@jbrowse/bandage-core 9.0.0 → 9.2.0

package/dist/chunks/chunk-ZDJDM77V.js

@@ -0,0 +1,273 @@
+import {
+  bubbleSubgraph
+} from "./chunk-VHW7FDHU.js";
+import {
+  coversGraph
+} from "./chunk-2AWUWGAD.js";
+import {
+  bubbleSegmentIds
+} from "./chunk-XKWD2RY3.js";
+import {
+  bubblesFromGraph,
+  walkIndexOf,
+  walkRoutes
+} from "./chunk-GOZYKNQ2.js";
+import {
+  SATURATED_PATH_COUNT
+} from "./chunk-FX4RDMDN.js";
+import {
+  strandSides
+} from "./chunk-2CVHXFK7.js";
+import {
+  isBackbone
+} from "./chunk-FYQWPEEY.js";
+
+// src/bubbles/superbubbles.ts
+var MAX_SUPERBUBBLES = 50;
+function slotGraph(graph, index) {
+  const slots = graph.nodes.length * 2;
+  const seen = /* @__PURE__ */ new Set();
+  const pairs = [];
+  const degree = new Int32Array(slots);
+  for (const e of graph.edges) {
+    const a = index.get(e.from);
+    const b = index.get(e.to);
+    if (a === void 0 || b === void 0) {
+      continue;
+    }
+    const sides = strandSides(e);
+    const ka = a * 2 + (sides.from === "end" ? 1 : 0);
+    const kb = b * 2 + (sides.to === "end" ? 1 : 0);
+    const id = Math.min(ka, kb) * slots + Math.max(ka, kb);
+    if (seen.has(id)) {
+      continue;
+    }
+    seen.add(id);
+    pairs.push(ka, kb);
+    degree[ka]++;
+    if (ka !== kb) {
+      degree[kb]++;
+    }
+  }
+  const offset = new Int32Array(slots + 1);
+  for (let k = 0; k < slots; k++) {
+    offset[k + 1] = offset[k] + degree[k];
+  }
+  const next = new Int32Array(offset[slots]);
+  const fill = offset.slice(0, slots);
+  for (let i = 0; i < pairs.length; i += 2) {
+    const ka = pairs[i];
+    const kb = pairs[i + 1];
+    next[fill[ka]++] = kb;
+    if (ka !== kb) {
+      next[fill[kb]++] = ka;
+    }
+  }
+  return { offset, next };
+}
+function searcher(nodes, offset, next) {
+  const visited = new Int32Array(nodes);
+  const pending = new Uint8Array(nodes * 2);
+  const stack = new Int32Array(nodes * 2);
+  const inside = new Int32Array(nodes);
+  const touched = [];
+  let stamp = 0;
+  return (start) => {
+    const s = start >> 1;
+    stamp++;
+    touched.length = 0;
+    let open = 0;
+    let top = 0;
+    let count = 0;
+    let found;
+    const expect = (k) => {
+      if (!pending[k]) {
+        pending[k] = 1;
+        open++;
+        touched.push(k);
+      }
+    };
+    expect(start);
+    stack[top++] = start;
+    search: while (top > 0) {
+      const k = stack[--top];
+      const v = k >> 1;
+      visited[v] = stamp;
+      if (v !== s) {
+        inside[count++] = k;
+      }
+      if (pending[k]) {
+        pending[k] = 0;
+        open--;
+      }
+      if (offset[k] === offset[k + 1]) {
+        break;
+      }
+      for (let p = offset[k]; p < offset[k + 1]; p++) {
+        const entry = next[p];
+        const u = entry >> 1;
+        if (u === s) {
+          break search;
+        }
+        expect(entry ^ 1);
+        if (visited[u] === stamp) {
+          continue;
+        }
+        let ready = true;
+        for (let q = offset[entry]; q < offset[entry + 1]; q++) {
+          if (visited[next[q] >> 1] !== stamp) {
+            ready = false;
+            break;
+          }
+        }
+        if (ready) {
+          stack[top++] = entry ^ 1;
+        }
+      }
+      if (top === 1 && open === 1) {
+        if (count > 0) {
+          found = {
+            source: start,
+            sink: stack[0],
+            inside: inside.slice(0, count)
+          };
+        }
+        break;
+      }
+    }
+    for (const k of touched) {
+      pending[k] = 0;
+    }
+    return found;
+  };
+}
+function reversed(f) {
+  return {
+    source: f.sink ^ 1,
+    sink: f.source ^ 1,
+    inside: f.inside.map((k) => k ^ 1).reverse()
+  };
+}
+var collator = new Intl.Collator(void 0, { numeric: true });
+function onReference(a, b) {
+  return isBackbone(a) && isBackbone(b) && a.stable.refName === b.stable.refName;
+}
+function forward(f, nodes) {
+  const a = nodes[f.source >> 1];
+  const b = nodes[f.sink >> 1];
+  const byRef = onReference(a, b) ? a.stable.start - b.stable.start : 0;
+  const bySide = ((f.sink ^ 1) & 1) - (f.source & 1);
+  return (byRef || bySide || collator.compare(a.name, b.name)) < 0;
+}
+function nodesOf(f) {
