks/chunk-SBMJNRTV.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-REE4GUDM.js";
+import "./chunks/chunk-TWRLC3KK.js";
 import "./chunks/chunk-PBENCR5L.js";
-import "./chunks/chunk-EMUUNWRU.js";
+import "./chunks/chunk-M6LK4GII.js";
 import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-BPLIXMH7.js";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "10.0.0",
+  "version": "10.1.0",
   "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": {
@@ -37,6 +37,7 @@
   "dependencies": {
     "@gmod/gbz-base": "^7.0.0",
     "@gmod/tabix": "^3.9.1",
+    "@jbrowse/graph-stress-layout": "^0.1.1",
     "@jbrowse/tubemap-core": "^0.2.4"
   },
   "devDependencies": {

package/dist/chunks/chunk-KAN2WTG5.js

@@ -1,226 +0,0 @@
-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);
-}
-function stepsOf(pieces, lengthOf) {
-  const steps = [];
-  let end;
-  for (const piece of pieces) {
-    if (end !== void 0 && piece.start !== void 0 && piece.start > end) {
-      steps.push(piece.start - end);
-    }
-    steps.push(...piece.nodeIds);
-    const bp = piece.nodeIds.reduce(
-      (sum, id) => sum + (lengthOf.get(id) ?? 0),
-      0
-    );
-    end = piece.start === void 0 ? void 0 : piece.start + bp;
-  }
-  return steps;
-}
-function stepSpans(pieces, lengthOf) {
-  const spans = [];
-  let end;
-  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) {
-      spans.push({ start: end, end: piece.start });
-    }
-    let pos = piece.start;
-    for (const id of piece.nodeIds) {
-      const len = lengthOf.get(id) ?? 0;
-      spans.push({ start: pos, end: pos + len });
-      pos += len;
-    }
-    end = pos;
-  }
-  return spans;
-}
-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((_, i) => {
-    const s = spanAt(i);
-    if (s) {
-      if (s.end <= region.start && s.end > bestEnd) {
-        bestEnd = s.end;
-        i0 = i;
-      }
-      if (s.start >= region.end && s.start < bestStart) {
-        bestStart = s.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 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) {
-    walks.set(path.name, [...walks.get(path.name) ?? [], path]);
-  }
-  const lengthOf = new Map(graph.nodes.map((n) => [n.id, n.length]));
-  const referenceStart = first.start ?? 0;
-  const cut = region && region.end > region.start ? region : void 0;
-  const span = /* @__PURE__ */ new Map();
-  for (const piece of referencePieces) {
-    let pos = piece.start ?? 0;
-    for (const id of piece.nodeIds) {
-      const len = lengthOf.get(id) ?? 0;
-      if (!span.has(id)) {
-        span.set(id, { start: pos, end: pos + len });
-      }
-      pos += len;
-    }
-  }
-  const flanked = cut === void 0 || [...span.values()].some((s) => s.end <= cut.start) && [...span.values()].some((s) => s.start >= cut.end);
-  const rowOf = (pieces) => {
-    const path = pieces[0];
-    const ordered = [...pieces].sort((a, b) => (a.start ?? 0) - (b.start ?? 0));
-    const { ids, complete, from, to, stop } = sliceBetween(
-      stepsOf(ordered, lengthOf),
-      span,
-      cut,
-      flanked
-    );
-    const spans = stepSpans(ordered, lengthOf);
-    const contig = path.contig ?? panSNContig(pathOrigin(path.name).name);
-    const axis = !spans?.length ? void 0 : from < 0 ? { contig, start: spans[0].start, reversed: false } : from < to ? { contig, start: spans[from].end, reversed: false } : { contig, start: spans[from].start, reversed: true };
-    const runs = [];
-    let bp = 0;
-    let offReferenceBp = 0;
-    let gapBp = 0;
-    let step = 0;
-    for (const id of ids) {
-      if (typeof id === "number") {
-        runs.push({ start: bp, bp: id, onReference: false, gap: true });
-        bp += id;
-        gapBp += id;
-        step = 0;
-        continue;
-      }
-      const len = lengthOf.get(id) ?? 0;
-      const s = span.get(id);
-      const last = runs.at(-1);
-      const at = last?.referenceStart;
-      const forward = s && at !== void 0 && step >= 0 && at + last.bp === s.start;
-      const backward = s && at !== void 0 && step <= 0 && s.end === at;
-      if (!s && last && !last.onReference && !last.gap) {
-        last.bp += len;
-      } else if (forward || backward) {
-        last.bp += len;
-        if (!forward) {
-          last.referenceStart = s.start;
-          last.reversed = true;
-        }
-        step = forward ? 1 : -1;
-      } else {
-        runs.push({
-          start: bp,
-          bp: len,
-          onReference: s !== void 0,
-          referenceStart: s?.start
-        });
-        step = 0;
-      }
-      bp += len;
-      if (!s) {
-        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),
-    rows: [...walks.values()].map(rowOf).sort(
-      (a, b) => Number(b.complete) - Number(a.complete) || b.bp - a.bp || a.label.localeCompare(b.label)
-    )
-  };
-}
-
-export {
-  filterSamples,
-  walkRows
-};