@genome-spy/core 0.51.0 → 0.53.0

package/dist/src/genome/genome.js

@@ -1,10 +1,9 @@
 import { bisect } from "d3-array";
 import { tsvParseRows } from "d3-dsv";
-import { loader } from "vega-loader";
 import { isObject } from "vega-util";
 import { formatRange } from "./locusFormat.js";
-
-const defaultBaseUrl = "https://genomespy.app/data/genomes/";
+import { getContigs } from "./genomes.js";
+import { concatUrl } from "../utils/url.js";
 
 /**
  * @typedef {import("../spec/genome.js").GenomeConfig} GenomeConfig
@@ -33,11 +32,17 @@ export default class Genome {
      * @param {GenomeConfig} config
      */
     constructor(config) {
-        this.config = config;
+        this.config = { name: "custom", ...config };
+
+        if ("baseUrl" in config) {
+            throw new Error(
+                "The `baseUrl` property in genome config has been removed in GenomeSpy v0.52.0. Use `url` instead. See https://genomespy.app/docs/genomic-data/genomic-coordinates/."
+            );
+        }
 
-        if (!this.config.contigs && typeof this.config.name !== "string") {
+        if (!isGenomeConfig(config)) {
             throw new Error(
-                "No name has been defined for the genome assembly!"
+                "Not a genome configuration: " + JSON.stringify(config)
             );
         }
 
@@ -55,8 +60,19 @@ export default class Genome {
 
         this.totalSize = 0;
 
-        if (this.config.contigs) {
+        if (isInlineGenomeConfig(this.config)) {
             this.setChromSizes(this.config.contigs);
+        } else if (isUrlGenomeConfig(this.config)) {
+            // Nop
+        } else {
+            const contigs = getContigs(this.config.name);
+            if (contigs) {
+                this.setChromSizes(contigs);
+            } else {
+                throw new Error(
+                    `Unknown genome: ${this.config.name}. Please provide contigs or a URL. See https://genomespy.app/docs/genomic-data/genomic-coordinates/.`
+                );
+            }
         }
     }
 
@@ -68,28 +84,21 @@ export default class Genome {
      * @param {string} baseUrl
      */
     async load(baseUrl) {
-        if (this.config.contigs) {
+        if (!isUrlGenomeConfig(this.config)) {
             return;
         }
 
-        if (this.config.baseUrl) {
-            this.baseUrl = /^http(s)?/.test(this.config.baseUrl)
-                ? this.config.baseUrl
-                : baseUrl + "/" + this.config.baseUrl;
-        } else {
-            this.baseUrl = defaultBaseUrl;
-        }
-
         try {
-            this.setChromSizes(
-                parseChromSizes(
-                    await loader({ baseURL: this.baseUrl }).load(
-                        `${this.config.name}/${this.name}.chrom.sizes`
-                    )
-                )
-            );
+            const fullUrl = concatUrl(baseUrl, this.config.url);
+            const result = await fetch(fullUrl);
+            if (!result.ok) {
+                throw new Error(`${result.status} ${result.statusText}`);
+            }
+            this.setChromSizes(parseChromSizes(await result.text()));
         } catch (e) {
-            throw new Error(`Could not load chrom sizes: ${e.message}`);
+            throw new Error(
+                `Could not load chrom sizes: ${this.config.url}. Reason: ${e.message}`
+            );
         }
     }
 
@@ -354,10 +363,10 @@ export default class Genome {
  * @param {string} chromSizesData
  */
 export function parseChromSizes(chromSizesData) {
-    // TODO: Support other organisms too
-    return tsvParseRows(chromSizesData)
-        .filter((row) => /^chr[0-9A-Z]+$/.test(row[0]))
-        .map(([name, size]) => ({ name, size: parseInt(size) }));
+    return tsvParseRows(chromSizesData).map(([name, size]) => ({
+        name,
+        size: parseInt(size),
+    }));
 }
 
 /**
@@ -377,3 +386,32 @@ export function isChromosomalLocus(value) {
 export function isChromosomalLocusInterval(value) {
     return value.every(isChromosomalLocus);
 }
+
+/**
+ * @param {any} value
+ * @returns {value is GenomeConfig}
+ */
+export function isGenomeConfig(value) {
+    return (
+        isObject(value) &&
+        ("name" in value ||
+            isUrlGenomeConfig(value) ||
+            isInlineGenomeConfig(value))
+    );
+}
+
+/**
+ * @param {any} value
+ * @returns {value is import("../spec/genome.js").UrlGenomeConfig               }
+ */
+export function isUrlGenomeConfig(value) {
+    return isGenomeConfig(value) && "url" in value;
+}
+
+/**
+ * @param {any} value
+ * @returns {value is import("../spec/genome.js").InlineGenomeConfig}
+ */
+export function isInlineGenomeConfig(value) {
+    return isGenomeConfig(value) && "contigs" in value;
+}

package/dist/src/genome/genome.test.js

@@ -1,4 +1,4 @@
-import { describe, expect, test } from "vitest";
+import { afterAll, describe, expect, test, vi } from "vitest";
 import Genome from "./genome.js";
 
 describe("Human genome, chromosome names prefixed with 'chr'", () => {
@@ -190,6 +190,48 @@ describe("C. elegans genome, chromosome names prefixed with 'chr'", () => {
     });
 });
 