+  return [f.source >> 1, ...Array.from(f.inside, (k) => k >> 1), f.sink >> 1];
+}
+function allSuperbubbles(graph) {
+  const { nodes } = graph;
+  const index = new Map(nodes.map((n, i) => [n.id, i]));
+  const { offset, next } = slotGraph(graph, index);
+  const find = searcher(nodes.length, offset, next);
+  const byEnds = /* @__PURE__ */ new Map();
+  for (let k = 0; k < nodes.length * 2; k++) {
+    const hit = find(k);
+    if (!hit) {
+      continue;
+    }
+    const a = hit.source >> 1;
+    const b = hit.sink >> 1;
+    const id = Math.min(a, b) * nodes.length + Math.max(a, b);
+    if (forward(hit, nodes) || !byEnds.has(id)) {
+      byEnds.set(id, hit);
+    }
+  }
+  const found = [...byEnds.values()].map(
+    (f) => forward(f, nodes) ? f : reversed(f)
+  );
+  return { found, offset, next };
+}
+function routesThrough(nodes, offset, next, f) {
+  const sink = f.sink >> 1;
+  const best = /* @__PURE__ */ new Map([
+    [f.source >> 1, { min: 0, max: 0, n: 1 }]
+  ]);
+  for (const k of [f.source, ...f.inside]) {
+    const cur = best.get(k >> 1);
+    if (!cur) {
+      continue;
+    }
+    for (let p = offset[k]; p < offset[k + 1]; p++) {
+      const u = next[p] >> 1;
+      const add = u === sink ? 0 : nodes[u].length;
+      const prev = best.get(u);
+      best.set(u, {
+        min: Math.min(prev?.min ?? Infinity, cur.min + add),
+        max: Math.max(prev?.max ?? -Infinity, cur.max + add),
+        n: Math.min(SATURATED_PATH_COUNT, cur.n + (prev?.n ?? 0))
+      });
+    }
+  }
+  return best.get(sink) ?? { min: 0, max: 0, n: 0 };
+}
+function superbubblesFromGraph(graph, span) {
+  const { nodes } = graph;
+  const { found, offset, next } = allSuperbubbles(graph);
+  const covers = found.map((f) => coversGraph(f.inside.length, nodes.length));
+  const members = found.map(nodesOf);
+  const holders = /* @__PURE__ */ new Map();
+  members.forEach((vs, i) => {
+    for (const v of vs) {
+      ;
+      (holders.get(v) ?? holders.set(v, []).get(v)).push(i);
+    }
+  });
+  const nested = (f, i) => holders.get(f.inside[0] >> 1).some(
+    (j) => j !== i && !covers[j] && members[j].length > members[i].length && members[i].every((v) => holders.get(v).includes(j))
+  );
+  const placed = (f) => span !== void 0 || onReference(nodes[f.source >> 1], nodes[f.sink >> 1]);
+  const outermost = found.filter((f, i) => !covers[i] && placed(f) && !nested(f, i)).sort((a, b) => b.inside.length - a.inside.length).slice(0, MAX_SUPERBUBBLES);
+  const byId = new Map(nodes.map((n) => [n.id, n]));
+  const walkIndex = walkIndexOf(graph);
+  return outermost.map((f) => {
+    const source = nodes[f.source >> 1];
+    const sink = nodes[f.sink >> 1];
+    const walked = walkIndex && walkRoutes(graph, byId, walkIndex, source.id, sink.id);
+    const crossed = walked?.n ? walked : void 0;
+    const routes = crossed ?? routesThrough(nodes, offset, next, f);
+    const placedOn = onReference(source, sink);
+    return {
+      refName: placedOn ? source.stable.refName : span.refName,
+      start: placedOn ? source.stable.start + source.length : span.start,
+      end: placedOn ? sink.stable.start : span.end,
+      segmentCount: f.inside.length + 2,
+      pathCount: routes.n,
+      inversion: false,
+      shortestAlleleLength: routes.min,
+      longestAlleleLength: routes.max,
+      segments: nodesOf(f).map((v) => nodes[v].name).join(","),
+      shortestAllele: void 0,
+      longestAllele: void 0,
+      partial: walked !== void 0 && walked.left > 0,
+      routes: crossed?.routes,
+      key: `${source.name}>${sink.name}`,
+      ...placedOn ? {} : { offReference: true }
+    };
+  }).sort(
+    (a, b) => a.start - b.start || a.end - b.end || collator.compare(a.key, b.key)
+  );
+}
+function graphBubbles(graph, span) {
+  const n = graph.nodes.length;
+  const reach = bubblesFromGraph(graph);
+  return reach.length === 0 ? superbubblesFromGraph(graph, span) : reach.flatMap(
+    (b) => coversGraph(b.segmentCount - 2, n) ? superbubblesFromGraph(
+      b.segmentCount === n ? graph : bubbleSubgraph(graph, bubbleSegmentIds(b)),
+      b
+    ) : [b]
+  );
+}
+
+export {
+  MAX_SUPERBUBBLES,
+  superbubblesFromGraph,
+  graphBubbles
+};

