gosling.js 0.13.1 → 0.13.2

package/dist/src/exported-utils.d.ts

@@ -1,3 +1,5 @@
 export { getRelativeGenomicPosition, computeChromSizes, getChromInterval, getChromTotalSize, parseGenomicPosition } from './core/utils/assembly';
 export { sanitizeChrName } from './data-fetchers/utils';
+export { convertToFlatTracks as _convertToFlatTracks } from './compiler/spec-preprocess';
+export { spreadTracksByData as _spreadTracksByData } from './core/utils/overlay';
 //# sourceMappingURL=exported-utils.d.ts.map

package/dist/src/exported-utils.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"exported-utils.d.ts","sourceRoot":"","sources":["../../src/exported-utils.ts"],"names":[],"mappings":"AAAA,OAAO,EACH,0BAA0B,EAC1B,iBAAiB,EACjB,gBAAgB,EAChB,iBAAiB,EACjB,oBAAoB,EACvB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAC;AAGxD,OAAO,EAAE,mBAAmB,IAAI,oBAAoB,EAAE,MAAM,4BAA4B,CAAC;AACzF,OAAO,EAAE,kBAAkB,IAAI,mBAAmB,EAAE,MAAM,sBAAsB,CAAC"}

package/dist/utils.js

@@ -1,12 +1,20 @@
-import { c, b, d, a, p, s } from "./exported-utils-068d7b17.js";
+import { ae, af, c, ab, ac, N, ad, s } from "./exported-utils-d4f1abea.js";
 import "d3-array";
 import "generic-filehandle";
+import "pixi.js";
+import "d3-color";
+import "bezier-js";
+import "d3-scale";
+import "lodash-es";
+import "d3-scale-chromatic";
 export {
+  ae as _convertToFlatTracks,
+  af as _spreadTracksByData,
   c as computeChromSizes,
-  b as getChromInterval,
-  d as getChromTotalSize,
-  a as getRelativeGenomicPosition,
-  p as parseGenomicPosition,
+  ab as getChromInterval,
+  ac as getChromTotalSize,
+  N as getRelativeGenomicPosition,
+  ad as parseGenomicPosition,
   s as sanitizeChrName
 };
 //# sourceMappingURL=utils.js.map

package/dist/utils.js.map

@@ -1 +1 @@
-{"version":3,"file":"utils.js","sources":[],"sourcesContent":[],"names":[],"mappings":";;;"}
+{"version":3,"file":"utils.js","sources":[],"sourcesContent":[],"names":[],"mappings":";;;;;;;;;"}

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "gosling.js",
   "author": "Sehi L'Yi",
-  "version": "0.13.1",
+  "version": "0.13.2",
   "license": "MIT",
   "repository": {
     "type": "git",
@@ -105,7 +105,6 @@
     "eslint-plugin-prettier": "^4.2.1",
     "eslint-plugin-react": "^7.30.1",
     "fetch-jsonp": "^1.1.3",
-    "gh-pages": "^3.1.0",
     "jsdom": "^19.0.0",
     "jsoncrush": "^1.1.6",
     "knip": "^2.30.0",
@@ -158,8 +157,6 @@
     "coverage": "vitest run --coverage",
     "format": "eslint src/ editor/ --fix && prettier 'editor/**/*.css' --write",
     "schema": "node scripts/generate-schemas.mjs",
-    "predeploy": "pnpm build-editor; echo \"gosling.js.org\" >> build/CNAME",
-    "deploy": "gh-pages -d build",
     "version": "conventional-changelog -p angular -i CHANGELOG.md -s && git add CHANGELOG.md",
     "knip": "knip --config knip.config.json",
     "e2e": "playwright test",

package/dist/exported-utils-068d7b17.js

@@ -1,438 +0,0 @@
-var __defProp = Object.defineProperty;
-var __defNormalProp = (obj, key, value) => key in obj ? __defProp(obj, key, { enumerable: true, configurable: true, writable: true, value }) : obj[key] = value;
-var __publicField = (obj, key, value) => {
-  __defNormalProp(obj, typeof key !== "symbol" ? key + "" : key, value);
-  return value;
-};
-import { bisector } from "d3-array";
-import { RemoteFile as RemoteFile$1 } from "generic-filehandle";
-const CHROM_SIZE_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
-};
-const CHROM_SIZE_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 CHROM_SIZE_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 CHROM_SIZE_HG17 = {
-  chr1: 245522847,
-  chr2: 243018229,
-  chr3: 199505740,
-  chr4: 191411218,
-  chr5: 180857866,
-  chr6: 170975699,
-  chr7: 158628139,
-  chr8: 146274826,
-  chr9: 138429268,
-  chr10: 135413628,
-  chr11: 134452384,
-  chr12: 132449811,
-  chr13: 114142980,
-  chr14: 106368585,
-  chr15: 100338915,
-  chr16: 88827254,
-  chr17: 78774742,
-  chr18: 76117153,
-  chr19: 63811651,
-  chr20: 62435964,
-  chr21: 46944323,
-  chr22: 49554710,
-  chrX: 154824264,
-  chrY: 57701691,
-  chrM: 16571
-};
-const CHROM_SIZE_HG16 = {
-  chr1: 246127941,
-  chr2: 243615958,
-  chr3: 199344050,
-  chr4: 191731959,
-  chr5: 181034922,
-  chr6: 170914576,