+describe("Load chrom.sizes file from a URL", () => {
+    const fetchSpy = vi.spyOn(global, "fetch");
+    fetchSpy.mockImplementation((/** @type {string} */ url) => {
+        if (url !== "http://example.com/chrom.sizes") {
+            throw new Error(`Unexpected URL: ${url}`);
+        }
+        return Promise.resolve(
+            // @ts-expect-error
+            {
+                text() {
+                    return Promise.resolve(
+                        "chr1\t1000\nchr2\t2000\nchr3\t3000\nchrX\t4000"
+                    );
+                },
+                ok: true,
+            }
+        );
+    });
+
+    afterAll(() => {
+        fetchSpy.mockRestore();
+    });
+
+    test("Throw if the deprecated baseUrl property is provided", () => {
+        expect(
+            () =>
+                new Genome({
+                    name: "random",
+                    // @ts-expect-error
+                    baseUrl: "http://example.com",
+                })
+        ).toThrow(/removed/);
+    });
+
+    test("Loads and parses a genome", async () => {
+        const g = new Genome({ name: "random", url: "chrom.sizes" });
+        await g.load("http://example.com");
+
+        expect(g.parseInterval("chr2")).toEqual([1000, 3000]);
+    });
+});
+
 describe("Parse interval strings", () => {
     const chromosomes = [
         { name: "chr1", size: 1000 },

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

@@ -0,0 +1,8 @@
+/**
+ * @param {string} assembly
+ */
+export function getContigs(assembly: string): {
+    name: string;
+    size: number;
+}[];
+//# sourceMappingURL=genomes.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"genomes.d.ts","sourceRoot":"","sources":["../../../src/genome/genomes.js"],"names":[],"mappings":"AAwJA;;GAEG;AACH,qCAFW,MAAM;;;IAUhB"}

package/dist/src/genome/genomes.js

@@ -0,0 +1,164 @@
+/*
+ * Based on chrom.sizes files from UCSC Genome Browser
+ * https://hgdownload.cse.ucsc.edu/goldenpath/
+ *
+ * Alternative loci, patches, and random contigs are not included.
+ */
+
+const dm6 = `chr3R	32079331
+chr3L	28110227
+chr2R	25286936
+chrX	23542271
+chr2L	23513712
+chrY	3667352
+chr4	1348131
+chrM	19524`;
+
+const hg18 = `chr1	247249719
+chr2	242951149
+chr3	199501827
+chr4	191273063
+chr5	180857866
+chr6	170899992
+chr7	158821424
+chr8	146274826
+chr9	140273252
+chr10	135374737
+chr11	134452384
+chr12	132349534
+chr13	114142980
+chr14	106368585
+chr15	100338915
+chr16	88827254
+chr17	78774742
+chr18	76117153
+chr19	63811651
+chr20	62435964
+chr21	46944323
+chr22	49691432
+chrX	154913754
+chrY	57772954
+chrM	16571`;
+
+const hg19 = `chr1	249250621
+chr2	243199373
+chr3	198022430
+chr4	191154276
+chr5	180915260
+chr6	171115067
+chr7	159138663
+chr8	146364022
+chr9	141213431
+chr10	135534747
+chr11	135006516
+chr12	133851895
+chr13	115169878
+chr14	107349540
+chr15	102531392
+chr16	90354753
+chr17	81195210
+chr18	78077248
+chr19	59128983
+chr20	63025520
+chr21	48129895
+chr22	51304566
+chrX	155270560
+chrY	59373566
+chrM	16571`;
+
+const hg38 = `chr1	248956422
+chr2	242193529
+chr3	198295559
+chr4	190214555
+chr5	181538259
+chr6	170805979
+chr7	159345973
+chr8	145138636
+chr9	138394717
+chr10	133797422
+chr11	135086622
+chr12	133275309
+chr13	114364328
+chr14	107043718
+chr15	101991189
+chr16	90338345
+chr17	83257441
+chr18	80373285
+chr19	58617616
+chr20	64444167
+chr21	46709983
+chr22	50818468
+chrX	156040895
+chrY	57227415
+chrM	16569`;
+
+const mm9 = `chr1	197195432
+chr2	181748087
+chr3	159599783
+chr4	155630120
+chr5	152537259
+chr6	149517037
+chr7	152524553
+chr8	131738871
+chr9	124076172
+chr10	129993255
+chr11	121843856
+chr12	121257530
+chr13	120284312
+chr14	125194864
+chr15	103494974
+chr16	98319150
+chr17	95272651
+chr18	90772031
+chr19	61342430
+chrX	166650296
+chrY	15902555
+chrM	16299`;
+
+const mm10 = `chr1	195471971
+chr2	182113224
+chr3	160039680
+chr4	156508116
+chr5	151834684
+chr6	149736546
+chr7	145441459
+chr8	129401213
+chr9	124595110
+chr10	130694993
+chr11	122082543
+chr12	120129022
+chr13	120421639
+chr14	124902244
+chr15	104043685
+chr16	98207768
+chr17	94987271
+chr18	90702639
+chr19	61431566
+chrX	171031299
+chrY	91744698
+chrM	16299`;
+
+/**
+ * @type {Record<string, string>}
+ */
+const assemblies = {
+    dm6,
+    hg18,
+    hg19,
+    hg38,
+    mm9,
+    mm10,
+};
+
+/**
+ * @param {string} assembly
+ */
+export function getContigs(assembly) {
+    if (!(assembly in assemblies))
+        throw new Error(`Unknown assembly: ${assembly}`);
+
+    return assemblies[assembly].split("\n").map((line) => {
+        const arr = line.split("\t");
+        return { name: arr[0], size: parseInt(arr[1]) };
+    });
+}

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

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=genomes.test.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"genomes.test.d.ts","sourceRoot":"","sources":["../../../src/genome/genomes.test.js"],"names":[],"mappings":""}

package/dist/src/genome/genomes.test.js

@@ -0,0 +1,8 @@
+import { expect, test } from "vitest";
+import { getContigs } from "./genomes.js";
+
+test("getContigs", () => {
+    expect(getContigs("mm10")[0]).toEqual({ name: "chr1", size: 195471971 });
+    expect(getContigs("mm10")[5]).toEqual({ name: "chr6", size: 149736546 });
+    expect(getContigs("hg38")[19]).toEqual({ name: "chr20", size: 64444167 });
+});

