@genome-spy/core 0.51.0 → 0.53.0

package/dist/bundle/{long-CYrAUkxh.js → long-D4tVjLLz.js}

@@ -1,4 +1,4 @@
-import { b as Pi } from "./index-C8lYPtq_.js";
+import { b as Pi } from "./index-B5cesONJ.js";
 import { g as Da } from "./_commonjsHelpers-BIiJCwQW.js";
 var re = {};
 (function(e) {
@@ -177,7 +177,7 @@ function aa(e) {
   e.bi_valid > 8 ? Ye(e, e.bi_buf) : e.bi_valid > 0 && (e.pending_buf[e.pending++] = e.bi_buf), e.bi_buf = 0, e.bi_valid = 0;
 }
 function Wa(e, i, t, a) {
-  aa(e), a && (Ye(e, t), Ye(e, ~t)), Ra.arraySet(e.pending_buf, e.window, i, t, e.pending), e.pending += t;
+  aa(e), Ye(e, t), Ye(e, ~t), Ra.arraySet(e.pending_buf, e.window, i, t, e.pending), e.pending += t;
 }
 function Jt(e, i, t, a) {
   var r = i * 2, n = t * 2;
@@ -282,7 +282,7 @@ function Qa(e) {
   ii || (Ga(), ii = !0), e.l_desc = new xt(e.dyn_ltree, ji), e.d_desc = new xt(e.dyn_dtree, Vi), e.bl_desc = new xt(e.bl_tree, Ji), e.bi_buf = 0, e.bi_valid = 0, ia(e);
 }
 function na(e, i, t, a) {
-  C(e, (Ua << 1) + (a ? 1 : 0), 3), Wa(e, i, t, !0);
+  C(e, (Ua << 1) + (a ? 1 : 0), 3), Wa(e, i, t);
 }
 function en(e) {
   C(e, Ki << 1, 3), ee(e, Ht, ne), Xa(e);
@@ -560,7 +560,7 @@ function ua(e, i, t, a, r, n) {
     return ue(e, X);
   a === 8 && (a = 9);
   var f = new Ln();
-  return e.state = f, f.strm = e, f.wrap = h, f.gzhead = null, f.w_bits = a, f.w_size = 1 << f.w_bits, f.w_mask = f.w_size - 1, f.hash_bits = r + 7, f.hash_size = 1 << f.hash_bits, f.hash_mask = f.hash_size - 1, f.hash_shift = ~~((f.hash_bits + S - 1) / S), f.window = new B.Buf8(f.w_size * 2), f.head = new B.Buf16(f.hash_size), f.prev = new B.Buf16(f.w_size), f.lit_bufsize = 1 << r + 6, f.pending_buf_size = f.lit_bufsize * 4, f.pending_buf = new B.Buf8(f.pending_buf_size), f.d_buf = 1 * f.lit_bufsize, f.l_buf = (1 + 2) * f.lit_bufsize, f.level = i, f.strategy = n, f.method = t, _a(e);
+  return e.state = f, f.strm = e, f.wrap = h, f.gzhead = null, f.w_bits = a, f.w_size = 1 << f.w_bits, f.w_mask = f.w_size - 1, f.hash_bits = r + 7, f.hash_size = 1 << f.hash_bits, f.hash_mask = f.hash_size - 1, f.hash_shift = ~~((f.hash_bits + S - 1) / S), f.window = new B.Buf8(f.w_size * 2), f.head = new B.Buf16(f.hash_size), f.prev = new B.Buf16(f.w_size), f.lit_bufsize = 1 << r + 6, f.pending_buf_size = f.lit_bufsize * 4, f.pending_buf = new B.Buf8(f.pending_buf_size), f.d_buf = 1 * f.lit_bufsize, f.l_buf = 3 * f.lit_bufsize, f.level = i, f.strategy = n, f.method = t, _a(e);
 }
 function Rn(e, i) {
   return ua(e, i, vt, pn, xn, gn);
@@ -1036,7 +1036,7 @@ var je = {}, j = {}, it = 30, Gn = 12, Wn = function(i, t) {
   if (i === ui ? (m = Je = f, x = 19) : i === mt ? (m = jn, I -= 257, Je = Vn, Gt -= 257, x = 256) : (m = Jn, Je = Qn, x = -1), z = 0, v = 0, o = d, p = h, w = g, k = 0, T = -1, N = 1 << g, y = N - 1, i === mt && N > oi || i === di && N > _i)
     return 1;
   for (; ; ) {
-    Wt = o - k, f[v] < x ? (Qe = 0, et = f[v]) : f[v] > x ? (Qe = Je[Gt + f[v]], et = m[I + f[v]]) : (Qe = 32 + 64, et = 0), E = 1 << o - k, c = 1 << w, d = c;
+    Wt = o - k, f[v] < x ? (Qe = 0, et = f[v]) : f[v] > x ? (Qe = Je[Gt + f[v]], et = m[I + f[v]]) : (Qe = 96, et = 0), E = 1 << o - k, c = 1 << w, d = c;
     do
       c -= E, n[p + (z >> k) + c] = Wt << 24 | Qe << 16 | et | 0;
     while (c !== 0);

package/dist/bundle/remoteFile-BkTxwFub.js

@@ -0,0 +1,90 @@
+import { b as d } from "./index-B5cesONJ.js";
+class b {
+  async getBufferFromResponse(e) {
+    const t = await e.arrayBuffer();
+    return d.Buffer.from(t);
+  }
+  constructor(e, t = {}) {
+    this.baseOverrides = {}, this.url = e;
+    const r = t.fetch || globalThis.fetch.bind(globalThis);
+    if (!r)
+      throw new TypeError("no fetch function supplied, and none found in global environment");
+    t.overrides && (this.baseOverrides = t.overrides), this.fetchImplementation = r;
+  }
+  async fetch(e, t) {
+    let r;
+    try {
+      r = await this.fetchImplementation(e, t);
+    } catch (s) {
+      if (`${s}`.includes("Failed to fetch"))
+        console.warn(`generic-filehandle: refetching ${e} to attempt to work around chrome CORS header caching bug`), r = await this.fetchImplementation(e, {
+          ...t,
+          cache: "reload"
+        });
+      else
+        throw s;
+    }
+    return r;
+  }
+  async read(e, t = 0, r, s = 0, h = {}) {
+    const { headers: n = {}, signal: c, overrides: a = {} } = h;
+    r < 1 / 0 ? n.range = `bytes=${s}-${s + r}` : r === 1 / 0 && s !== 0 && (n.range = `bytes=${s}-`);
+    const l = {
+      ...this.baseOverrides,
+      ...a,
+      headers: {
+        ...n,
+        ...a.headers,
+        ...this.baseOverrides.headers
+      },
+      method: "GET",
+      redirect: "follow",
+      mode: "cors",
+      signal: c
+    }, i = await this.fetch(this.url, l);
+    if (!i.ok)
+      throw new Error(`HTTP ${i.status} ${i.statusText} ${this.url}`);
+    if (i.status === 200 && s === 0 || i.status === 206) {
+      const f = await this.getBufferFromResponse(i), u = f.copy(e, t, 0, Math.min(r, f.length)), w = i.headers.get("content-range"), o = /\/(\d+)$/.exec(w || "");
+      return o != null && o[1] && (this._stat = { size: parseInt(o[1], 10) }), { bytesRead: u, buffer: e };
+    }
+    throw i.status === 200 ? new Error("${this.url} fetch returned status 200, expected 206") : new Error(`HTTP ${i.status} fetching ${this.url}`);
+  }
+  async readFile(e = {}) {
+    let t, r;
+    typeof e == "string" ? (t = e, r = {}) : (t = e.encoding, r = e, delete r.encoding);
+    const { headers: s = {}, signal: h, overrides: n = {} } = r, c = {
+      headers: s,
+      method: "GET",
+      redirect: "follow",
+      mode: "cors",
+      signal: h,
+      ...this.baseOverrides,
+      ...n
+    }, a = await this.fetch(this.url, c);
+    if (!a)
+      throw new Error("generic-filehandle failed to fetch");
+    if (a.status !== 200)
+      throw Object.assign(new Error(`HTTP ${a.status} fetching ${this.url}`), {
+        status: a.status
+      });
+    if (t === "utf8")
+      return a.text();
+    if (t)
+      throw new Error(`unsupported encoding: ${t}`);
+    return this.getBufferFromResponse(a);
+  }
+  async stat() {
+    if (!this._stat) {
+      const e = d.Buffer.allocUnsafe(10);
+      if (await this.read(e, 0, 10, 0), !this._stat)
+        throw new Error(`unable to determine size of file at ${this.url}`);
+    }
+    return this._stat;
+  }
+  async close() {
+  }
+}
+export {
+  b as R
+};