package/dist/cli/figure.js

@@ -4,18 +4,26 @@ import {
   genesFromGff3Lines,
   genesFromText
 } from "../chunks/chunk-BXEPA4KS.js";
+import {
+  LAYOUT_ENGINE_VALUES,
+  isLayoutEngineKind,
+  layoutEngine
+} from "../chunks/chunk-6EJIU6IA.js";
+import "../chunks/chunk-UNOE2NDN.js";
+import "../chunks/chunk-LYJ4US66.js";
 import {
   LAYOUT_MODES,
   layoutModeByValue
-} from "../chunks/chunk-WNUZP3WQ.js";
+} from "../chunks/chunk-M7SRZJ32.js";
+import "../chunks/chunk-LOEA5IHZ.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-7XHHVYG7.js";
 import {
   HPRC_GBZ,
   cutGbzRegion,
@@ -25,43 +33,35 @@ import {
 } from "../chunks/chunk-73RSLGZT.js";
 import "../chunks/chunk-LTUWJKHD.js";
 import "../chunks/chunk-WSIFAZU7.js";
-import {
-  LAYOUT_ENGINE_VALUES,
-  isLayoutEngineKind,
-  layoutEngine
-} from "../chunks/chunk-6EJIU6IA.js";
-import "../chunks/chunk-UNOE2NDN.js";
-import "../chunks/chunk-LYJ4US66.js";
-import "../chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "../chunks/chunk-TLQ7F2ZT.js";
+} from "../chunks/chunk-HOOVOF2Y.js";
+import "../chunks/chunk-UD5FOCI2.js";
+import "../chunks/chunk-WBCOREDZ.js";
+import "../chunks/chunk-4BYTEJGW.js";
 import "../chunks/chunk-LOCJN3BZ.js";
 import "../chunks/chunk-47DYCZOK.js";
-import "../chunks/chunk-WDTXW7T2.js";
 import {
   genesOnRow,
   placeRowGenes
-} from "../chunks/chunk-MIW3HYPE.js";
-import "../chunks/chunk-2WNBVB55.js";
-import "../chunks/chunk-4BYTEJGW.js";
-import "../chunks/chunk-3S3YVOJ7.js";
+} from "../chunks/chunk-GFRPX6M2.js";
 import "../chunks/chunk-BUBZ32IC.js";
-import "../chunks/chunk-MBB7ATM6.js";
-import "../chunks/chunk-DPV2CUIE.js";
+import "../chunks/chunk-3S3YVOJ7.js";
+import "../chunks/chunk-XKM5OHQQ.js";
+import "../chunks/chunk-LFKMASER.js";
+import "../chunks/chunk-XPT66H6H.js";
 import "../chunks/chunk-2LQ5BWT7.js";
-import "../chunks/chunk-6ZNQJ5ZD.js";
-import "../chunks/chunk-HBEKUQO4.js";
+import "../chunks/chunk-OXTR3BVF.js";
+import "../chunks/chunk-BR25DGIJ.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-AMS3MAFP.js";
-import "../chunks/chunk-TL4B342F.js";
+import "../chunks/chunk-FM6XRXPX.js";
 import "../chunks/chunk-3C5UXR2U.js";
 import {
   filterSamples,
   walkRows
 } from "../chunks/chunk-MAUEPAMG.js";
-import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-7GBL7SJY.js";
+import "../chunks/chunk-PBENCR5L.js";
 import {
   featuresOnBackbone,
   graphBackbone,
@@ -80,18 +80,18 @@ import {
   engineSettingsOf,
   forceLayout,
   loadGraph
-} from "../chunks/chunk-5OIVTEF7.js";
+} from "../chunks/chunk-ZGRYFUXE.js";
 import "../chunks/chunk-PUG7LXDF.js";
 import "../chunks/chunk-IGVV37VI.js";
 import "../chunks/chunk-OCMBULGN.js";
+import "../chunks/chunk-OA7RIMZ2.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-CDLPYR5O.js";
-import "../chunks/chunk-OA7RIMZ2.js";
+import "../chunks/chunk-JVLURPFW.js";
 import "../chunks/chunk-ES2N6V56.js";
 import "../chunks/chunk-ST2IBUAN.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-TAMCZHLW.js";
-import "../chunks/chunk-JVLURPFW.js";
 import "../chunks/chunk-UVBGRJQX.js";
 import "../chunks/chunk-6JEWNXCQ.js";
 import "../chunks/chunk-N6FECAXP.js";