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

@@ -1 +1 @@
-{"version":3,"file":"genomeSpy.d.ts","sourceRoot":"","sources":["../../src/genomeSpy.js"],"names":[],"mappings":"AA6CA;IACI;;;;;OAKG;IAEH;;;;;OAKG;IACH,uBAJW,WAAW,qDAEX,OAAO,qBAAqB,EAAE,YAAY,EA6FpD;IA1FG,uBAA0B;IAC1B,oDAAsB;IAItB,6BAA6B;IAC7B,uBADW,CAAC,MAAM,IAAI,CAAC,EAAE,CACM;IAE/B,sCAAsC;IACtC,wCAAgB;IAEhB,yBAAoC;IAEpC,4CAA4C;IAC5C,oBADW,QAAU,MAAM,KAAE,MAAM,EAAE,CAAC,EAAE,CACZ;IAE5B,mBAAoD;IAEpD,0BAA0B;IAC1B,aADW,WAAW,CACM;IAE5B;;;;;OAKG;IACH,qEAF0B,OAAO,CAE8B;IAE/D,2CAA2C;IAC3C,mBADW,4BAA4B,CACL;IAClC,2CAA2C;IAC3C,iBADW,4BAA4B,CACP;IAEhC,oDAAoD;IACpD,6BAAgC;IAEhC;;;OAGG;IACH,eAFU;QAAE,IAAI,EAAE,OAAO,iBAAiB,EAAE,OAAO,CAAC;QAAC,KAAK,EAAE,OAAO,oBAAoB,EAAE,KAAK,CAAC;QAAC,QAAQ,EAAE,MAAM,CAAA;KAAE,CAEpF;IAE9B,uBAA+C;IAE/C;;;OAGG;IACH,oBAFU,IAAI,MAAM,EAAE,QAAU,aAAa,KAAE,IAAI,CAAC,EAAE,CAAC,CAEpB;IAEnC;;;;;;OAMG;IACH,yCAFkC,GAAG,KAAK,IAAI,GAEd;IAEhC;;;OAGG;IACH,kDAFkC,GAAG,KAAK,IAAI,GAEL;IAEzC,oFAAoF;IACpF,iBADW,OAAO,MAAM,EAAE,OAAO,6BAA6B,EAAE,cAAc,CAAC,CAK9E;IAED,mBAAmB;IACnB,2CAAyB;IAEzB;;;;OAIG;IACH;gBAF8B,OAAO,wBAAwB,EAAE,iBAAiB;iBAAW,MAAM;OAEnE;IAE9B;;OAEG;IACH,wBAFU,WAAW,CAEkB;IAEvC,oBAAoB;IACpB,kBADW,KAAK,CACiB;IA2CrC;;;OAGG;IACH,2CAFkB,MAAM,KAAK,GAAG,EAAE,QAIjC;IAED;;OAEG;IACH,+BAFW,MAAM,YAShB;IAED;;;;OAIG;IACH,sBAHW,MAAM,QACN,GAAG,EAAE,QAaf;IAED;;;;;OAKG;IACH,gBAHW,kBAAkB,YAClB,GAAG,QAQb;IAED;;;OAGG;IACH,iCAwDC;IA4DG,uBAQC;IAGD,mCAGE;IAOF,sCAEE;IAGF,iBAA0C;IAW9C;;OAEG;IACH,gBAuBC;IAED,sCA6MC;IAED;;;OAGG;IACH,UAFa,QAAQ,OAAO,CAAC,CA6B5B;IAED,4BA8JC;IAvIe,iCAAoC;IAyIpD;;;OAGG;IACH,kBAHW,MAAM,KACN,MAAM,QAqEhB;IAED;;;;;;;OAOG;IACH,oDAHuB,QAAQ,MAAM,GAAG,WAAW,GAAG,OAAO,KAAK,EAAE,cAAc,CAAC,QAYlF;IAED,sBA6CC;IAED,kBAIC;IAED,iCAOC;IAED,iCASC;IAED,qFAWC;;CACJ;;;;iCAt8BY,eAAe,GAAG,YAAY,GAAG,QAAQ,GAAG,gBAAgB;4BAP7B,uBAAuB;qBAZ9C,qBAAqB;wBAIlB,yBAAyB;yCARR,yDAAyD;oBAYvD,oBAAoB;kBAT7C,wBAAwB;wBALlB,qBAAqB;oBATzB,uBAAuB;qBAOtB,oBAAoB"}