package/dist/schema.json

@@ -2843,19 +2843,21 @@
       "type": "object"
     },
     "GenomeConfig": {
-      "additionalProperties": false,
-      "properties": {
-        "baseUrl": {
-          "description": "Base url of data files: chromsizes, cytobands, and gene annotations.\n\n**Default:** `\"https://genomespy.app/data/genomes/\"`",
-          "type": "string"
+      "anyOf": [
+        {
+          "$ref": "#/definitions/UrlGenomeConfig"
         },
-        "contigs": {
-          "description": "As an alternative for chromSizes, the contigs can be provided inline.",
-          "items": {
-            "$ref": "#/definitions/Contig"
-          },
-          "type": "array"
+        {
+          "$ref": "#/definitions/InlineGenomeConfig"
         },
+        {
+          "$ref": "#/definitions/GenomeConfigBase"
+        }
+      ]
+    },
+    "GenomeConfigBase": {
+      "additionalProperties": false,
+      "properties": {
         "name": {
           "description": "Name of the genome assembly, e.g., `hg19` or `hg38`.",
           "type": "string"
@@ -3286,6 +3288,27 @@
         }
       ]
     },
+    "InlineGenomeConfig": {
+      "additionalProperties": false,
+      "properties": {
+        "contigs": {
+          "description": "An array of contigs/sequences in the genome assembly.",
+          "items": {
+            "$ref": "#/definitions/Contig"
+          },
+          "type": "array"
+        },
+        "name": {
+          "description": "Name of the genome assembly, e.g., `hg19` or `hg38`.",
+          "type": "string"
+        }
+      },
+      "required": [
+        "contigs",
+        "name"
+      ],
+      "type": "object"
+    },
     "IntervalSelectionConfig": {
       "additionalProperties": false,
       "properties": {
@@ -7109,7 +7132,7 @@
           "description": "Extending the domain so that it starts and ends on nice round values. This method typically modifies the scale’s domain, and may only extend the bounds to the nearest round value. Nicing is useful if the domain is computed from data and may be irregular. For example, for a domain of _[0.201479…, 0.996679…]_, a nice domain might be _[0.2, 1.0]_.\n\nFor quantitative scales such as linear, `nice` can be either a boolean flag or a number. If `nice` is a number, it will represent a desired tick count. This allows greater control over the step size used to extend the bounds, guaranteeing that the returned ticks will exactly cover the domain.\n\n__Default value:__ `true` for unbinned _quantitative_ fields; `false` otherwise."
         },
         "padding": {
-          "description": "For _[continuous](https://vega.github.io/vega-lite/docs/scale.html#continuous)_ scales, expands the scale domain to accommodate the specified number of pixels on each of the scale range. The scale range must represent pixels for this parameter to function as intended. Padding adjustment is performed prior to all other adjustments, including the effects of the `zero`, `nice`, `domainMin`, and `domainMax` properties.\n\nFor _[band](https://vega.github.io/vega-lite/docs/scale.html#band)_ scales, shortcut for setting `paddingInner` and `paddingOuter` to the same value.\n\nFor _[point](https://vega.github.io/vega-lite/docs/scale.html#point)_ scales, alias for `paddingOuter`.\n\n__Default value:__ For _continuous_ scales, derived from the [scale config](https://vega.github.io/vega-lite/docs/scale.html#config)'s `continuousPadding`. For _band and point_ scales, see `paddingInner` and `paddingOuter`.  By default, Vega-Lite sets padding such that _width/height = number of unique values * step_.",
+          "description": "For _[continuous](https://vega.github.io/vega-lite/docs/scale.html#continuous)_ scales, expands the scale domain to accommodate the specified number of pixels on each of the scale range. The scale range must represent pixels for this parameter to function as intended. Padding adjustment is performed prior to all other adjustments, including the effects of the `zero`, `nice`, `domainMin`, and `domainMax` properties.\n\nFor _[band](https://vega.github.io/vega-lite/docs/scale.html#band)_ scales, shortcut for setting `paddingInner` and `paddingOuter` to the same value.\n\nFor _[point](https://vega.github.io/vega-lite/docs/scale.html#point)_ scales, alias for `paddingOuter`.\n\n__Default value:__ For _continuous_ scales, derived from the [scale config](https://vega.github.io/vega-lite/docs/scale.html#config)'s `continuousPadding`. For _band and point_ scales, see `paddingInner` and `paddingOuter`.  By default, Vega-Lite sets padding such that _width/height = number of unique values * step_.",
           "minimum": 0,
           "type": "number"
         },
@@ -8385,6 +8408,24 @@
       ],
       "type": "object"
     },
+    "UrlGenomeConfig": {
+      "additionalProperties": false,
+      "properties": {
+        "name": {
+          "description": "Name of the genome assembly, e.g., `hg19` or `hg38`.",
+          "type": "string"
+        },
+        "url": {
+          "description": "A URL to a `chrom.sizes` file, which is a tab-separated file with two columns: the sequence name and its size.\n\nYou may want to strip alternative loci, haplotypes, and other non-canonical contigs from the file.\n\nExample: `\"https://genomespy.app/data/genomes/hg19/chrom.sizes\"`",
+          "type": "string"
+        }
+      },
+      "required": [
+        "name",
+        "url"
+      ],
+      "type": "object"
+    },
     "UrlImport": {
       "additionalProperties": false,
       "properties": {