-  chr7: 158545518,
-  chr8: 146308819,
-  chr9: 136372045,
-  chr10: 135037215,
-  chr11: 134482954,
-  chr12: 132078379,
-  chr13: 113042980,
-  chr14: 105311216,
-  chr15: 100256656,
-  chr16: 90041932,
-  chr17: 81860266,
-  chr18: 76115139,
-  chr19: 63811651,
-  chr20: 63741868,
-  chr21: 46976097,
-  chr22: 49396972,
-  chrX: 153692391,
-  chrY: 50286555,
-  chrM: 16571
-};
-const CHROM_SIZE_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
-};
-const CHROM_SIZE_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
-};
-function getRelativeGenomicPosition(absPos, assembly, returnWithinAssembly = false) {
-  const chrSizes = Object.entries(computeChromSizes(assembly).interval);
-  const minPosChr = { chromosome: "unknown", position: Infinity };
-  const maxPosChr = { chromosome: "unknown", position: 0 };
-  for (const chrSize of chrSizes) {
-    const [chromosome, absInterval] = chrSize;
-    const [start, end] = absInterval;
-    if (start <= absPos && absPos < end) {
-      return { chromosome, position: absPos - start };
-    }
-    if (start < minPosChr.position) {
-      minPosChr.chromosome = chromosome;
-      minPosChr.position = start;
-    }
-    if (end > maxPosChr.position) {
-      maxPosChr.chromosome = chromosome;
-      maxPosChr.position = end;
-    }
-  }
-  if (returnWithinAssembly) {
-    if (absPos < minPosChr.position) {
-      return minPosChr;
-    } else {
-      return maxPosChr;
-    }
-  } else {
-    return { chromosome: "unknown", position: absPos };
-  }
-}
-function createChromSizesUrl(chromSizes) {
-  const text = chromSizes.map((d) => d.join("	")).join("\n");
-  const tsv = new Blob([text], { type: "text/tsv" });
-  return URL.createObjectURL(tsv);
-}
-function computeChromSizes(assembly) {
-  if (assembly && typeof assembly === "string" && assembly in CRHOM_SIZES) {
-    return CRHOM_SIZES[assembly];
-  } else if (Array.isArray(assembly) && assembly.length !== 0) {
-    const size = Object.fromEntries(assembly);
-    return {
-      size,
-      interval: getChromInterval(size),
-      total: getChromTotalSize(size),
-      path: createChromSizesUrl(assembly)
-    };
-  } else {
-    return CRHOM_SIZES.hg38;
-  }
-}
-const basePath = (assembly) => `https://s3.amazonaws.com/gosling-lang.org/data/${assembly}.chrom.sizes`;
-const CRHOM_SIZES = Object.freeze({
-  hg38: {
-    size: CHROM_SIZE_HG38,
-    interval: getChromInterval(CHROM_SIZE_HG38),
-    total: getChromTotalSize(CHROM_SIZE_HG38),
-    path: basePath("hg38")
-  },
-  hg19: {
-    size: CHROM_SIZE_HG19,
-    interval: getChromInterval(CHROM_SIZE_HG19),
-    total: getChromTotalSize(CHROM_SIZE_HG19),
-    path: basePath("hg19")
-  },
-  hg18: {
-    size: CHROM_SIZE_HG18,
-    interval: getChromInterval(CHROM_SIZE_HG18),
-    total: getChromTotalSize(CHROM_SIZE_HG18),
-    path: basePath("hg18")
-  },
-  hg17: {
-    size: CHROM_SIZE_HG17,
-    interval: getChromInterval(CHROM_SIZE_HG17),
-    total: getChromTotalSize(CHROM_SIZE_HG17),
-    path: basePath("hg17")
-  },
-  hg16: {
-    size: CHROM_SIZE_HG16,
-    interval: getChromInterval(CHROM_SIZE_HG16),
-    total: getChromTotalSize(CHROM_SIZE_HG16),
-    path: basePath("hg16")
-  },
-  mm10: {
-    size: CHROM_SIZE_MM10,
-    interval: getChromInterval(CHROM_SIZE_MM10),
-    total: getChromTotalSize(CHROM_SIZE_MM10),
-    path: basePath("mm10")
-  },
-  mm9: {
-    size: CHROM_SIZE_MM9,
-    interval: getChromInterval(CHROM_SIZE_MM9),
-    total: getChromTotalSize(CHROM_SIZE_MM9),
-    path: basePath("mm9")
-  },
-  // `unknown` assembly contains only one chromosome with max length
-  unknown: {
-    size: { chr: Number.MAX_VALUE },
-    interval: { chr: [0, Number.MAX_VALUE] },
-    total: Number.MAX_VALUE,
-    path: basePath("hg38")
-    // just to ensure this does not make crash
-  }
-});
-function getAutoCompleteId(assembly) {
-  switch (assembly) {
-    case "hg19":
-      return "OHJakQICQD6gTD7skx4EWA";
-    case "mm10":
-      return "QDutvmyiSrec5nX4pA5WGQ";
-    case "mm9":
-      return "GUm5aBiLRCyz2PsBea7Yzg";
-    case "hg38":
-    default:
-      return "P0PLbQMwTYGy-5uPIQid7A";
-  }
-}
-function getChromInterval(chromSize) {
-  const interval = {};
-  Object.keys(chromSize).reduce((sum, k) => {