+{"version":3,"file":"genomeSpy.d.ts","sourceRoot":"","sources":["../../src/genomeSpy.js"],"names":[],"mappings":"AA6CA;IACI;;;;;OAKG;IAEH;;;;;OAKG;IACH,uBAJW,WAAW,qDAEX,OAAO,qBAAqB,EAAE,YAAY,EA6FpD;IA1FG,uBAA0B;IAC1B,oDAAsB;IAItB,6BAA6B;IAC7B,uBADW,CAAC,MAAM,IAAI,CAAC,EAAE,CACM;IAE/B,sCAAsC;IACtC,wCAAgB;IAEhB,yBAAoC;IAEpC,4CAA4C;IAC5C,oBADW,QAAU,MAAM,KAAE,MAAM,EAAE,CAAC,EAAE,CACZ;IAE5B,mBAAoD;IAEpD,0BAA0B;IAC1B,aADW,WAAW,CACM;IAE5B;;;;;OAKG;IACH,qEAF0B,OAAO,CAE8B;IAE/D,2CAA2C;IAC3C,mBADW,4BAA4B,CACL;IAClC,2CAA2C;IAC3C,iBADW,4BAA4B,CACP;IAEhC,oDAAoD;IACpD,6BAAgC;IAEhC;;;OAGG;IACH,eAFU;QAAE,IAAI,EAAE,OAAO,iBAAiB,EAAE,OAAO,CAAC;QAAC,KAAK,EAAE,OAAO,oBAAoB,EAAE,KAAK,CAAC;QAAC,QAAQ,EAAE,MAAM,CAAA;KAAE,CAEpF;IAE9B,uBAA+C;IAE/C;;;OAGG;IACH,oBAFU,IAAI,MAAM,EAAE,QAAU,aAAa,KAAE,IAAI,CAAC,EAAE,CAAC,CAEpB;IAEnC;;;;;;OAMG;IACH,iBAFU,IAAI,MAAM,EAAE,IAAI,CAAC,KAAK,EAAE,GAAG,KAAK,IAAI,CAAC,CAAC,CAEhB;IAEhC;;;OAGG;IACH,0BAFU,IAAI,MAAM,EAAE,IAAI,CAAC,KAAK,EAAE,GAAG,KAAK,IAAI,CAAC,CAAC,CAEP;IAEzC,oFAAoF;IACpF,iBADW,OAAO,MAAM,EAAE,OAAO,6BAA6B,EAAE,cAAc,CAAC,CAK9E;IAED,mBAAmB;IACnB,2CAAyB;IAEzB;;;;OAIG;IACH;gBAF8B,OAAO,wBAAwB,EAAE,iBAAiB;iBAAW,MAAM;OAEnE;IAE9B;;OAEG;IACH,wBAFU,WAAW,CAEkB;IAEvC,oBAAoB;IACpB,kBADW,KAAK,CACiB;IA2CrC;;;OAGG;IACH,oCAFW,CAAC,IAAI,EAAE,MAAM,KAAK,GAAG,EAAE,QAIjC;IAED;;OAEG;IACH,+BAFW,MAAM,YAShB;IAED;;;;OAIG;IACH,sBAHW,MAAM,QACN,GAAG,EAAE,QAaf;IAED;;;;;OAKG;IACH,gBAHW,kBAAkB,YAClB,GAAG,QAQb;IAED;;;OAGG;IACH,iCAwDC;IA4DG,uBAQC;IAGD,mCAGE;IAOF,sCAEE;IAGF,iBAA0C;IAW9C;;OAEG;IACH,gBAuBC;IAED,sCA6MC;IAED;;;OAGG;IACH,UAFa,QAAQ,OAAO,CAAC,CA6B5B;IAED,4BA8JC;IAvIe,iCAAoC;IAyIpD;;;OAGG;IACH,kBAHW,MAAM,KACN,MAAM,QAqEhB;IAED;;;;;;;OAOG;IACH,oDAHuB,QAAQ,MAAM,GAAG,WAAW,GAAG,OAAO,KAAK,EAAE,cAAc,CAAC,QAYlF;IAED,sBA6CC;IAED,kBAIC;IAED,iCAOC;IAED,iCASC;IAED,qFAWC;;CACJ;;;;iCAt8BY,eAAe,GAAG,YAAY,GAAG,QAAQ,GAAG,gBAAgB;4BAP7B,uBAAuB;qBAZ9C,qBAAqB;wBAIlB,yBAAyB;yCARR,yDAAyD;oBAYvD,oBAAoB;kBAT7C,wBAAwB;wBALlB,qBAAqB;oBATzB,uBAAuB;qBAOtB,oBAAoB"}