package/dist/src/data/sources/dataUtils.d.ts

@@ -19,6 +19,11 @@ export function getFormat(params: import("../../spec/data.js").DataSource): {
 } | {
     type: string;
 };
+/**
+ * @param {string} type
+ * @returns {string}
+ */
+export function responseType(type: string): string;
 /**
  * @param {string | string[]} url
  */

package/dist/src/data/sources/dataUtils.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"dataUtils.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/dataUtils.js"],"names":[],"mappings":"AAGA;;;;;;GAMG;AACH,kCAHW,OAAO,oBAAoB,EAAE,UAAU;;;;;;;;;;;;;EAsBjD;AAED;;GAEG;AACH,wCAFW,MAAM,GAAG,MAAM,EAAE,UAU3B;AAWD;;;GAGG;AACH,4CAHW,OAAO,oBAAoB,EAAE,UAAU,4DAKjD;AAED;;;GAGG;AACH,4CAHW,OAAO,oBAAoB,EAAE,UAAU,4DAKjD;AAED;;;GAGG;AACH,6CAHW,OAAO,oBAAoB,EAAE,UAAU,6DAKjD;AAED;;;;GAIG;AACH,sCAHW,OAAO,oBAAoB,EAAE,UAAU,sDAKjD;AAxCM,+BAAgC,GAAG,QAI3B,OAAO,uBAAuB,EAAE,MAAM;;UAGtB,OAAO,gBAAgB,EAAE,KAAK,qCANR"}
+{"version":3,"file":"dataUtils.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/dataUtils.js"],"names":[],"mappings":"AAIA;;;;;;GAMG;AACH,kCAHW,OAAO,oBAAoB,EAAE,UAAU;;;;;;;;;;;;;EAsBjD;AAED;;;GAGG;AACH,mCAHW,MAAM,GACJ,MAAM,CAIlB;AAED;;GAEG;AACH,wCAFW,MAAM,GAAG,MAAM,EAAE,UAU3B;AAWD;;;GAGG;AACH,4CAHW,OAAO,oBAAoB,EAAE,UAAU,4DAKjD;AAED;;;GAGG;AACH,4CAHW,OAAO,oBAAoB,EAAE,UAAU,4DAKjD;AAED;;;GAGG;AACH,6CAHW,OAAO,oBAAoB,EAAE,UAAU,6DAKjD;AAED;;;;GAIG;AACH,sCAHW,OAAO,oBAAoB,EAAE,UAAU,sDAKjD;AAxCM,+BAAgC,GAAG,QAI3B,OAAO,uBAAuB,EAAE,MAAM;;UAGtB,OAAO,gBAAgB,EAAE,KAAK,qCANR"}

package/dist/src/data/sources/dataUtils.js

@@ -1,3 +1,4 @@
+import { formats } from "vega-loader";
 import { withoutExprRef } from "../../view/paramMediator.js";
 import { isInlineData } from "./inlineSource.js";
 
@@ -29,6 +30,14 @@ export function getFormat(params) {
     return format;
 }
 
+/**
+ * @param {string} type
+ * @returns {string}
+ */
+export function responseType(type) {
+    return formats(type)?.responseType ?? "text";
+}
+
 /**
  * @param {string | string[]} url
  */

package/dist/src/data/sources/lazy/axisTickSource.js

@@ -47,8 +47,8 @@ export default class AxisTickSource extends SingleAxisLazySource {
         // synchronously to ensure that the new ticks are available before the next frame is drawn.
 
         const scale = this.scaleResolution.scale;
+        const axisLength = this.scaleResolution.getAxisLength();
         const axisParams = this.params.axis;
-        const axisLength = this.getAxisLength();
 
         /**
          * Make ticks more dense in small plots.

package/dist/src/data/sources/lazy/bamSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"bamSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/bamSource.js"],"names":[],"mappings":"AAGA;IAeI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,OAAO,QACvC,OAAO,uBAAuB,EAAE,OAAO,EAmDjD;IAhED;;;;;;;;OAQG;IACH,sBAFgB,MAAM,KAAK,MAAM,CAEH;IAkB1B,gDAAgC;IAQhC,iCA4BE;;CAmCT;qCAxGoC,+BAA+B"}
+{"version":3,"file":"bamSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/bamSource.js"],"names":[],"mappings":"AAGA;IAeI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,OAAO,QACvC,OAAO,uBAAuB,EAAE,OAAO,EAmDjD;IAhED;;;;;;;;OAQG;IACH,gBAFU,CAAC,GAAG,EAAE,MAAM,KAAK,MAAM,CAEH;IAkB1B,gDAAgC;IAQhC,iCA4BE;;CAmCT;qCAxGoC,+BAA+B"}

package/dist/src/data/sources/lazy/bigBedSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"bigBedSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/bigBedSource.js"],"names":[],"mappings":"AAOA;IAUI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,UAAU,QAC1C,OAAO,uBAAuB,EAAE,OAAO,EAmCjD;IA9CD,0CAA0C;IAC1C,QADW,OAAO,WAAW,EAAE,OAAO,CAC/B;IAEP,yCAAyC;IACzC,KADW,OAAO,WAAW,EAAE,MAAM,CACjC;IAEJ,4GAA4G;IAC5G,mBADmB,MAAM,UAAU;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,GAAG,EAAE,MAAM,CAAC;QAAC,IAAI,CAAC,EAAE,MAAM,CAAA;KAAE,KAAK,OAAO,MAAM,EAAE,GAAG,CAAC,CAC9F;IA8BN,mDAA6B;;CAoFpC;qCA5HoC,+BAA+B"}
+{"version":3,"file":"bigBedSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/bigBedSource.js"],"names":[],"mappings":"AAOA;IAUI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,UAAU,QAC1C,OAAO,uBAAuB,EAAE,OAAO,EAmCjD;IA9CD,0CAA0C;IAC1C,QADW,OAAO,WAAW,EAAE,OAAO,CAC/B;IAEP,yCAAyC;IACzC,KADW,OAAO,WAAW,EAAE,MAAM,CACjC;IAEJ,4GAA4G;IAC5G,WADW,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,GAAG,EAAE,MAAM,CAAC;QAAC,IAAI,CAAC,EAAE,MAAM,CAAA;KAAE,KAAK,OAAO,MAAM,EAAE,GAAG,CAAC,CAC9F;IA8BN,mDAA6B;;CAoFpC;qCA5HoC,+BAA+B"}

package/dist/src/data/sources/lazy/bigWigSource.js

@@ -111,7 +111,7 @@ export default class BigWigSource extends SingleAxisWindowedSource {
         await this.initializedPromise;
 