-    interval[k] = [sum, sum + chromSize[k]];
-    return sum + chromSize[k];
-  }, 0);
-  return interval;
-}
-function getChromTotalSize(chromSize) {
-  return Object.values(chromSize).reduce((sum, current) => sum + current, 0);
-}
-function parseGenomicPosition(position) {
-  const [chromosome, intervalString] = position.split(":");
-  if (intervalString) {
-    const [start, end] = intervalString.split("-").map((s) => +s.replace(/,/g, ""));
-    if (!Number.isNaN(start) && !Number.isNaN(end)) {
-      return { chromosome, start, end };
-    }
-  }
-  return { chromosome };
-}
-class GenomicPositionHelper {
-  constructor(chromosome, start, end) {
-    this.chromosome = chromosome;
-    this.start = start;
-    this.end = end;
-  }
-  static fromString(str) {
-    const result = parseGenomicPosition(str);
-    return new GenomicPositionHelper(result.chromosome, result.start, result.end);
-  }
-  toAbsoluteCoordinates(assembly, padding = 0) {
-    const info = computeChromSizes(assembly);
-    const size = info.size[this.chromosome];
-    const interval = info.interval[this.chromosome];
-    if (size === void 0 || interval === void 0) {
-      throw new Error(`Chromosome name ${this.chromosome} is not valid`);
-    }
-    let { start, end } = this;
-    if (start === void 0 || end === void 0) {
-      [start, end] = [1, size];
-    }
-    const offset = interval[0];
-    return [start + offset - padding, end + offset + padding];
-  }
-}
-function filterUsingGenoPos(data, [minX, maxX], config) {
-  const { x, xe, x1, x1e } = config;
-  const definedXFields = [x, xe, x1, x1e].filter((f) => f);
-  return data.filter((d) => {
-    if (definedXFields.length === 0) {
-      return true;
-    } else if (definedXFields.length === 1) {
-      const value = +d[definedXFields[0]];
-      return typeof value === "number" && minX < value && value <= maxX;
-    } else {
-      const values = definedXFields.map((f) => +d[f]).filter((v) => !isNaN(v));
-      const minValue = Math.min(...values);
-      const maxValue = Math.max(...values);
-      return minX <= maxValue && minValue <= maxX;
-    }
-  });
-}
-bisector((d) => d.pos).left;
-function sanitizeChrName(chrName, assembly, chromosomePrefix) {
-  if (Array.isArray(assembly)) {
-    return chrName;
-  }
-  if (chromosomePrefix) {
-    chrName = chrName.replace(chromosomePrefix, "chr");
-  } else if (!chrName.includes("chr")) {
-    chrName = `chr${chrName}`;
-  }
-  return chrName;
-}
-class RemoteFile extends RemoteFile$1 {
-  constructor() {
-    super(...arguments);
-    // Overrides `read` to eagerly read 200 or 206 response
-    // from https://github.com/GMOD/generic-filehandle/blob/0e8209be25e3097307bd15e964edd8c017e808d7/src/remoteFile.ts#L100-L162
-    __publicField(this, "read", async (buffer, offset = 0, length, position = 0, opts = {}) => {
-      const { headers = {}, signal, overrides = {} } = opts;
-      if (length < Infinity) {
-        headers.range = `bytes=${position}-${position + length}`;
-      } else if (length === Infinity && position !== 0) {
-        headers.range = `bytes=${position}-`;
-      }
-      const args = {
-        // @ts-expect-error private property
-        ...this.baseOverrides,
-        ...overrides,
-        headers: {
-          ...headers,
-          ...overrides.headers,
-          // @ts-expect-error private property
-          ...this.baseOverrides.headers
-        },
-        method: "GET",
-        redirect: "follow",
-        mode: "cors",
-        signal
-      };
-      const response = await this.fetch(this.url, args);
-      if (!response.ok) {
-        throw new Error(`HTTP ${response.status} ${response.statusText} ${this.url}`);
-      }
-      if (response.status === 200 || response.status === 206) {
-        const responseData = await this.getBufferFromResponse(response);
-        const bytesCopied = responseData.copy(buffer, offset, 0, Math.min(length, responseData.length));
-        const res = response.headers.get("content-range");
-        const sizeMatch = /\/(\d+)$/.exec(res || "");
-        if (sizeMatch && sizeMatch[1]) {
-          this._stat = { size: parseInt(sizeMatch[1], 10) };
-        }
-        return { bytesRead: bytesCopied, buffer };
-      }