package/dist/cli/fold.js

@@ -0,0 +1,72 @@
+#!/usr/bin/env node
+import {
+  writeRgfa
+} from "../chunks/chunk-B4YH42OP.js";
+import {
+  foldVariants
+} from "../chunks/chunk-B4645SM2.js";
+import {
+  loadGraph
+} from "../chunks/chunk-ZGRYFUXE.js";
+import "../chunks/chunk-PUG7LXDF.js";
+import "../chunks/chunk-IGVV37VI.js";
+import "../chunks/chunk-OCMBULGN.js";
+import "../chunks/chunk-OA7RIMZ2.js";
+import "../chunks/chunk-QYBZZI5H.js";
+import "../chunks/chunk-CDLPYR5O.js";
+import "../chunks/chunk-JVLURPFW.js";
+import "../chunks/chunk-ES2N6V56.js";
+import "../chunks/chunk-ST2IBUAN.js";
+import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-TAMCZHLW.js";
+import "../chunks/chunk-UVBGRJQX.js";
+import "../chunks/chunk-6JEWNXCQ.js";
+import "../chunks/chunk-N6FECAXP.js";
+import "../chunks/chunk-2CVHXFK7.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-FYQWPEEY.js";
+
+// src/cli/fold.ts
+import { readFile, writeFile } from "node:fs/promises";
+import { parseArgs } from "node:util";
+import { gunzipSync } from "node:zlib";
+var USAGE = "usage: bandage-fold <graph.gfa[.gz] | -> --below <bp> [-o out.gfa]";
+async function readInput(location) {
+  const bytes = await readFile(location === "-" ? "/dev/stdin" : location);
+  const gzipped = bytes[0] === 31 && bytes[1] === 139;
+  return new TextDecoder().decode(gzipped ? gunzipSync(bytes) : bytes);
+}
+async function main() {
+  const { values, positionals } = parseArgs({
+    allowPositionals: true,
+    options: {
+      below: { type: "string" },
+      out: { type: "string", short: "o" },
+      reference: { type: "string" }
+    }
+  });
+  const below = Number(values.below);
+  const input = positionals[0];
+  if (!input || !(below > 0)) {
+    throw new Error(USAGE);
+  }
+  const graph = loadGraph(await readInput(input), input, {
+    referencePath: values.reference
+  });
+  const folded = foldVariants({ ...graph, paths: void 0 }, below);
+  const text = writeRgfa(folded);
+  if (values.out) {
+    await writeFile(values.out, text);
+  } else {
+    process.stdout.write(text);
+  }
+  process.stderr.write(
+    `${graph.nodes.length} segments, ${graph.edges.length} links -> ${folded.nodes.length} segments, ${folded.edges.length} links
+`
+  );
+}
+main().catch((e) => {
+  process.stderr.write(`${e instanceof Error ? e.message : String(e)}
+`);
+  process.exit(1);
+});

