@genome-spy/core 0.43.0 → 0.43.1

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

@@ -8,6 +8,12 @@ export default class BigBedSource extends SingleAxisWindowedSource {
     parser: import("@gmod/bed").default;
     /** @type {import("@gmod/bbi").BigBed} */
     bbi: import("@gmod/bbi").BigBed;
+    /** @type {(chrom: string, fields: { start: number, end: number, rest?: string }) => Record<string, any>} */
+    parseLine: (chrom: string, fields: {
+        start: number;
+        end: number;
+        rest?: string;
+    }) => Record<string, any>;
     params: import("../../../spec/data.js").BigBedData;
     initializedPromise: Promise<any>;
 }

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":"AAGA;IAOI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,UAAU,QAC1C,OAAO,uBAAuB,EAAE,OAAO,EA4CjD;IApDD,0CAA0C;IAC1C,QADW,OAAO,WAAW,EAAE,OAAO,CAC/B;IAEP,yCAAyC;IACzC,KADW,OAAO,WAAW,EAAE,MAAM,CACjC;IAkBA,mDAAgC;IAQhC,iCAqBE;CA4BT;qCAlFoC,+BAA+B"}
+{"version":3,"file":"bigBedSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/bigBedSource.js"],"names":[],"mappings":"AAGA;IAUI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,UAAU,QAC1C,OAAO,uBAAuB,EAAE,OAAO,EAsDjD;IAjED,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;IAkBN,mDAAgC;IAQhC,iCA+BE;CAuBT;qCA1FoC,+BAA+B"}

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

@@ -8,6 +8,9 @@ export default class BigBedSource extends SingleAxisWindowedSource {
     /** @type {import("@gmod/bbi").BigBed} */
     bbi;
 
+    /** @type {(chrom: string, fields: { start: number, end: number, rest?: string }) => Record<string, any>} */
+    parseLine;
+
     /**
      * @param {import("../../../spec/data.js").BigBedData} params
      * @param {import("../../../view/view.js").default} view
@@ -49,6 +52,16 @@ export default class BigBedSource extends SingleAxisWindowedSource {
                 this.bbi.getHeader().then(async (header) => {
                     // @ts-ignore TODO: Fix
                     this.parser = new BED({ autoSql: header.autoSql });
+                    try {
+                        const fastParser = makeFastParser(this.parser);
+                        this.parseLine = (chrom, f) =>
+                            fastParser(chrom, f.start, f.end, f.rest);
+                    } catch (e) {
+                        this.parseLine = (chrom, f) =>
+                            this.parser.parseLine(
+                                `${chrom}\t${f.start}\t${f.end}\t${f.rest}`
+                            );
+                    }
 
                     resolve();
                 });
@@ -68,12 +81,7 @@ export default class BigBedSource extends SingleAxisWindowedSource {
                         signal,
                     })
                     .then((features) =>
-                        features.map((f) =>
-                            this.parser.parseLine(
-                                `${d.chrom}\t${f.start}\t${f.end}\t${f.rest}`,
-                                { uniqueId: f.uniqueId }
-                            )
-                        )
+                        features.map((f) => this.parseLine(d.chrom, f))
                     )
         );
 
@@ -82,3 +90,117 @@ export default class BigBedSource extends SingleAxisWindowedSource {
         }
     }
 }
+
+/**
+ * A specific optimization for Hautaniemi Lab's Methylation project, where
+ * we have hundreds of columns having small integers (0-100).
+ * This parser avoids generating piles of garbage to be collected by the GC.
+ * We don't split the line into an array of strings, but instead parse the
+ * integer fields directly from the original string.
+ * This parser doesn't support arrays, etc. at the moment.
+ *
+ * @param {import("@gmod/bed").default} bed
+ */
+function makeFastParser(bed) {
+    // Skip the first three fields: chrom, chromStart, chromEnd
+    const fields = bed.autoSql.fields.filter((field) => field.type).slice(3);
+
+    let i = 0;
+    let currentLine = "";
+    let lineLength = 0;
+
+    /** @type {Record<string, any>} */
+    let currentObject = {};
+
+    const delimiter = "\t";
+    const delimiterCode = delimiter.charCodeAt(0);
+    const zero = "0".charCodeAt(0);
+    const minusCode = "-".charCodeAt(0);
+
+    function parseString() {
+        let end = currentLine.indexOf(delimiter, i);
+        if (end < 0) {
+            end = lineLength;
+        }
+        const str = currentLine.substring(i, end);
+        i = end + 1;
+        return str;
+    }
+
+    function parseInt() {
+        let value = 0;
+
+        let charCode = currentLine.charCodeAt(i);
+        let sign = 1;
+
+        if (charCode === minusCode) {
+            sign = -1;
+            i++;
+            charCode = currentLine.charCodeAt(i);
+        }
+
+        do {
+            if (charCode === delimiterCode) {
+                i++;
+                break;
+            }
+            value = value * 10 + charCode - zero;
+            charCode = currentLine.charCodeAt(++i);
+        } while (i < lineLength);
+
+        return value * sign;
+    }
+
+    const fieldParsers = fields.map((field) => {
+        const { name, type } = field;
+
+        if (["ubyte", "int", "uint"].includes(type)) {
+            return () => {
+                currentObject[name] = parseInt();
+            };
+        } else if (field.isNumeric) {
+            return () => {
+                currentObject[name] = Number(parseString());
+            };
+        } else if (["char", "string", "lstring"].includes(type)) {
+            return () => {
+                currentObject[name] = parseString();
+            };
+        } else {
+            throw new Error("Unsupported type: " + type);
+        }
+    });
+
+    /**
+     * @param {string} line
+     */
+    function setLine(line) {
+        currentLine = line;
+        lineLength = line.length;
+        i = 0;
+    }
+
+    /**
+     * @param {string} chrom
+     * @param {number} chromStart
+     * @param {number} chromEnd
+     * @param {string} rest
+     */
+    function parseLine(chrom, chromStart, chromEnd, rest) {
+        setLine(rest);
+
+        currentObject = {
+            chrom,
+            chromStart,
+            chromEnd,
+        };
+
+        for (let j = 0, n = fieldParsers.length; j < n; j++) {
+            fieldParsers[j]();
+        }
+
+        return currentObject;
+    }
+
+    return parseLine;
+}

