@jbrowse/bandage-core 0.1.19 → 4.0.24

package/dist/cli/figure.js

@@ -0,0 +1,152 @@
+#!/usr/bin/env node
+import {
+  cutWindowGFA,
+  figureSvg,
+  forceLayout,
+  haplotypeWanted,
+  layoutModeByValue,
+  loadBandage,
+  loadGraph,
+  referencePathQuery,
+  referenceSamplesOf,
+  resolveReferenceSample
+} from "../chunks/chunk-4AOHEU76.js";
+
+// src/cli/figure.ts
+import { open, readFile, writeFile } from "node:fs/promises";
+import path from "node:path";
+import { parseArgs } from "node:util";
+import { gunzipSync } from "node:zlib";
+import { GBZBase } from "@gmod/gbz-base";
+var HPRC = {
+  db: "https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.gbz.db",
+  index: "https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.haplotype-index.anchored.db"
+};
+var WALK_LIMIT = 1e5;
+function parseRegion(text) {
+  const m = /^\s*([^:\s]+):([\d,]+)-([\d,]+)\s*$/.exec(text);
+  if (!m) {
+    throw new Error(
+      `"${text}" is not a region like chr6:160,614,798-160,647,758`
+    );
+  }
+  const n = (s) => Number(s.replaceAll(",", ""));
+  return { refName: m[1], start: n(m[2]), end: n(m[3]) };
+}
+var isUrl = (s) => /^https?:\/\//.test(s);
+function byteSource(location) {
+  if (isUrl(location)) {
+    return {
+      async read(length, position) {
+        const res = await fetch(location, {
+          headers: { range: `bytes=${position}-${position + length - 1}` }
+        });
+        if (!res.ok) {
+          throw new Error(`HTTP ${res.status} reading ${location}`);
+        }
+        return new Uint8Array(await res.arrayBuffer());
+      },
+      async stat() {
+        const res = await fetch(location, { method: "HEAD" });
+        return { size: Number(res.headers.get("content-length")) };
+      }
+    };
+  }
+  const handle = open(location);
+  return {
+    async read(length, position) {
+      const buffer = new Uint8Array(length);
+      const { bytesRead } = await (await handle).read(buffer, 0, length, position);
+      return buffer.subarray(0, bytesRead);
+    },
+    async stat() {
+      return { size: (await (await handle).stat()).size };
+    }
+  };
+}
+async function gfaText(location) {
+  const bytes = isUrl(location) ? new Uint8Array(await (await fetch(location)).arrayBuffer()) : await readFile(location);
+  const gzipped = bytes[0] === 31 && bytes[1] === 139;
+  return new TextDecoder().decode(gzipped ? gunzipSync(bytes) : bytes);
+}
+async function cutGbz(gbz) {
+  const { db, index } = gbz.db === "hprc" ? HPRC : gbz;
+  const base = await GBZBase.open(
+    byteSource(db),
+    index ? { haplotypeIndex: byteSource(index) } : {}
+  );
+  const samples = await referenceSamplesOf(base);
+  const sample = resolveReferenceSample({
+    configured: "",
+    anchorPrefix: gbz.referenceSample ?? samples[0] ?? "",
+    referenceSamples: samples
+  });
+  const region = parseRegion(gbz.region);
+  const query = await referencePathQuery(base, sample, region.refName);
+  if (!query) {
+    throw new Error(`${sample} has no indexed path named ${region.refName}`);
+  }
+  const wanted = gbz.haplotypes?.length ? gbz.haplotypes : void 0;
+  const text = await cutWindowGFA(base, query, region.start, region.end, {
+    context: 1e3,
+    snarls: "contained",
+    limit: WALK_LIMIT,
+    ...wanted ? { keep: (name) => haplotypeWanted(name, wanted) } : {}
+  });
+  return { text, region, name: `${sample} ${gbz.region}` };
+}
+var engine = async (request) => {
+  const bandage = await loadBandage();
+  const start = performance.now();
+  const result = bandage.computeLayout(request.graph, request.options);
+  return { result, duration: performance.now() - start };
+};
+async function renderSpec(spec, base = ".") {
+  const source = spec.gbz ? await cutGbz(spec.gbz) : spec.gfa ? {
+    text: await gfaText(
+      isUrl(spec.gfa) ? spec.gfa : path.resolve(base, spec.gfa)
+    ),
+    region: spec.region ? parseRegion(spec.region) : void 0,
+    name: path.basename(spec.gfa)
+  } : void 0;
+  if (!source) {
+    throw new Error("a spec names its graph as `gfa` or `gbz`");
+  }
+  const graph = loadGraph(source.text, source.name, {
+    referencePath: spec.referencePath
+  });
+  const layout = layoutModeByValue(spec.layout ?? "force").run(graph, source.region) ?? (await forceLayout(
+    graph,
+    {
+      quality: spec.quality ?? 2,
+      linearLayout: false,
+      bubbleSpread: spec.bubbleSpread ?? "auto"
+    },
+    engine
+  )).result;
+  return figureSvg(graph, layout, {
+    ...spec,
+    walks: spec.walks?.map((w) => typeof w === "string" ? { walk: w } : w),
+    region: source.region,
+    metadata: JSON.stringify(spec)
+  });
+}
+async function main() {
+  const { positionals, values } = parseArgs({
+    allowPositionals: true,
+    options: { out: { type: "string", short: "o" } }
+  });
+  const file = positionals[0];
+  if (!file) {
+    console.error("usage: bandage-figure <spec.json> [-o figure.svg]");
+    process.exit(2);
+  }
+  const spec = JSON.parse(await readFile(file, "utf8"));
+  const svg = await renderSpec(spec, path.dirname(file));
+  if (values.out) {
+    await writeFile(values.out, svg);
+  } else {
+    process.stdout.write(svg);
+  }
+}
+await main();