         // TODO: Postpone the initial load until layout is computed and remove 700.
-        const length = this.getAxisLength() || 700;
+        const length = this.scaleResolution.getAxisLength() || 700;
 
         const reductionLevel = findReductionLevel(
             domain,

package/dist/src/data/sources/lazy/singleAxisLazySource.d.ts

@@ -15,11 +15,6 @@ export default class SingleAxisLazySource extends DataSource {
     /** @type {import("../../../spec/channel.js").PrimaryPositionalChannel}  */
     channel: import("../../../spec/channel.js").PrimaryPositionalChannel;
     scaleResolution: import("../../../view/scaleResolution.js").default;
-    /**
-     * Returns the length of the axis in pixels. Chooses the smallest of the views.
-     * They should all be the same, but some exotic configuration might break that assumption.
-     */
-    getAxisLength(): number;
     /**
      * Convenience getter for genome.
      *
@@ -42,7 +37,10 @@ export default class SingleAxisLazySource extends DataSource {
      */
     protected requestRender(): void;
     /**
-     * Resets the data flow and propagates the data.
+     * Resets the data flow and propagates the data, which should be an array of data chunks.
+     * A chunk is an ordinary array of data objects. Typically all data objects are stored
+     * in a single chunk, but sometimes they may be split into multiple chunks, e.g., one per
+     * chromosome.
      *
      * @param {import("../../flowNode.js").Datum[][]} chunks An array of data chunks.
      * @protected

package/dist/src/data/sources/lazy/singleAxisLazySource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"singleAxisLazySource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/singleAxisLazySource.js"],"names":[],"mappings":"AAIA;;GAEG;AACH;IAOI;;;OAGG;IACH,kBAHW,OAAO,uBAAuB,EAAE,OAAO,WACvC,OAAO,0BAA0B,EAAE,wBAAwB,EA+CrE;IAvDD;;;OAGG;IACH,4CAAuC;IAmBnC,2EAA2E;IAC3E,SADW,OAAO,0BAA0B,EAAE,wBAAwB,CAChD;IAEtB,oEAA4D;IA+BhE;;;OAGG;IACH,wBAWC;IAED;;;;OAIG;IACH,oEAEC;IAED;;;;;;OAMG;IACH,wBAJW,MAAM,EAAE,iBACR,OAAO,yBAAyB,EAAE,gBAAgB,EAAE,QAK9D;IAED;;;;;OAKG;IACH,gCAGC;IAQD;;;;;OAKG;IACH,8BAHW,OAAO,mBAAmB,EAAE,KAAK,EAAE,EAAE,QAgB/C;CACJ;uBA1IsB,kBAAkB"}
+{"version":3,"file":"singleAxisLazySource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/singleAxisLazySource.js"],"names":[],"mappings":"AAIA;;GAEG;AACH;IAOI;;;OAGG;IACH,kBAHW,OAAO,uBAAuB,EAAE,OAAO,WACvC,OAAO,0BAA0B,EAAE,wBAAwB,EA+CrE;IAvDD;;;OAGG;IACH,4CAAuC;IAmBnC,2EAA2E;IAC3E,SADW,OAAO,0BAA0B,EAAE,wBAAwB,CAChD;IAEtB,oEAA4D;IA+BhE;;;;OAIG;IACH,oEAEC;IAED;;;;;;OAMG;IACH,wBAJW,MAAM,EAAE,iBACR,OAAO,yBAAyB,EAAE,gBAAgB,EAAE,QAK9D;IAED;;;;;OAKG;IACH,gCAGC;IAQD;;;;;;;;OAQG;IACH,8BAHW,OAAO,mBAAmB,EAAE,KAAK,EAAE,EAAE,QAgB/C;CACJ;uBA5HsB,kBAAkB"}

package/dist/src/data/sources/lazy/singleAxisLazySource.js

@@ -63,23 +63,6 @@ export default class SingleAxisLazySource extends DataSource {
         );
     }
 
-    /**
-     * Returns the length of the axis in pixels. Chooses the smallest of the views.
-     * They should all be the same, but some exotic configuration might break that assumption.
-     */
-    getAxisLength() {
-        const lengths = this.scaleResolution.members
-            .map(
-                (m) =>
-                    m.view.coords?.[this.channel === "x" ? "width" : "height"]
-            )
-            .filter((len) => len > 0);
-
-        return lengths.length
-            ? lengths.reduce((a, b) => Math.min(a, b), 10000)
-            : 0;
-    }
-
     /**
      * Convenience getter for genome.
      *
@@ -118,7 +101,10 @@ export default class SingleAxisLazySource extends DataSource {
     }
 
     /**
-     * Resets the data flow and propagates the data.
+     * Resets the data flow and propagates the data, which should be an array of data chunks.
+     * A chunk is an ordinary array of data objects. Typically all data objects are stored
+     * in a single chunk, but sometimes they may be split into multiple chunks, e.g., one per
+     * chromosome.
      *
      * @param {import("../../flowNode.js").Datum[][]} chunks An array of data chunks.
      * @protected

package/dist/src/data/sources/urlSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"urlSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/urlSource.js"],"names":[],"mappings":"AASA;;;GAGG;AACH,gCAHW,QAAQ,OAAO,oBAAoB,EAAE,IAAI,CAAC,gDAKpD;AAED;IACI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,OAAO,QACpC,OAAO,oBAAoB,EAAE,OAAO,EAU9C;IALG,6CAEC;IAED,gBAAiC;CAiExC;uBA5FsB,iBAAiB"}
+{"version":3,"file":"urlSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/urlSource.js"],"names":[],"mappings":"AASA;;;GAGG;AACH,gCAHW,QAAQ,OAAO,oBAAoB,EAAE,IAAI,CAAC,gDAKpD;AAED;IACI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,OAAO,QACpC,OAAO,oBAAoB,EAAE,OAAO,EAU9C;IALG,6CAEC;IAED,gBAAiC;CAsExC;uBAjGsB,iBAAiB"}

package/dist/src/data/sources/urlSource.js

@@ -1,5 +1,5 @@
 import { read } from "vega-loader";
-import { getFormat } from "./dataUtils.js";
+import { getFormat, responseType } from "./dataUtils.js";
 import DataSource from "./dataSource.js";
 import {
     activateExprRefProps,
@@ -40,6 +40,9 @@ export default class UrlSource extends DataSource {
         /** @type {string[]} */
         const urls = Array.isArray(url) ? url : [url];
 
+        const format = getFormat(this.params);
+        const type = responseType(format.type);
+
         if (urls.length === 0 || !urls[0]) {
             this.reset();
             this.complete();
@@ -54,8 +57,11 @@ export default class UrlSource extends DataSource {
                 if (!result.ok) {
                     throw new Error(`${result.status} ${result.statusText}`);
                 }
-                // TODO: what about binary data (for arrow), etc?
-                return result.text();
+                // @ts-ignore
+                return typeof result[type] == "function"
+                    ? // @ts-ignore
+                      result[type]()
+                    : result.text();
             } catch (e) {
                 throw new Error(
                     `Could not load data: ${url}. Reason: ${e.message}`
@@ -64,13 +70,13 @@ export default class UrlSource extends DataSource {
         };
 