package/dist/src/gl/dataToVertices.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"dataToVertices.d.ts","sourceRoot":"","sources":["../../../src/gl/dataToVertices.js"],"names":[],"mappings":"AAgBA;;;;;GAKG;AACH;IACI;;;OAGG;IAEH;;;;;;OAMG;IACH;;qBAJW,MAAM,EAAE;sBACR,MAAM;OAyFhB;IArFG,8FAAwB;IAIxB,sGAQK;IAQL,0BAAoC;IAEpC,8BAAoD;IA2DpD,mBAAmB;IAEnB,yFAAyF;IACzF,UADW,IAAI,GAAG,EAAE,UAAU,CAAC,CACkB;IAGrD;;;;OAIG;IACH,mBAFW,GAAG,QAcb;IAED;;OAEG;IACH,oBAFW,IAAI,GAAG,EAAE,MAAM,EAAE,CAAC,QAM5B;IAED;;;OAGG;IACH,cAHW,GAAG,QACH,MAAM,EAAE,kCAYlB;IAED;;;;OAIG;IACH,sBAJW,OAAO,qBAAqB,EAAE,IAAI,OAClC,MAAM,OACN,MAAM,QAgEhB;IAED;;;;;OAKG;IACH,mBAFW,OAAO,qBAAqB,EAAE,KAAK,QAI7C;IAhEO;;;MAAyB;IAkEjC;QAEQ,kJAAkJ;gBAAvI,OAAO,MAAM,EAAE;YAAC,IAAI,EAAE,WAAW,GAAG,UAAU,GAAG,WAAW,GAAG,UAAU,GAAG,YAAY,CAAC;YAAC,aAAa,EAAE,MAAM,CAAC;YAAC,OAAO,CAAC,EAAE,MAAM,CAAA;SAAC,CAAC;QAE9I,8BAA8B;;QAE9B,8CAA8C;;;MAIrD;CACJ;AAED;IACI;;;;;;OAMG;IACH;;oBAHW,MAAM,EAAE;mBACR,MAAM;OA+BhB;IAnBG,qBAkBW;CA8BlB;AAED;IACI;;;;;;;;;OASG;IACH;;oBANW,MAAM,EAAE;gCACR,MAAM;uBAEN,MAAM,EAAE;mBACR,MAAM;OAwBhB;IARG,uBAAgC;IAEhC,8BAA8D;IAE9D,6CAA+D;IAC/D,4CAA6D;CA6CpE;AAED;IACI;;;;;;OAMG;IACH;;oBAHW,MAAM,EAAE;mBACR,MAAM;OAShB;CACJ;AAED;IACI;;;;;OAKG;IACH;;oBAHW,MAAM,EAAE;mBACR,MAAM;OAShB;CAYJ;AAED;IACI;;;;;;;;;OASG;IACH;;oBANW,MAAM,EAAE;qBACR,OAAO,2BAA2B,EAAE,aAAa;oBACjD,OAAO,MAAM,EAAE,GAAG,CAAC;wBACnB,MAAM;sBACN,OAAO;OA6CjB;IA9BG,4DAA2B;IAC3B,2DAA0B;IAE1B,gCAA4B;IAO5B,qCAAqC;IACrC,sBADmB,GAAG,KAAK,MAAM,CAMf;IAElB,oDAGC;IACD,qDAGC;IAED,8CAAiE;CAgJxE;;;;;;;;YAnnBS,MAAM;;;;WACN,MAAM;YACN,OAAO,yBAAyB,EAAE,MAAM;;yBAjBzB,mBAAmB"}
+{"version":3,"file":"dataToVertices.d.ts","sourceRoot":"","sources":["../../../src/gl/dataToVertices.js"],"names":[],"mappings":"AAgBA;;;;;GAKG;AACH;IACI;;;OAGG;IAEH;;;;;;OAMG;IACH;;qBAJW,MAAM,EAAE;sBACR,MAAM;OAyFhB;IArFG,8FAAwB;IAIxB,sGAQK;IAQL,0BAAoC;IAEpC,8BAAoD;IA2DpD,mBAAmB;IAEnB,yFAAyF;IACzF,UADW,IAAI,GAAG,EAAE,UAAU,CAAC,CACkB;IAGrD;;;;OAIG;IACH,mBAFW,GAAG,QAcb;IAED;;OAEG;IACH,oBAFW,IAAI,GAAG,EAAE,MAAM,EAAE,CAAC,QAM5B;IAED;;;OAGG;IACH,cAHW,GAAG,QACH,MAAM,EAAE,kCAYlB;IAED;;;;OAIG;IACH,sBAJW,OAAO,qBAAqB,EAAE,IAAI,OAClC,MAAM,OACN,MAAM,QAgEhB;IAED;;;;;OAKG;IACH,mBAFW,OAAO,qBAAqB,EAAE,KAAK,QAI7C;IAhEO;;;MAAyB;IAkEjC;QAEQ,kJAAkJ;gBAAvI,OAAO,MAAM,EAAE;YAAC,IAAI,EAAE,WAAW,GAAG,UAAU,GAAG,WAAW,GAAG,UAAU,GAAG,YAAY,CAAC;YAAC,aAAa,EAAE,MAAM,CAAC;YAAC,OAAO,CAAC,EAAE,MAAM,CAAA;SAAC,CAAC;QAE9I,8BAA8B;;QAE9B,8CAA8C;;;MAIrD;CACJ;AAED;IACI;;;;;;OAMG;IACH;;oBAHW,MAAM,EAAE;mBACR,MAAM;OA+BhB;IAnBG,qBAkBW;CA8BlB;AAED;IACI;;;;;;;;;OASG;IACH;;oBANW,MAAM,EAAE;gCACR,MAAM;uBAEN,MAAM,EAAE;mBACR,MAAM;OAwBhB;IARG,uBAAgC;IAEhC,8BAA8D;IAE9D,6CAA+D;IAC/D,4CAA6D;CA6CpE;AAED;IACI;;;;;;OAMG;IACH;;oBAHW,MAAM,EAAE;mBACR,MAAM;OAShB;CACJ;AAED;IACI;;;;;OAKG;IACH;;oBAHW,MAAM,EAAE;mBACR,MAAM;OAShB;CAYJ;AAED;IACI;;;;;;;;;OASG;IACH;;oBANW,MAAM,EAAE;qBACR,OAAO,2BAA2B,EAAE,aAAa;oBACjD,OAAO,MAAM,EAAE,GAAG,CAAC;wBACnB,MAAM;sBACN,OAAO;OA6CjB;IA9BG,4DAA2B;IAC3B,2DAA0B;IAE1B,gCAA4B;IAO5B,qCAAqC;IACrC,cADW,CAAC,KAAK,EAAE,GAAG,KAAK,MAAM,CAMf;IAElB,oDAGC;IACD,qDAGC;IAED,8CAAiE;CAgJxE;;;;;;;;YAnnBS,MAAM;;;;WACN,MAAM;YACN,OAAO,yBAAyB,EAAE,MAAM;;yBAjBzB,mBAAmB"}