-      throw new Error(`HTTP ${response.status} fetching ${this.url}`);
-    });
-  }
-}
-export {
-  GenomicPositionHelper as G,
-  RemoteFile as R,
-  getRelativeGenomicPosition as a,
-  getChromInterval as b,
-  computeChromSizes as c,
-  getChromTotalSize as d,
-  filterUsingGenoPos as f,
-  getAutoCompleteId as g,
-  parseGenomicPosition as p,
-  sanitizeChrName as s
-};
-//# sourceMappingURL=exported-utils-068d7b17.js.map

package/dist/exported-utils-068d7b17.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"exported-utils-068d7b17.js","sources":["../src/core/utils/chrom-size.ts","../src/core/utils/assembly.ts","../src/data-fetchers/utils.ts"],"sourcesContent":["export const CHROM_SIZE_HG38 = {\n    chr1: 248956422,\n    chr2: 242193529,\n    chr3: 198295559,\n    chr4: 190214555,\n    chr5: 181538259,\n    chr6: 170805979,\n    chr7: 159345973,\n    chr8: 145138636,\n    chr9: 138394717,\n    chr10: 133797422,\n    chr11: 135086622,\n    chr12: 133275309,\n    chr13: 114364328,\n    chr14: 107043718,\n    chr15: 101991189,\n    chr16: 90338345,\n    chr17: 83257441,\n    chr18: 80373285,\n    chr19: 58617616,\n    chr20: 64444167,\n    chr21: 46709983,\n    chr22: 50818468,\n    chrX: 156040895,\n    chrY: 57227415\n};\n\nexport const CHROM_SIZE_HG19 = {\n    chr1: 249250621,\n    chr2: 243199373,\n    chr3: 198022430,\n    chr4: 191154276,\n    chr5: 180915260,\n    chr6: 171115067,\n    chr7: 159138663,\n    chr8: 146364022,\n    chr9: 141213431,\n    chr10: 135534747,\n    chr11: 135006516,\n    chr12: 133851895,\n    chr13: 115169878,\n    chr14: 107349540,\n    chr15: 102531392,\n    chr16: 90354753,\n    chr17: 81195210,\n    chr18: 78077248,\n    chr19: 59128983,\n    chr20: 63025520,\n    chr21: 48129895,\n    chr22: 51304566,\n    chrX: 155270560,\n    chrY: 59373566,\n    chrM: 16571\n};\n\nexport const CHROM_SIZE_HG18 = {\n    chr1: 247249719,\n    chr2: 242951149,\n    chr3: 199501827,\n    chr4: 191273063,\n    chr5: 180857866,\n    chr6: 170899992,\n    chr7: 158821424,\n    chr8: 146274826,\n    chr9: 140273252,\n    chr10: 135374737,\n    chr11: 134452384,\n    chr12: 132349534,\n    chr13: 114142980,\n    chr14: 106368585,\n    chr15: 100338915,\n    chr16: 88827254,\n    chr17: 78774742,\n    chr18: 76117153,\n    chr19: 63811651,\n    chr20: 62435964,\n    chr21: 46944323,\n    chr22: 49691432,\n    chrX: 154913754,\n    chrY: 57772954,\n    chrM: 16571\n};\n\nexport const CHROM_SIZE_HG17 = {\n    chr1: 245522847,\n    chr2: 243018229,\n    chr3: 199505740,\n    chr4: 191411218,\n    chr5: 180857866,\n    chr6: 170975699,\n    chr7: 158628139,\n    chr8: 146274826,\n    chr9: 138429268,\n    chr10: 135413628,\n    chr11: 134452384,\n    chr12: 132449811,\n    chr13: 114142980,\n    chr14: 106368585,\n    chr15: 100338915,\n    chr16: 88827254,\n    chr17: 78774742,\n    chr18: 76117153,\n    chr19: 63811651,\n    chr20: 62435964,\n    chr21: 46944323,\n    chr22: 49554710,\n    chrX: 154824264,\n    chrY: 57701691,\n    chrM: 16571\n};\n\nexport const CHROM_SIZE_HG16 = {\n    chr1: 246127941,\n    chr2: 243615958,\n    chr3: 199344050,\n    chr4: 191731959,\n    chr5: 181034922,\n    chr6: 170914576,\n    chr7: 158545518,\n    chr8: 146308819,\n    chr9: 136372045,\n    chr10: 135037215,\n    chr11: 134482954,\n    chr12: 132078379,\n    chr13: 113042980,\n    chr14: 105311216,\n    chr15: 100256656,\n    chr16: 90041932,\n    chr17: 81860266,\n    chr18: 76115139,\n    chr19: 63811651,\n    chr20: 63741868,\n    chr21: 46976097,\n    chr22: 49396972,\n    chrX: 153692391,\n    chrY: 50286555,\n    chrM: 16571\n};\n\nexport const CHROM_SIZE_MM10 = {\n    chr1: 195471971,\n    chr2: 182113224,\n    chr3: 160039680,\n    chr4: 156508116,\n    chr5: 151834684,\n    chr6: 149736546,\n    chr7: 145441459,\n    chr8: 129401213,\n    chr9: 124595110,\n    chr10: 130694993,\n    chr11: 122082543,\n    chr12: 120129022,\n    chr13: 120421639,\n    chr14: 124902244,\n    chr15: 104043685,\n    chr16: 98207768,\n    chr17: 94987271,\n    chr18: 90702639,\n    chr19: 61431566,\n    chrX: 171031299,\n    chrY: 91744698,\n    chrM: 16299\n};\n\nexport const CHROM_SIZE_MM9 = {\n    chr1: 197195432,\n    chr2: 181748087,\n    chr3: 159599783,\n    chr4: 155630120,\n    chr5: 