package/dist/figure.js

@@ -1,26 +1,26 @@
 import {
   figureSvg
-} from "./chunks/chunk-TLQ7F2ZT.js";
+} from "./chunks/chunk-HOOVOF2Y.js";
+import "./chunks/chunk-UD5FOCI2.js";
+import "./chunks/chunk-WBCOREDZ.js";
+import "./chunks/chunk-4BYTEJGW.js";
 import "./chunks/chunk-LOCJN3BZ.js";
 import "./chunks/chunk-47DYCZOK.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";
+import "./chunks/chunk-GFRPX6M2.js";
 import "./chunks/chunk-BUBZ32IC.js";
-import "./chunks/chunk-MBB7ATM6.js";
-import "./chunks/chunk-DPV2CUIE.js";
+import "./chunks/chunk-3S3YVOJ7.js";
+import "./chunks/chunk-XKM5OHQQ.js";
+import "./chunks/chunk-LFKMASER.js";
+import "./chunks/chunk-XPT66H6H.js";
 import "./chunks/chunk-2LQ5BWT7.js";
-import "./chunks/chunk-6ZNQJ5ZD.js";
-import "./chunks/chunk-HBEKUQO4.js";
+import "./chunks/chunk-OXTR3BVF.js";
+import "./chunks/chunk-BR25DGIJ.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-AMS3MAFP.js";
-import "./chunks/chunk-TL4B342F.js";
+import "./chunks/chunk-FM6XRXPX.js";
 import "./chunks/chunk-3C5UXR2U.js";
 import "./chunks/chunk-MAUEPAMG.js";
-import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-7GBL7SJY.js";
+import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-RAKOB6IV.js";
 import "./chunks/chunk-GJMC3PGM.js";
 import "./chunks/chunk-FP4H7SFT.js";
@@ -31,18 +31,18 @@ import "./chunks/chunk-AB35TJST.js";
 import "./chunks/chunk-JKJWSY4V.js";
 import "./chunks/chunk-NNODIW4U.js";
 import "./chunks/chunk-XV4P5KEQ.js";
-import "./chunks/chunk-5OIVTEF7.js";
+import "./chunks/chunk-ZGRYFUXE.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-OCMBULGN.js";
+import "./chunks/chunk-OA7RIMZ2.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-OA7RIMZ2.js";
+import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
-import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-UVBGRJQX.js";
 import "./chunks/chunk-6JEWNXCQ.js";
 import "./chunks/chunk-N6FECAXP.js";

package/dist/figureSettings.js

@@ -1,19 +1,19 @@
 import {
   FIGURE_DEFAULTS,
   figureSpecSettings
-} from "./chunks/chunk-6VBDMZBZ.js";
-import "./chunks/chunk-5OIVTEF7.js";
+} from "./chunks/chunk-BLRJ6IGK.js";
+import "./chunks/chunk-ZGRYFUXE.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-OCMBULGN.js";
+import "./chunks/chunk-OA7RIMZ2.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-OA7RIMZ2.js";
+import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
-import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-UVBGRJQX.js";
 import "./chunks/chunk-6JEWNXCQ.js";
 import "./chunks/chunk-N6FECAXP.js";

package/dist/foldVariants.js

@@ -0,0 +1,9 @@
+import {
+  foldVariants
+} from "./chunks/chunk-B4645SM2.js";
+import "./chunks/chunk-2CVHXFK7.js";
+import "./chunks/chunk-CPMHA4W5.js";
+import "./chunks/chunk-FYQWPEEY.js";
+export {
+  foldVariants
+};

package/dist/gfa/writeRgfa.js

@@ -0,0 +1,6 @@
+import {
+  writeRgfa
+} from "../chunks/chunk-B4YH42OP.js";
+export {
+  writeRgfa
+};