package/dist/src/gl/glslScaleGenerator.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"glslScaleGenerator.d.ts","sourceRoot":"","sources":["../../../src/gl/glslScaleGenerator.js"],"names":[],"mappings":";AAqDA;;;;;GAKG;AACH,kDAJW,OAAO,mBACP,MAAM,GACJ,MAAM,CAIlB;AAED;;;;;;;;;;GAUG;AAEH;;;;;;;GAOG;AACH,mDALW,OAAO,mBACP,MAAM,SACN,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,GAAG,OAAO,GAClC,aAAa,CA4CzB;AAED;;;;;;;GAOG;AACH,4DAJW,OAAO,mBACP,MAAM,GACJ,aAAa,CAkCzB;AAED;;;;;;GAMG;AACH,0CANW,OAAO,SACP,GAAG,mBACH,MAAM,+BACN,OAAO,EAAE,GACP,aAAa,CA+BzB;AACD;;;;;GAKG;AACH,qDALW,OAAO,SACP,GAAG,mBACH,MAAM,GACJ,aAAa,CAyBzB;AAED;;;;;GAKG;AAEH,2CALW,OAAO,SACP,GAAG,cACH,OAAO,oBAAoB,EAAE,UAAU;;;;;;EAwQjD;AAED;;;;GAIG;AACH,wDAHW,OAAO,aACP,OAAO,qBAAqB,EAAE,QAAQ,EAAE,UAuClD;AAmED;;GAEG;AACH,qDAFW,OAAO,6BAQjB;AA+CD;;;;GAIG;AACH,iDAHW,OAAO,qBAAqB,EAAE,SAAS,WACvC,OAAO,oBAAoB,EAAE,OAAO;mBAQjB,MAAM;sBAAoB,sBAAsB,GAAG,sBAAsB,GAAG,uBAAuB;;;;;;EAkBhI;AAED;;;;GAIG;AACH,2CAFW,MAAM,WAIhB;AAED;;;;GAIG;AACH,sCAFW,MAAM,EAAE,WAIlB;AAMD;;;GAGG;AACH,sCAHW,MAAM,QACN,MAAM,EAAE,YAYlB;AAED;;;GAGG;AACH,2CAHW,MAAM,QACN,MAAM,EAAE,YAUlB;AAYD;;GAEG;AACH,qDAFW,MAAM,EAAE,YAIlB;AAED;;GAEG;AAEH;;;;;GAKG;AACH,+CAFW,QAAQ,OAAO,OAAO,oBAAoB,EAAE,OAAO,EAAE,OAAO,qBAAqB,EAAE,OAAO,CAAC,CAAC,+DA4BtG;AAED;;GAEG;AACH,2CAFW,OAAO,oBAAoB,EAAE,OAAO,GAAG,OAAO,oBAAoB,EAAE,OAAO,EAAE,UAIvF;AAwBD;;;;GAIG;AACH,uCAJW,MAAM,EAAE,cACR,MAAM,EAAE,GACN,MAAM,CAgClB;AAr1BD,uCAAwC;AACxC,uCAAwC;AACxC,oCAAqC;AACrC,mDAAoD;AACpD,6CAA8C;AAC9C,kDAAmD;AACnD,oDAAqD;AACrD,qCAAsC;AAmyB/B,uCAJI,GAAG,WACH,OAAO,GACL,MAAM,EAAE,CAQF;sBAnyBN,OAAO,oBAAoB,EAAE,OAAO;;aA+BvC,OAAO;kBACP,MAAM;0BACN,MAAM;oBACN,MAAM;oBACN,MAAM;kBACN,MAAM;kBACN,MAAM;mBACF,GAAG,KAAK,GAAG;;;;;8BA6fZ,MAAM,GAAG;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,aAAa,EAAE,MAAM,CAAA;CAAE;;;;uBAgMhD,CAAC,MAAM,EAAE,OAAO,CAAC;0BApvBJ,WAAW"}
+{"version":3,"file":"glslScaleGenerator.d.ts","sourceRoot":"","sources":["../../../src/gl/glslScaleGenerator.js"],"names":[],"mappings":";AAqDA;;;;;GAKG;AACH,kDAJW,OAAO,mBACP,MAAM,GACJ,MAAM,CAIlB;AAED;;;;;;;;;;GAUG;AAEH;;;;;;;GAOG;AACH,mDALW,OAAO,mBACP,MAAM,SACN,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,GAAG,OAAO,GAClC,aAAa,CA4CzB;AAED;;;;;;;GAOG;AACH,4DAJW,OAAO,mBACP,MAAM,GACJ,aAAa,CAkCzB;AAED;;;;;;GAMG;AACH,0CANW,OAAO,SACP,GAAG,mBACH,MAAM,+BACN,OAAO,EAAE,GACP,aAAa,CA+BzB;AACD;;;;;GAKG;AACH,qDALW,OAAO,SACP,GAAG,mBACH,MAAM,GACJ,aAAa,CAyBzB;AAED;;;;;GAKG;AAEH,2CALW,OAAO,SACP,GAAG,cACH,OAAO,oBAAoB,EAAE,UAAU;;;;;;EAwQjD;AAED;;;;GAIG;AACH,wDAHW,OAAO,aACP,OAAO,qBAAqB,EAAE,QAAQ,EAAE,UAuClD;AAmED;;GAEG;AACH,qDAFW,OAAO,6BAQjB;AA+CD;;;;GAIG;AACH,iDAHW,OAAO,qBAAqB,EAAE,SAAS,WACvC,OAAO,oBAAoB,EAAE,OAAO;mBAQjB,MAAM;sBAAoB,sBAAsB,GAAG,sBAAsB,GAAG,uBAAuB;;;;;;EAkBhI;AAED;;;;GAIG;AACH,2CAFW,MAAM,WAIhB;AAED;;;;GAIG;AACH,sCAFW,MAAM,EAAE,WAIlB;AAMD;;;GAGG;AACH,sCAHW,MAAM,QACN,MAAM,EAAE,YAYlB;AAED;;;GAGG;AACH,2CAHW,MAAM,QACN,MAAM,EAAE,YAUlB;AAYD;;GAEG;AACH,qDAFW,MAAM,EAAE,YAIlB;AAED;;GAEG;AAEH;;;;;GAKG;AACH,+CAFW,QAAQ,OAAO,OAAO,oBAAoB,EAAE,OAAO,EAAE,OAAO,qBAAqB,EAAE,OAAO,CAAC,CAAC,+DA4BtG;AAED;;GAEG;AACH,2CAFW,OAAO,oBAAoB,EAAE,OAAO,GAAG,OAAO,oBAAoB,EAAE,OAAO,EAAE,UAIvF;AAwBD;;;;GAIG;AACH,uCAJW,MAAM,EAAE,cACR,MAAM,EAAE,GACN,MAAM,CAgClB;AAr1BD,uCAAwC;AACxC,uCAAwC;AACxC,oCAAqC;AACrC,mDAAoD;AACpD,6CAA8C;AAC9C,kDAAmD;AACnD,oDAAqD;AACrD,qCAAsC;AAmyB/B,uCAJI,GAAG,WACH,OAAO,GACL,MAAM,EAAE,CAQF;sBAnyBN,OAAO,oBAAoB,EAAE,OAAO;;aA+BvC,OAAO;kBACP,MAAM;0BACN,MAAM;oBACN,MAAM;oBACN,MAAM;kBACN,MAAM;kBACN,MAAM;eACN,CAAC,CAAC,EAAE,GAAG,KAAK,GAAG;;;;;8BA6fZ,MAAM,GAAG;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,aAAa,EAAE,MAAM,CAAA;CAAE;;;;uBAgMhD,CAAC,MAAM,EAAE,OAAO,CAAC;0BApvBJ,WAAW"}