152537259,\n    chr6: 149517037,\n    chr7: 152524553,\n    chr8: 131738871,\n    chr9: 124076172,\n    chr10: 129993255,\n    chr11: 121843856,\n    chr12: 121257530,\n    chr13: 120284312,\n    chr14: 125194864,\n    chr15: 103494974,\n    chr16: 98319150,\n    chr17: 95272651,\n    chr18: 90772031,\n    chr19: 61342430,\n    chrX: 166650296,\n    chrY: 15902555,\n    chrM: 16299\n};\n\nexport type Chromosome =\n    | '1'\n    | '2'\n    | '3'\n    | '4'\n    | '5'\n    | '6'\n    | '7'\n    | '8'\n    | '9'\n    | '10'\n    | '11'\n    | '12'\n    | '13'\n    | '14'\n    | '15'\n    | '16'\n    | '17'\n    | '18'\n    | '19'\n    | '20'\n    | '21'\n    | '22'\n    | 'X'\n    | 'Y'\n    | 'M'\n    | 'chr1'\n    | 'chr2'\n    | 'chr3'\n    | 'chr4'\n    | 'chr5'\n    | 'chr6'\n    | 'chr7'\n    | 'chr8'\n    | 'chr9'\n    | 'chr10'\n    | 'chr11'\n    | 'chr12'\n    | 'chr13'\n    | 'chr14'\n    | 'chr15'\n    | 'chr16'\n    | 'chr17'\n    | 'chr18'\n    | 'chr19'\n    | 'chr20'\n    | 'chr21'\n    | 'chr22'\n    | 'chrX'\n    | 'chrY'\n    | 'chrM';\n","import type { Assembly, ChromSizes, GenomicPosition } from '@gosling-lang/gosling-schema';\nimport {\n    CHROM_SIZE_HG16,\n    CHROM_SIZE_HG17,\n    CHROM_SIZE_HG18,\n    CHROM_SIZE_HG19,\n    CHROM_SIZE_HG38,\n    CHROM_SIZE_MM10,\n    CHROM_SIZE_MM9\n} from './chrom-size';\n\nexport interface ChromSize {\n    size: { [chr: string]: number };\n    interval: { [chr: string]: [number, number] };\n    total: number;\n    path: string;\n}\n\n/**\n * Get relative chromosome position (e.g., `100` => `{ chromosome: 'chr1', position: 100 }`)\n * @param absPos number which is the absolute chromosome position\n * @param assembly the assembly used to calculate which chromosome position\n * @param returnWithinAssembly If true, then if the absolute position is before the first chromosome, it returns the\n * first position of the first chromosome. If the absolute position is after the last chromosome, it returns the last\n * position of the last chromosome\n * @returns the genomic position of the absPos\n */\nexport function getRelativeGenomicPosition(\n    absPos: number,\n    assembly?: Assembly,\n    returnWithinAssembly = false\n): GenomicPosition {\n    const chrSizes = Object.entries(computeChromSizes(assembly).interval);\n    const minPosChr = { chromosome: 'unknown', position: Infinity } as GenomicPosition;\n    const maxPosChr = { chromosome: 'unknown', position: 0 } as GenomicPosition;\n    for (const chrSize of chrSizes) {\n        const [chromosome, absInterval] = chrSize;\n        const [start, end] = absInterval;\n        // absPos was found within this chromosome\n        if (start <= absPos && absPos < end) {\n            return { chromosome, position: absPos - start } as GenomicPosition;\n        }\n        // Update the min and max chromosomes found\n        if (start < minPosChr.position) {\n            minPosChr.chromosome = chromosome;\n            minPosChr.position = start;\n        }\n        if (end > maxPosChr.position) {\n            maxPosChr.chromosome = chromosome;\n            maxPosChr.position = end;\n        }\n    }\n    if (returnWithinAssembly) {\n        // Return either the min or max chromosome position\n        if (absPos < minPosChr.position) {\n            return minPosChr;\n        } else {\n            return maxPosChr;\n        }\n    } else {\n        return { chromosome: 'unknown', position: absPos };\n    }\n}\n\n/**\n * Generate a URL for custom chrom sizes\n * @param chromSizes A custom assembly that specifies chromosomes and their sizes\n */\nfunction createChromSizesUrl(chromSizes: ChromSizes): string {\n    const text = chromSizes.map(d => d.join('\\t')).join('\\n');\n    const tsv = new Blob([text], { type: 'text/tsv' });\n    return URL.createObjectURL(tsv);\n}\n\n/**\n * Get chromosome sizes.\n * @param assembly (default: 'hg38')\n */\nexport function computeChromSizes(assembly?: Assembly): ChromSize {\n    if (assembly && typeof assembly === 'string' && assembly in CRHOM_SIZES) {\n        return CRHOM_SIZES[assembly];\n    } else if (Array.isArray(assembly) && assembly.length !