         /**
-         * @param {string} text
+         * @param {any} content
          * @param {string} [url]
          */
-        const readAndParse = (text, url) => {
+        const readAndParse = (content, url) => {
             try {
                 /** @type {any[]} */
-                const data = read(text, getFormat(this.params));
+                const data = read(content, format);
                 this.beginBatch({ type: "file", url: url });
                 for (const d of data) {
                     this._propagate(d);
@@ -89,7 +95,6 @@ export default class UrlSource extends DataSource {
         } catch (e) {
             this.setLoadingStatus("error", e.message);
         }
-
         this.complete();
     }
 }

package/dist/src/data/transforms/clone.d.ts

@@ -3,14 +3,13 @@
  */
 export default class CloneTransform extends FlowNode {
     constructor();
-    /** @param {any} datum */
-    handle: (datum: any) => void;
     /**
      * Signals that a new batch of data will be propagated.
      *
      * @param {import("../../types/flowBatch.js").FlowBatch} [flowBatch]
      */
     beginBatch: (flowBatch?: import("../../types/flowBatch.js").FlowBatch) => void;
+    #private;
 }
 import FlowNode from "../flowNode.js";
 //# sourceMappingURL=clone.d.ts.map

package/dist/src/data/transforms/clone.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"clone.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/clone.js"],"names":[],"mappings":"AAGA;;GAEG;AACH;IAKI,cA2BC;IApBO,yBAAyB;IACzB,gBALQ,GAAG,UAK2C;IAO1D;;;;OAIG;IACH,yBAFW,OAAO,0BAA0B,EAAE,SAAS,UAQtD;CAER;qBAtCsD,gBAAgB"}
+{"version":3,"file":"clone.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/clone.js"],"names":[],"mappings":"AAIA;;GAEG;AACH;IAWI,cAmCC;IAXG;;;;OAIG;IACH,yBAFW,OAAO,0BAA0B,EAAE,SAAS,UAOtD;;CAER;qBApDsD,gBAAgB"}

package/dist/src/data/transforms/clone.js

@@ -1,4 +1,5 @@
-import createCloner from "../../utils/cloner.js";
+import { shallowArrayEquals } from "../../utils/arrayUtils.js";
+import createCloner, { getAllProperties } from "../../utils/cloner.js";
 import FlowNode, { BEHAVIOR_CLONES, isFileBatch } from "../flowNode.js";
 
 /**
@@ -9,13 +10,28 @@ export default class CloneTransform extends FlowNode {
         return BEHAVIOR_CLONES;
     }
 
+    /** @type {string[]} */
+    #lastBatchFields;
+
+    /** @type {(datum: import("../flowNode.js").Datum) => import("../flowNode.js").Datum} */
+    #clone = (datum) => datum;
+
     constructor() {
         super();
 
-        /** @param {any} datum */
+        /** @param {import("../flowNode.js").Datum} datum */
         const setupCloner = (datum) => {
-            const clone = createCloner(datum);
+            // Create a new cloner if the fields have changed
+            const fields = getAllProperties(datum);
+            if (
+                !this.#lastBatchFields ||
+                !shallowArrayEquals(fields, this.#lastBatchFields)
+            ) {
+                this.#lastBatchFields = fields;
+                this.#clone = createCloner(datum);
+            }
 
+            const clone = this.#clone;
             /** @param {any} datum */
             this.handle = (datum) => this._propagate(clone(datum));
 
@@ -31,7 +47,6 @@ export default class CloneTransform extends FlowNode {
          */
         this.beginBatch = (flowBatch) => {
             if (isFileBatch(flowBatch)) {
-                // TODO: Only create new cloner if the props change
                 this.handle = setupCloner;
             }
             super.beginBatch(flowBatch);

package/dist/src/data/transforms/filterScoredLabels.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"filterScoredLabels.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filterScoredLabels.js"],"names":[],"mappings":"AAMA;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,wBAAwB,QAC1D,OAAO,oBAAoB,EAAE,OAAO,EA2C9C;IAtCG,mEAAoB;IAEpB,oBAAoB;IACpB,OADW,GAAG,EAAE,CACD;IAEf,mBAAoC;IAMpC,iDAAyC;IACzC,mDAA6C;IAC7C,mDAA6C;IAC7C,mDAA6C;IAC7C,gCAAgC;IAChC,qBADoB,GAAG,KAAE,GAAG,CAGd;IACd,gBAAuC;IAEvC,uCAAuC;IACvC,iBADW,IAAI,GAAG,EAAE,cAAc,CAAC,CACH;IAEhC,4DAAuD;IAIvD,qBAAuE;IAgBvE,eAAiD;IAWrD,4BA4CC;IAKG,sBAAuB;CAU9B;qBApI2C,gBAAgB;2BAEjC,+BAA+B"}
+{"version":3,"file":"filterScoredLabels.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filterScoredLabels.js"],"names":[],"mappings":"AAMA;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,wBAAwB,QAC1D,OAAO,oBAAoB,EAAE,OAAO,EA2C9C;IAtCG,mEAAoB;IAEpB,oBAAoB;IACpB,OADW,GAAG,EAAE,CACD;IAEf,mBAAoC;IAMpC,iDAAyC;IACzC,mDAA6C;IAC7C,mDAA6C;IAC7C,mDAA6C;IAC7C,gCAAgC;IAChC,qBADoB,GAAG,KAAE,GAAG,CAGd;IACd,gBAAuC;IAEvC,uCAAuC;IACvC,iBADW,IAAI,GAAG,EAAE,cAAc,CAAC,CACH;IAEhC,4DAAuD;IAIvD,qBAAuE;IAgBvE,eAAiD;IAWrD,4BAyCC;IAKG,sBAAuB;CAU9B;qBAjI2C,gBAAgB;2BAEjC,+BAA+B"}

package/dist/src/data/transforms/filterScoredLabels.js

@@ -76,10 +76,7 @@ export default class FilterScoredLabelsTransform extends FlowNode {
         super.reset();
 
         const scale = this.resolution.scale;
-        const rangeSpan =
-            this.resolution.members[0].view.coords?.[
-                this.channel == "x" ? "width" : "height"
-            ];
+        const rangeSpan = this.resolution.getAxisLength();
         if (!rangeSpan) {
             // The view size is not (yet) available
             return;

package/dist/src/data/transforms/transformFactory.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"transformFactory.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/transformFactory.js"],"names":[],"mappings":"AA+CA;;;GAGG;AACH,gDAHW,OAAO,yBAAyB,EAAE,mBAAmB,SACrD,OAAO,oBAAoB,EAAE,OAAO,oCAS9C;AAtCD;;;;GAIG;AACH,qDAFsC,GAAG,SAAS,OAAO,oBAAoB,EAAE,OAAO,KAAK,OAAO,gBAAgB,EAAE,OAAO,EAsBzH"}
+{"version":3,"file":"transformFactory.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/transformFactory.js"],"names":[],"mappings":"AA+CA;;;GAGG;AACH,gDAHW,OAAO,yBAAyB,EAAE,mBAAmB,SACrD,OAAO,oBAAoB,EAAE,OAAO,oCAS9C;AAtCD;;;;GAIG;AACH,yBAFU,OAAO,MAAM,EAAE,KAAK,MAAM,EAAE,GAAG,EAAE,IAAI,CAAC,EAAE,OAAO,oBAAoB,EAAE,OAAO,KAAK,OAAO,gBAAgB,EAAE,OAAO,CAAC,CAsB1H"}