package/dist/src/spec/axis.d.ts

@@ -135,9 +135,7 @@ export interface Axis extends BaseAxis {
 
 export interface BaseAxis<
     N = number,
-    NS = number,
     B = boolean,
-    BNS = number | boolean,
     S = string,
     C = string,
     FW = string,

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

@@ -3,25 +3,38 @@ export interface Contig {
     size: number;
 }
 
-export interface GenomeConfig {
+export interface GenomeConfigBase {
     /**
      * Name of the genome assembly, e.g., `hg19` or `hg38`.
      */
     name: string;
+}
 
+export interface UrlGenomeConfig extends GenomeConfigBase {
     /**
-     * Base url of data files: chromsizes, cytobands, and gene annotations.
+     * A URL to a `chrom.sizes` file, which is a tab-separated file with two
+     * columns: the sequence name and its size.
+     *
+     * You may want to strip alternative loci, haplotypes, and other
+     * non-canonical contigs from the file.
      *
-     * **Default:** `"https://genomespy.app/data/genomes/"`
+     * Example: `"https://genomespy.app/data/genomes/hg19/chrom.sizes"`
      */
-    baseUrl?: string;
+    url: string;
+}
 
+export interface InlineGenomeConfig extends GenomeConfigBase {
     /**
-     * As an alternative for chromSizes, the contigs can be provided inline.
+     * An array of contigs/sequences in the genome assembly.
      */
-    contigs?: Contig[];
+    contigs: Contig[];
 }
 
+export type GenomeConfig =
+    | UrlGenomeConfig
+    | InlineGenomeConfig
+    | GenomeConfigBase;
+
 export interface ChromosomalLocus {
     /**
      * The name of the chromosome. For example: `"chr1"`, `"CHR1"`, or `"1"`.

package/dist/src/spec/scale.d.ts

@@ -130,7 +130,7 @@ export interface Scale {
     round?: boolean;
 
     /**
-     * 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.
+     * 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.
      *
      * For _[band](https://vega.github.io/vega-lite/docs/scale.html#band)_ scales, shortcut for setting `paddingInner` and `paddingOuter` to the same value.
      *

package/dist/src/utils/addBaseUrl.d.ts

@@ -3,4 +3,10 @@
  * @param {string} baseUrl
  */
 export default function addBaseUrl(url: string, baseUrl: string): string;
+/**
+ *
+ * @param {string} url
+ * @returns {string}
+ */
+export function endWithSlash(url: string): string;
 //# sourceMappingURL=addBaseUrl.d.ts.map

package/dist/src/utils/addBaseUrl.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"addBaseUrl.d.ts","sourceRoot":"","sources":["../../../src/utils/addBaseUrl.js"],"names":[],"mappings":"AAAA;;;GAGG;AACH,wCAHW,MAAM,WACN,MAAM,UAgBhB"}
+{"version":3,"file":"addBaseUrl.d.ts","sourceRoot":"","sources":["../../../src/utils/addBaseUrl.js"],"names":[],"mappings":"AAAA;;;GAGG;AACH,wCAHW,MAAM,WACN,MAAM,UAgBhB;AAED;;;;GAIG;AACH,kCAHW,MAAM,GACJ,MAAM,CAalB"}

package/dist/src/utils/addBaseUrl.js

@@ -17,3 +17,21 @@ export default function addBaseUrl(url, baseUrl) {
 
     return url;
 }
+
+/**
+ *
+ * @param {string} url
+ * @returns {string}
+ */
+export function endWithSlash(url) {
+    if (!url) {
+        return url;
+    }
+
+    if (/[?#]/.test(url)) {
+        throw new Error(
+            `Invalid base URL: ${url} - cannot contain query or hash.`
+        );
+    }
+    return url.endsWith("/") ? url : url + "/";
+}

package/dist/src/utils/addBaseUrl.test.js

@@ -1,5 +1,5 @@
 import { expect, test } from "vitest";
-import addBaseUrl from "./addBaseUrl.js";
+import addBaseUrl, { endWithSlash } from "./addBaseUrl.js";
 