== 0) {\n        // custom assembly\n        const size = Object.fromEntries(assembly);\n        return {\n            size,\n            interval: getChromInterval(size),\n            total: getChromTotalSize(size),\n            path: createChromSizesUrl(assembly)\n        };\n    } else {\n        // We do not have that assembly prepared, so return a default one.\n        return CRHOM_SIZES.hg38;\n    }\n}\n\nconst basePath = (assembly: string) => `https://s3.amazonaws.com/gosling-lang.org/data/${assembly}.chrom.sizes`;\nconst CRHOM_SIZES: { [assembly: string]: ChromSize } = Object.freeze({\n    hg38: {\n        size: CHROM_SIZE_HG38,\n        interval: getChromInterval(CHROM_SIZE_HG38),\n        total: getChromTotalSize(CHROM_SIZE_HG38),\n        path: basePath('hg38')\n    },\n    hg19: {\n        size: CHROM_SIZE_HG19,\n        interval: getChromInterval(CHROM_SIZE_HG19),\n        total: getChromTotalSize(CHROM_SIZE_HG19),\n        path: basePath('hg19')\n    },\n    hg18: {\n        size: CHROM_SIZE_HG18,\n        interval: getChromInterval(CHROM_SIZE_HG18),\n        total: getChromTotalSize(CHROM_SIZE_HG18),\n        path: basePath('hg18')\n    },\n    hg17: {\n        size: CHROM_SIZE_HG17,\n        interval: getChromInterval(CHROM_SIZE_HG17),\n        total: getChromTotalSize(CHROM_SIZE_HG17),\n        path: basePath('hg17')\n    },\n    hg16: {\n        size: CHROM_SIZE_HG16,\n        interval: getChromInterval(CHROM_SIZE_HG16),\n        total: getChromTotalSize(CHROM_SIZE_HG16),\n        path: basePath('hg16')\n    },\n    mm10: {\n        size: CHROM_SIZE_MM10,\n        interval: getChromInterval(CHROM_SIZE_MM10),\n        total: getChromTotalSize(CHROM_SIZE_MM10),\n        path: basePath('mm10')\n    },\n    mm9: {\n        size: CHROM_SIZE_MM9,\n        interval: getChromInterval(CHROM_SIZE_MM9),\n        total: getChromTotalSize(CHROM_SIZE_MM9),\n        path: basePath('mm9')\n    },\n    // `unknown` assembly contains only one chromosome with max length\n    unknown: {\n        size: { chr: Number.MAX_VALUE },\n        interval: { chr: [0, Number.MAX_VALUE] },\n        total: Number.MAX_VALUE,\n        path: basePath('hg38') // just to ensure this does not make crash\n    }\n});\n\n/**\n * Some presets of auto-complete IDs (`autocompleteId`) to search for genes using the HiGlass server.\n */\nexport function getAutoCompleteId(assembly?: Assembly) {\n    switch (assembly) {\n        case 'hg19':\n            return 'OHJakQICQD6gTD7skx4EWA';\n        case 'mm10':\n            return 'QDutvmyiSrec5nX4pA5WGQ';\n        case 'mm9':\n            return 'GUm5aBiLRCyz2PsBea7Yzg';\n        case 'hg38':\n        default:\n            return 'P0PLbQMwTYGy-5uPIQid7A';\n    }\n}\n\n/**\n * Calculate cumulative interval of each chromosome.\n */\nexport function getChromInterval(chromSize: { [k: string]: number }) {\n    const interval: { [k: string]: [number, number] } = {};\n\n    Object.keys(chromSize).reduce((sum, k) => {\n        interval[k] = [sum, sum + chromSize[k]];\n        return sum + chromSize[k];\n    }, 0);\n\n    return interval;\n}\n\n/**\n * Calculate total size of entire chromosomes.\n */\nexport function getChromTotalSize(chromSize: { [k: string]: number }) {\n    return Object.values(chromSize).reduce((sum, current) => sum + current, 0);\n}\n\nexport function parseGenomicPosition(position: string): { chromosome: string; start?: number; end?: number } {\n    const [chromosome, intervalString] = position.split(':');\n    if (intervalString) {\n        const [start, end] = intervalString.split('-').map(s => +s.replace(/,/g, ''));\n        // only return if both are valid\n        if (!Number.isNaN(start) && !Number.isNaN(end)) {\n            return { chromosome, start, end };\n        }\n    }\n    return { chromosome };\n}\n\n/**\n * A class that consistently manage and convert genomics positions.