package/dist/src/encoder/encoder.d.ts

@@ -105,7 +105,7 @@ export function getPrimaryChannel(channel: import("../spec/channel.js").Channel)
  *
  * @param {import("../spec/channel.js").Channel} channel
  */
-export function getChannelWithSecondarys(channel: import("../spec/channel.js").Channel): ("search" | "fill" | "stroke" | "angle" | "sample" | "color" | "fillOpacity" | "opacity" | "strokeOpacity" | "strokeWidth" | "text" | "size" | "x" | "y" | "x2" | "y2" | "shape" | "dx" | "dy" | "uniqueId" | "facetIndex" | "semanticScore")[];
+export function getChannelWithSecondarys(channel: import("../spec/channel.js").Channel): ("search" | "fill" | "stroke" | "angle" | "sample" | "color" | "fillOpacity" | "opacity" | "strokeOpacity" | "strokeWidth" | "x" | "y" | "text" | "size" | "x2" | "y2" | "shape" | "dx" | "dy" | "uniqueId" | "facetIndex" | "semanticScore")[];
 /**
  * @param {import("../spec/channel.js").Channel} channel
  */

package/dist/src/encoder/encoder.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"encoder.d.ts","sourceRoot":"","sources":["../../../src/encoder/encoder.js"],"names":[],"mappings":"AAEA;;;;;;;;GAQG;AACH,iDAJW,OAAO,qBAAqB,EAAE,OAAO,YACrC,OAAO,oBAAoB,EAAE,QAAQ,gGAgC/C;AAED;;;;GAIG;AACH,4DAJW,OAAO,qBAAqB,EAAE,QAAQ,EAAE,yBAC9B,OAAO,oBAAoB,EAAE,gBAAgB,KAAK,OAAO,qBAAqB,EAAE,SAAS,yCAqC7G;AAED;;;;GAIG;AACH,4IAHqB,OAAO,oBAAoB,EAAE,gBAAgB,KAAK,OAAO,qBAAqB,EAAE,SAAS,yCAqC7G;AAED;;;;;GAKG;AACH,uCAHW,OAAO,oBAAoB,EAAE,UAAU,4FAKjD;AAED;;;GAGG;AACH,uCAHW,OAAO,oBAAoB,EAAE,UAAU,2DAKjD;AAED;;;GAGG;AACH,uCAHW,OAAO,oBAAoB,EAAE,UAAU,qIAKjD;AAED;;;GAGG;AACH,kDAHW,OAAO,oBAAoB,EAAE,UAAU,kEAWjD;AAED;;;GAGG;AACH,6CAHW,OAAO,qBAAqB,EAAE,OAAO,WACrC,OAAO,oBAAoB,EAAE,OAAO,s9CAS9C;AAED;;;GAGG;AACH,iDAHW,OAAO,oBAAoB,EAAE,UAAU,4FAKjD;AAED;;;GAGG;AACH,0CAHW,OAAO,oBAAoB,EAAE,UAAU,0DAKjD;AAED;;;GAGG;AACH,sCAHW,OAAO,oBAAoB,EAAE,UAAU,sDAKjD;AAED;;;GAGG;AACH,2DAHW,OAAO,oBAAoB,EAAE,UAAU,wMAQjD;AAED;;;GAGG;AACH,oDAHW,OAAO,oBAAoB,EAAE,UAAU,wGAKjD;AAoBD;;;GAGG;AACH,oDAHW,OAAO,oBAAoB,EAAE,OAAO,oEAM9C;AAED;;;GAGG;AACH,6CAHW,OAAO,oBAAoB,EAAE,OAAO,6DAM9C;AAqBD;;;GAGG;AACH,4CAFW,MAAM,WAIhB;AAED;;;;GAIG;AACH,oDAFW,OAAO,oBAAoB,EAAE,OAAO,2DAS9C;AAED;;;;;GAKG;AACH,2CAFW,OAAO,oBAAoB,EAAE,OAAO,wCAI9C;AAED;;;;GAIG;AACH,kDAFW,OAAO,oBAAoB,EAAE,OAAO,mPAM9C;AAED;;GAEG;AACH,wCAFW,OAAO,oBAAoB,EAAE,OAAO,WAI9C;AAED;;;;GAIG;AACH,2CAFW,OAAO,oBAAoB,EAAE,OAAO,WAI9C;AAED;;;GAGG;AACH,4CAHW,OAAO,oBAAoB,EAAE,OAAO,4DAsB9C;AAED;;;;;GAKG;AACH,0CAHW,OAAO,oBAAoB,EAAE,OAAO,GAClC,GAAG,EAAE,CAsBjB;AAED;;;GAGG;AACH,gDAHW,OAAO,oBAAoB,EAAE,OAAO,UACzB,GAAG,KAAE,MAAM,CAmBhC;AA5LD;;GAEG;AACH,wCAFU,OAAO,oBAAoB,EAAE,wBAAwB,EAAE,CAEb;AAEpD;;GAEG;AACH,0CAFU,OAAO,oBAAoB,EAAE,0BAA0B,EAAE,CAEX;AAExD;;GAEG;AACH,iCAFU,OAAO,oBAAoB,EAAE,iBAAiB,EAAE,CAKxD;AAoBF;;;;GAIG;AACH,gCAFU,QAAQ,OAAO,OAAO,oBAAoB,EAAE,OAAO,EAAE,OAAO,oBAAoB,EAAE,0BAA0B,CAAC,CAAC,CAKtH;AAEF;;;;GAIG;AACH,8BAFU,QAAQ,OAAO,OAAO,oBAAoB,EAAE,OAAO,EAAE,OAAO,oBAAoB,EAAE,OAAO,CAAC,CAAC,CAInG"}
+{"version":3,"file":"encoder.d.ts","sourceRoot":"","sources":["../../../src/encoder/encoder.js"],"names":[],"mappings":"AAEA;;;;;;;;GAQG;AACH,iDAJW,OAAO,qBAAqB,EAAE,OAAO,YACrC,OAAO,oBAAoB,EAAE,QAAQ,gGAgC/C;AAED;;;;GAIG;AACH,4DAJW,OAAO,qBAAqB,EAAE,QAAQ,EAAE,eACxC,CAAC,OAAO,EAAE,OAAO,oBAAoB,EAAE,gBAAgB,KAAK,OAAO,qBAAqB,EAAE,SAAS,yCAqC7G;AAED;;;;GAIG;AACH,kIAHW,CAAC,OAAO,EAAE,OAAO,oBAAoB,EAAE,gBAAgB,KAAK,OAAO,qBAAqB,EAAE,SAAS,yCAqC7G;AAED;;;;;GAKG;AACH,uCAHW,OAAO,oBAAoB,EAAE,UAAU,4FAKjD;AAED;;;GAGG;AACH,uCAHW,OAAO,oBAAoB,EAAE,UAAU,2DAKjD;AAED;;;GAGG;AACH,uCAHW,OAAO,oBAAoB,EAAE,UAAU,qIAKjD;AAED;;;GAGG;AACH,kDAHW,OAAO,oBAAoB,EAAE,UAAU,kEAWjD;AAED;;;GAGG;AACH,6CAHW,OAAO,qBAAqB,EAAE,OAAO,WACrC,OAAO,oBAAoB,EAAE,OAAO,s9CAS9C;AAED;;;GAGG;AACH,iDAHW,OAAO,oBAAoB,EAAE,UAAU,4FAKjD;AAED;;;GAGG;AACH,0CAHW,OAAO,oBAAoB,EAAE,UAAU,0DAKjD;AAED;;;GAGG;AACH,sCAHW,OAAO,oBAAoB,EAAE,UAAU,sDAKjD;AAED;;;GAGG;AACH,2DAHW,OAAO,oBAAoB,EAAE,UAAU,wMAQjD;AAED;;;GAGG;AACH,oDAHW,OAAO,oBAAoB,EAAE,UAAU,wGAKjD;AAoBD;;;GAGG;AACH,oDAHW,OAAO,oBAAoB,EAAE,OAAO,oEAM9C;AAED;;;GAGG;AACH,6CAHW,OAAO,oBAAoB,EAAE,OAAO,6DAM9C;AAqBD;;;GAGG;AACH,4CAFW,MAAM,WAIhB;AAED;;;;GAIG;AACH,oDAFW,OAAO,oBAAoB,EAAE,OAAO,2DAS9C;AAED;;;;;GAKG;AACH,2CAFW,OAAO,oBAAoB,EAAE,OAAO,wCAI9C;AAED;;;;GAIG;AACH,kDAFW,OAAO,oBAAoB,EAAE,OAAO,mPAM9C;AAED;;GAEG;AACH,wCAFW,OAAO,oBAAoB,EAAE,OAAO,WAI9C;AAED;;;;GAIG;AACH,2CAFW,OAAO,oBAAoB,EAAE,OAAO,WAI9C;AAED;;;GAGG;AACH,4CAHW,OAAO,oBAAoB,EAAE,OAAO,4DAsB9C;AAED;;;;;GAKG;AACH,0CAHW,OAAO,oBAAoB,EAAE,OAAO,GAClC,GAAG,EAAE,CAsBjB;AAED;;;GAGG;AACH,gDAHW,OAAO,oBAAoB,EAAE,OAAO,UACzB,GAAG,KAAE,MAAM,CAmBhC;AA5LD;;GAEG;AACH,wCAFU,OAAO,oBAAoB,EAAE,wBAAwB,EAAE,CAEb;AAEpD;;GAEG;AACH,0CAFU,OAAO,oBAAoB,EAAE,0BAA0B,EAAE,CAEX;AAExD;;GAEG;AACH,iCAFU,OAAO,oBAAoB,EAAE,iBAAiB,EAAE,CAKxD;AAoBF;;;;GAIG;AACH,gCAFU,QAAQ,OAAO,OAAO,oBAAoB,EAAE,OAAO,EAAE,OAAO,oBAAoB,EAAE,0BAA0B,CAAC,CAAC,CAKtH;AAEF;;;;GAIG;AACH,8BAFU,QAAQ,OAAO,OAAO,oBAAoB,EAAE,OAAO,EAAE,OAAO,oBAAoB,EAAE,OAAO,CAAC,CAAC,CAInG"}