 test("addBaseUrl adds baseUrl when needed", () => {
     expect(addBaseUrl("foo.html", "https://site.com/")).toEqual(
@@ -20,3 +20,11 @@ test("addBaseUrl doesn't add baseUrl when not needed", () => {
     expect(addBaseUrl("/foo.html", "https://site.com/")).toEqual("/foo.html");
     expect(addBaseUrl("foo.html", undefined)).toEqual("foo.html");
 });
+
+test("endWithSlash adds slash when needed", () => {
+    expect(endWithSlash(null)).toBeNull();
+    expect(endWithSlash("https://site.com")).toEqual("https://site.com/");
+    expect(endWithSlash("https://site.com/")).toEqual("https://site.com/");
+    expect(() => endWithSlash("https://site.com/foo?bar")).toThrow();
+    expect(() => endWithSlash("https://site.com/foo#bar")).toThrow();
+});

package/dist/src/utils/cloner.d.ts

@@ -8,9 +8,15 @@
  *
  * @param {T} template The template object that
  * @returns {(function(T):T) & { properties: string[] }}
- * @template T
+ * @template {object} [T=object]
  */
-export default function createCloner<T>(template: T): ((arg0: T) => T) & {
+export default function createCloner<T extends object = object>(template: T): ((arg0: T) => T) & {
     properties: string[];
 };
+/**
+ * Needed for proxied Apache Arrow tables.
+ *
+ * @param {object} obj
+ */
+export function getAllProperties(obj: object): string[];
 //# sourceMappingURL=cloner.d.ts.map

package/dist/src/utils/cloner.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"cloner.d.ts","sourceRoot":"","sources":["../../../src/utils/cloner.js"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AACH;gBAH6C,MAAM,EAAE;EAwBpD"}
+{"version":3,"file":"cloner.d.ts","sourceRoot":"","sources":["../../../src/utils/cloner.js"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AACH;gBAH6C,MAAM,EAAE;EAwBpD;AAED;;;;GAIG;AACH,sCAFW,MAAM,YAYhB"}

package/dist/src/utils/cloner.js

@@ -8,12 +8,12 @@
  *
  * @param {T} template The template object that
  * @returns {(function(T):T) & { properties: string[] }}
- * @template T
+ * @template {object} [T=object]
  */
 export default function createCloner(template) {
     // TODO: Check that only properties, not methods get cloned
     const properties = /** @type {string[]} */ (
-        Object.keys(template).filter((k) => typeof k == "string")
+        getAllProperties(template).filter((k) => typeof k == "string")
     );
 
     const cloner = /** @type {(function(T):T) & { properties: string[] }} */ (
@@ -32,3 +32,20 @@ export default function createCloner(template) {
 
     return cloner;
 }
+
+/**
+ * Needed for proxied Apache Arrow tables.
+ *
+ * @param {object} obj
+ */
+export function getAllProperties(obj) {
+    /** @type {string[]} */
+    let props = [];
+    do {
+        props = props.concat(Object.keys(obj));
+        obj = Object.getPrototypeOf(obj);
+    } while (obj && obj !== Object.prototype); // Traverse until the end of the prototype chain
+
+    const uniqueProps = Array.from(new Set(props));
+    return uniqueProps;
+}

package/dist/src/utils/cloner.test.js

@@ -1,10 +1,11 @@
 import { expect, test } from "vitest";
-import createCloner from "./cloner.js";
+import createCloner, { getAllProperties } from "./cloner.js";
 
 const template = {
+    1: "iddqd",
     a: 1,
-    b: "xyzzy",
-    3: "iddqd",
+    c: "xyzzy",
+    b: "idclip",
 };
 
 test("Cloner clones object properly", () => {
@@ -14,11 +15,21 @@ test("Cloner clones object properly", () => {
     expect(makeClone(template)).not.toBe(template);
 
     const another = {
+        1: "hello",
         a: 2,
-        b: "idkfa",
-        3: "hello",
+        c: "idkfa",
+        b: "idclip",
     };
 
     expect(makeClone(another)).toEqual(another);
     expect(makeClone(another)).not.toBe(another);
 });
+
+test("getAllProperties", () => {
+    expect(getAllProperties(template)).toEqual(["1", "a", "c", "b"]);
+
+    const obj = Object.create(template);
+    obj.d = 42;
+
+    expect(getAllProperties(obj)).toEqual(["d", "1", "a", "c", "b"]);
+});

package/dist/src/utils/expression.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"expression.d.ts","sourceRoot":"","sources":["../../../src/utils/expression.js"],"names":[],"mappings":"AA2DA;;;;;;;;;;GAUG;AACH,6CAHW,MAAM,sBACJ,kBAAkB,CAgC9B;;YAvCU,MAAM,EAAE;aACR,MAAM,EAAE;UACR,MAAM;;2CAEO,OAAO,qBAAqB,EAAE,KAAK,KAAK,GAAG"}
+{"version":3,"file":"expression.d.ts","sourceRoot":"","sources":["../../../src/utils/expression.js"],"names":[],"mappings":"AA2DA;;;;;;;;;;GAUG;AACH,6CAHW,MAAM,sBACJ,kBAAkB,CAgC9B;;YAvCU,MAAM,EAAE;aACR,MAAM,EAAE;UACR,MAAM;;iCAEH,CAAC,CAAC,KAAK,CAAC,EAAE,OAAO,qBAAqB,EAAE,KAAK,KAAK,GAAG,CAAC,GAAG,eAAe"}

package/dist/src/utils/ui/tooltip.d.ts

@@ -17,7 +17,7 @@ export default class Tooltip {
     /**
      * @param {boolean} visible
      */
-    set visible(arg: boolean);
+    set visible(visible: boolean);
     get visible(): boolean;
     get enabled(): boolean;
     /**