\n */\nexport class GenomicPositionHelper {\n    constructor(public chromosome: string, public start?: number, public end?: number) {}\n    static fromString(str: string) {\n        const result = parseGenomicPosition(str);\n        return new GenomicPositionHelper(result.chromosome, result.start, result.end);\n    }\n    toAbsoluteCoordinates(assembly?: Assembly, padding = 0): [number, number] {\n        const info = computeChromSizes(assembly);\n        const size = info.size[this.chromosome];\n        const interval = info.interval[this.chromosome];\n        if (size === undefined || interval === undefined) {\n            throw new Error(`Chromosome name ${this.chromosome} is not valid`);\n        }\n        let { start, end } = this;\n        if (start === undefined || end === undefined) {\n            // if only a chromosome name is specified, set to the extent of the chromosome\n            [start, end] = [1, size];\n        }\n        const offset = interval[0];\n        return [start + offset - padding, end + offset + padding];\n    }\n}\n","import { bisector } from 'd3-array';\nimport { RemoteFile as _RemoteFile } from 'generic-filehandle';\n\nimport type * as HiGlass from '@higlass/types';\nimport type { Assembly, ChromSizes, Datum } from '@gosling-lang/gosling-schema';\n\nexport type CommonDataConfig = {\n    assembly: Assembly;\n    x?: string;\n    xe?: string;\n    x1?: string;\n    x1e?: string;\n    urlFetchOptions?: RequestInit;\n};\n\nexport class DataSource<File, Options> {\n    chromInfo: ExtendedChromInfo;\n    tilesetInfo: ReturnType<typeof tilesetInfoFromChromInfo>;\n\n    constructor(public file: File, chromSizes: ChromSizes, public options: Options) {\n        this.chromInfo = sizesToChromInfo(chromSizes);\n        this.tilesetInfo = tilesetInfoFromChromInfo(this.chromInfo);\n    }\n}\n\n/**\n * Filter data before sending to a track considering the visible genomic area in the track.\n * TODO(2022-Jul-13): Consider genomic `y` channels as well.\n */\nexport function filterUsingGenoPos(\n    data: Datum[],\n    [minX, maxX]: [number, number],\n    config: Omit<CommonDataConfig, 'assembly'>\n) {\n    const { x, xe, x1, x1e } = config;\n    const definedXFields = [x, xe, x1, x1e].filter(f => f) as string[];\n    return data.filter((d: Datum) => {\n        if (definedXFields.length === 0) {\n            // no filter applies\n            return true;\n        } else if (definedXFields.length === 1) {\n            // filter based on one genomic position\n            const value = +d[definedXFields[0]];\n            return typeof value === 'number' && minX < value && value <= maxX;\n        } else {\n            // filter based on two genomic positions, i.e., check overlaps\n            const values = definedXFields.map(f => +d[f]).filter(v => !isNaN(v));\n            const minValue = Math.min(...values);\n            const maxValue = Math.max(...values);\n            return minX <= maxValue && minValue <= maxX;\n        }\n    });\n}\n\nconst chromInfoBisector = bisector((d: { pos: number }) => d.pos).left;\n\nconst chrToAbs = (chrom: string, chromPos: number, chromInfo: HiGlass.ChromInfo) =>\n    chromInfo.chrPositions[chrom].pos + chromPos;\n\nconst absToChr = (absPosition: number, chromInfo: HiGlass.ChromInfo) => {\n    if (!chromInfo || !chromInfo.cumPositions || !chromInfo.cumPositions.length) {\n        return null;\n    }\n\n    let insertPoint = chromInfoBisector(chromInfo.cumPositions, absPosition);\n    const lastChr = chromInfo.cumPositions[chromInfo.cumPositions.length - 1].chr;\n    const lastLength = chromInfo.chromLengths[lastChr];\n\n    // @ts-expect-error\n    insertPoint -= insertPoint > 0 && 1;\n\n    let chrPosition = Math.floor(absPosition - chromInfo.cumPositions[insertPoint].pos);\n    let offset = 0;\n\n    if (chrPosition < 0) {\n        // before the start of the genome\n        offset = chrPosition - 1;\n        chrPosition = 1;\n    }\n\n    if (insertPoint === chromInfo.cumPositions.length - 1 && chrPosition > lastLength) {\n        // beyond the last chromosome\n        offset = chrPosition - lastLength;\n        chrPosition = lastLength;\n    }\n\n    return [chromInfo.cumPositions[insertPoint].chr, chrPosition, offset, insertPoint] as const;\n};\n\n/**\n * Get a chromosome name for the consistentcy, e.g., `1` --> `chr1`.