package/dist/src/fonts/bmFontMetrics.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"bmFontMetrics.d.ts","sourceRoot":"","sources":["../../../src/fonts/bmFontMetrics.js"],"names":[],"mappings":"AAIA;;;;;;;;;;;;;;;;;;;GAmBG;AACH,2CAHW,OAAO,oBAAoB,EAAE,MAAM,GACjC,aAAa,CAqFzB;AA3GD,4BAA6B;;;;;;;mBAUhB,OAAO,oBAAoB,EAAE,IAAI;;;;;;;;yBAG7B,MAAM,aAAa,MAAM,KAAK,MAAM;8BAChC,MAAM,KAAK,IAAI;oBACnB,MAAM,KAAK,IAAI;aACtB,MAAM;eACN,MAAM;aACN,MAAM;YACN,OAAO,oBAAoB,EAAE,MAAM"}
+{"version":3,"file":"bmFontMetrics.d.ts","sourceRoot":"","sources":["../../../src/fonts/bmFontMetrics.js"],"names":[],"mappings":"AAIA;;;;;;;;;;;;;;;;;;;GAmBG;AACH,2CAHW,OAAO,oBAAoB,EAAE,MAAM,GACjC,aAAa,CAqFzB;AA3GD,4BAA6B;;;;;;;mBAUhB,OAAO,oBAAoB,EAAE,IAAI;;;;;;;;kBAGpC,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,CAAC,EAAE,MAAM,KAAK,MAAM;mBAC3C,CAAC,QAAQ,EAAE,MAAM,KAAK,IAAI;aAC1B,CAAC,IAAI,EAAE,MAAM,KAAK,IAAI;aACtB,MAAM;eACN,MAAM;aACN,MAAM;YACN,OAAO,oBAAoB,EAAE,MAAM"}

package/dist/src/genome/genome.d.ts

@@ -18,6 +18,21 @@ export function isChromosomalLocus(value: any): value is import("../spec/genome.
  * @return {value is ChromosomalLocus[]}
  */
 export function isChromosomalLocusInterval(value: any[]): value is import("../spec/genome.js").ChromosomalLocus[];
+/**
+ * @param {any} value
+ * @returns {value is GenomeConfig}
+ */
+export function isGenomeConfig(value: any): value is import("../spec/genome.js").GenomeConfig;
+/**
+ * @param {any} value
+ * @returns {value is import("../spec/genome.js").UrlGenomeConfig               }
+ */
+export function isUrlGenomeConfig(value: any): value is import("../spec/genome.js").UrlGenomeConfig;
+/**
+ * @param {any} value
+ * @returns {value is import("../spec/genome.js").InlineGenomeConfig}
+ */
+export function isInlineGenomeConfig(value: any): value is import("../spec/genome.js").InlineGenomeConfig;
 /**
  * @typedef {import("../spec/genome.js").GenomeConfig} GenomeConfig
  * @typedef {import("../spec/genome.js").ChromosomalLocus} ChromosomalLocus
@@ -44,7 +59,15 @@ export default class Genome {
      * @param {GenomeConfig} config
      */
     constructor(config: GenomeConfig);
-    config: import("../spec/genome.js").GenomeConfig;
+    config: {
+        name: string;
+    } | {
+        url: string;
+        name: string;
+    } | {
+        contigs: import("../spec/genome.js").Contig[];
+        name: string;
+    };
     /** @type {(Chromosome & ChromosomeAnnotation)[]} */
     chromosomes: (Chromosome & ChromosomeAnnotation)[];
     /** @type {Map<string | number, number>} */
@@ -59,7 +82,6 @@ export default class Genome {
      * @param {string} baseUrl
      */
     load(baseUrl: string): Promise<void>;
-    baseUrl: string;
     hasChrPrefix(): boolean;
     /**
      *

package/dist/src/genome/genome.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"genome.d.ts","sourceRoot":"","sources":["../../../src/genome/genome.js"],"names":[],"mappings":"AA+VA;;;GAGG;AACH,gDAFW,MAAM;;;IAOhB;AAED;;;;GAIG;AACH,0CAHW,GAAG,yDAKb;AAED;;;;GAIG;AACH,kDAHW,GAAG,EAAE,2DAKf;AAlXD;;;;;;;;;;;;;;;;;;;;GAoBG;AAEH;IACI;;OAEG;IACH,oBAFW,YAAY,EA4BtB;IAzBG,iDAAoB;IAQpB,oDAAoD;IACpD,aADW,CAAC,UAAU,GAAG,oBAAoB,CAAC,EAAE,CAC3B;IAErB,2CAA2C;IAC3C,0BADW,IAAI,MAAM,GAAG,MAAM,EAAE,MAAM,CAAC,CACE;IAEzC,sEAAsE;IACtE,mBADW,IAAI,MAAM,GAAG,MAAM,EAAE,UAAU,GAAG,oBAAoB,CAAC,CAChC;IAElC,uBAAuB;IACvB,cADW,MAAM,EAAE,CACG;IAEtB,kBAAkB;IAOtB,mBAEC;IAED;;OAEG;IACH,cAFW,MAAM,iBA0BhB;IAlBO,gBAEyC;IAkBjD,wBAEC;IAED;;;OAGG;IACH,0BAFW,UAAU,EAAE,QA2CtB;IAED,sBAEC;IAED;;;;;OAKG;IACH,oBAHW,MAAM,GAAG,MAAM,OACf,MAAM,UAShB;IAED;;;OAGG;IACH,4BAFW,MAAM,qCAgBhB;IAED;;;;OAIG;IACH,6BAHW,MAAM,GACJ,gBAAgB,CAY5B;IAED;;;OAGG;IACH,oBAFW,MAAM,qCAIhB;IAED;;;;;;;;;;OAUG;IACH,yBAHW,MAAM,EAAE,GACN,MAAM,CAIlB;IAED;;;OAGG;IACH,gCAHW,MAAM,EAAE,GACN,CAAC,gBAAgB,EAAE,gBAAgB,CAAC,CAUhD;IAED;;;;;;OAMG;IACH,kCAFW,gBAAgB,EAAE,YAgB5B;IAED;;;;;OAKG;IACH,wCAHW,CAAC,gBAAgB,EAAE,gBAAgB,CAAC,GAClC,0BAA0B,EAAE,CAiCxC;IAED;;;;OAIG;IACH,4DAFW,MAAM,EAAE,gCAOlB;IAED;;;;OAIG;IACH,mBAHW,MAAM,GACJ,CAAC,MAAM,EAAE,MAAM,CAAC,CAgC5B;CACJ;2BApVY,OAAO,mBAAmB,EAAE,YAAY;+BACxC,OAAO,mBAAmB,EAAE,gBAAgB;;UAG/C,MAAM;UACN,MAAM;;;;;;WAGN,MAAM;;;;YACN,MAAM;;;;qBACN,MAAM;;;;mBACN,MAAM;wBACN,MAAM,EAAE;;;;SACR,OAAO;;;WAGP,MAAM;cACN,MAAM;YACN,MAAM"}
+{"version":3,"file":"genome.d.ts","sourceRoot":"","sources":["../../../src/genome/genome.js"],"names":[],"mappings":"AAwWA;;;GAGG;AACH,gDAFW,MAAM;;;IAOhB;AAED;;;;GAIG;AACH,0CAHW,GAAG,yDAKb;AAED;;;;GAIG;AACH,kDAHW,GAAG,EAAE,2DAKf;AAED;;;GAGG;AACH,sCAHW,GAAG,qDAUb;AAED;;;GAGG;AACH,yCAHW,GAAG,wDAKb;AAED;;;GAGG;AACH,4CAHW,GAAG,2DAKb;AAzZD;;;;;;;;;;;;;;;;;;;;GAoBG;AAEH;IACI;;OAEG;IACH,oBAFW,YAAY,EA6CtB;IA1CG;;;;;;;;MAA2C;IAc3C,oDAAoD;IACpD,aADW,CAAC,UAAU,GAAG,oBAAoB,CAAC,EAAE,CAC3B;IAErB,2CAA2C;IAC3C,0BADW,IAAI,MAAM,GAAG,MAAM,EAAE,MAAM,CAAC,CACE;IAEzC,sEAAsE;IACtE,mBADW,IAAI,MAAM,GAAG,MAAM,EAAE,UAAU,GAAG,oBAAoB,CAAC,CAChC;IAElC,uBAAuB;IACvB,cADW,MAAM,EAAE,CACG;IAEtB,kBAAkB;IAkBtB,mBAEC;IAED;;OAEG;IACH,cAFW,MAAM,iBAmBhB;IAED,wBAEC;IAED;;;OAGG;IACH,0BAFW,UAAU,EAAE,QA2CtB;IAED,sBAEC;IAED;;;;;OAKG;IACH,oBAHW,MAAM,GAAG,MAAM,OACf,MAAM,UAShB;IAED;;;OAGG;IACH,4BAFW,MAAM,qCAgBhB;IAED;;;;OAIG;IACH,6BAHW,MAAM,GACJ,gBAAgB,CAY5B;IAED;;;OAGG;IACH,oBAFW,MAAM,qCAIhB;IAED;;;;;;;;;;OAUG;IACH,yBAHW,MAAM,EAAE,GACN,MAAM,CAIlB;IAED;;;OAGG;IACH,gCAHW,MAAM,EAAE,GACN,CAAC,gBAAgB,EAAE,gBAAgB,CAAC,CAUhD;IAED;;;;;;OAMG;IACH,kCAFW,gBAAgB,EAAE,YAgB5B;IAED;;;;;OAKG;IACH,wCAHW,CAAC,gBAAgB,EAAE,gBAAgB,CAAC,GAClC,0BAA0B,EAAE,CAiCxC;IAED;;;;OAIG;IACH,4DAFW,MAAM,EAAE,gCAOlB;IAED;;;;OAIG;IACH,mBAHW,MAAM,GACJ,CAAC,MAAM,EAAE,MAAM,CAAC,CAgC5B;CACJ;2BA9VY,OAAO,mBAAmB,EAAE,YAAY;+BACxC,OAAO,mBAAmB,EAAE,gBAAgB;;UAG/C,MAAM;UACN,MAAM;;;;;;WAGN,MAAM;;;;YACN,MAAM;;;;qBACN,MAAM;;;;mBACN,MAAM;wBACN,MAAM,EAAE;;;;SACR,OAAO;;;WAGP,MAAM;cACN,MAAM;YACN,MAAM"}