\n * @param chrName A chromosome name to be sanitized\n * @param assembly A genome assembly of the data\n * @param chromosomePrefix A prefix string that can be replaced to 'chr'\n * @returns\n */\nexport function sanitizeChrName(chrName: string, assembly: Assembly, chromosomePrefix?: string) {\n    if (Array.isArray(assembly)) {\n        // this is a custom assembly, so use this as is\n        return chrName;\n    }\n\n    // For assemblies in Gosling, we use the `chr` prefix consistently\n    if (chromosomePrefix) {\n        // `hs1` --> `chr1`\n        chrName = chrName.replace(chromosomePrefix, 'chr');\n    } else if (!chrName.includes('chr')) {\n        // `1` --> `chr1`\n        chrName = `chr${chrName}`;\n    }\n    return chrName;\n}\n\nexport type ExtendedChromInfo = HiGlass.ChromInfo & {\n    absToChr(absPos: number): ReturnType<typeof absToChr> | null;\n    chrToAbs(chr: [name: string, pos: number]): number | null;\n};\n\nexport function tilesetInfoFromChromInfo(chromInfo: ExtendedChromInfo, tileSize = 1024) {\n    return {\n        tile_size: tileSize,\n        bins_per_dimension: tileSize,\n        max_zoom: Math.ceil(Math.log(chromInfo.totalLength / tileSize) / Math.log(2)),\n        max_width: chromInfo.totalLength,\n        min_pos: [0],\n        max_pos: [chromInfo.totalLength]\n    };\n}\n\nexport function sizesToChromInfo(sizes: [string, number][]): ExtendedChromInfo {\n    const info: HiGlass.ChromInfo = {\n        cumPositions: [],\n        chromLengths: {},\n        chrPositions: {},\n        totalLength: 0\n    };\n\n    sizes.forEach(([chr, length], i) => {\n        const chrPosition = { id: i, chr, pos: info.totalLength };\n        info.chrPositions[chr] = chrPosition;\n        info.chromLengths[chr] = length;\n        info.cumPositions.push(chrPosition);\n        info.totalLength += length;\n    });\n\n    return {\n        ...info,\n        absToChr: absPos => (info.chrPositions ? absToChr(absPos, info) : null),\n        chrToAbs: ([chrName, chrPos]) => (info.chrPositions ? chrToAbs(chrName, chrPos, info) : null)\n    };\n}\n\nexport class RemoteFile extends _RemoteFile {\n    // Overrides `read` to eagerly read 200 or 206 response\n    // from https://github.com/GMOD/generic-filehandle/blob/0e8209be25e3097307bd15e964edd8c017e808d7/src/remoteFile.ts#L100-L162\n    public read: _RemoteFile['read'] = async (\n        buffer,\n        offset = 0,\n        length,\n        position = 0,\n        opts = {}\n    ): Promise<{ bytesRead: number; buffer: Buffer }> => {\n        const { headers = {}, signal, overrides = {} } = opts;\n\n        if (length < Infinity) {\n            headers.range = `bytes=${position}-${position + length}`;\n        } else if (length === Infinity && position !== 0) {\n            headers.range = `bytes=${position}-`;\n        }\n        const args = {\n            // @ts-expect-error private property\n            ...this.baseOverrides,\n            ...overrides,\n            headers: {\n                ...headers,\n                ...overrides.headers,\n                // @ts-expect-error private property\n                ...this.baseOverrides.headers\n            },\n            method: 'GET',\n            redirect: 'follow',\n            mode: 'cors',\n            signal\n        };\n        const response = await this.fetch(this.url, args);\n\n        if (!response.ok) {\n            throw new Error(`HTTP ${response.status} ${response.statusText} ${this.url}`);\n        }\n\n        // Just read the response if it was successful.\n        if (response.status === 200 || response.status === 206) {\n            // @ts-expect-error private method\n            const responseData = await this.getBufferFromResponse(response);\n            const bytesCopied = responseData.copy(buffer, offset, 0, Math.min(length, responseData.length));\n\n            // try to parse out the size of the remote file\n            const res = response.headers.get('content-range');\n            const sizeMatch = /\\/(\\d+)$/.exec(res || '');\n            if (sizeMatch && sizeMatch[1]) {\n                // @ts-expect-error private property\n                this._stat = { size: parseInt(sizeMatch[1], 10) };\n            }\n\n            return { bytesRead: bytesCopied, buffer };\n        }\n\n        // TODO: try harder here to gather more information about what the problem is\n        throw new Error(`HTTP ${response.status} fetching ${this.url}`);\n    };\n}\n\nexport interface TabularDataFetcher<Tile> {\n    getTabularData(tileIds: string[]): Promise<Tile[]>;\n    MAX_TILE_WIDTH?: 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