package/dist/src/gl/arrayBuilder.d.ts

@@ -5,6 +5,7 @@
  * @prop {function(object):any} f The converter
  * @prop {number[]} [arrayReference] An optimization for fp64 mainly
  * @prop {number} [numComponents]
+ * @prop {typeof Uint16Array | typeof Int16Array | typeof Uint32Array | typeof Int32Array | typeof Float32Array} [targetArrayType] Defaults to Float32Array
  */
 export default class ArrayBuilder {
     /**
@@ -13,10 +14,10 @@ export default class ArrayBuilder {
      */
     constructor(size: number);
     size: number;
-    /** @type {Object.<string, {data: number[] | Float32Array, numComponents: number, divisor?: number}>} */
+    /** @type {Object.<string, {data: Uint16Array | Int16Array | Uint32Array | Int32Array | Float32Array, numComponents: number, divisor?: number}>} */
     arrays: {
         [x: string]: {
-            data: number[] | Float32Array;
+            data: Uint16Array | Int16Array | Uint32Array | Int32Array | Float32Array;
             numComponents: number;
             divisor?: number;
         };
@@ -26,6 +27,7 @@ export default class ArrayBuilder {
     /** @type {(function(any):void)[]} */
     dataUpdaters: ((arg0: any) => void)[];
     vertexCount: number;
+    configure(): void;
     /**
      *
      * @param {string} attribute
@@ -36,13 +38,13 @@ export default class ArrayBuilder {
      *
      * @param {string} attributeName
      * @param {number} numComponents
+     * @param {typeof Uint16Array | typeof Int16Array | typeof Uint32Array | typeof Int32Array | typeof Float32Array} [targetArrayType]
      * @param {number[]} [arrayReference]
      * @return {function(number|number[])}
      */
-    createUpdater(attributeName: string, numComponents: number, arrayReference?: number[]): (arg0: number | number[]) => any;
+    createUpdater(attributeName: string, numComponents: number, targetArrayType?: typeof Uint16Array | typeof Int16Array | typeof Uint32Array | typeof Int32Array | typeof Float32Array, arrayReference?: number[]): (arg0: number | number[]) => any;
     pushAll(): void;
     /**
-     *
      * @param {object} datum
      */
     updateFromDatum(datum: object): void;
@@ -51,6 +53,7 @@ export default class ArrayBuilder {
      * @param {object} datum
      */
     pushFromDatum(datum: object): void;
+    #private;
 }
 /**
  * A function that extracts a raw attribute from a datum (optionally) converts
@@ -66,5 +69,9 @@ export type ConverterMetadata = {
      */
     arrayReference?: number[];
     numComponents?: number;
+    /**
+     * Defaults to Float32Array
+     */
+    targetArrayType?: typeof Uint16Array | typeof Int16Array | typeof Uint32Array | typeof Int32Array | typeof Float32Array;
 };
 //# sourceMappingURL=arrayBuilder.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"arrayBuilder.d.ts","sourceRoot":"","sources":["../../../src/gl/arrayBuilder.js"],"names":[],"mappings":"AASA;;;;;;;GAOG;AACH;IAGI;;;OAGG;IACH,kBAFW,MAAM,EAehB;IAZG,aAAgB;IAEhB,wGAAwG;IACxG;YADmB,MAAM,GAAE;YAAC,IAAI,EAAE,MAAM,EAAE,GAAG,YAAY,CAAC;YAAC,aAAa,EAAE,MAAM,CAAC;YAAC,OAAO,CAAC,EAAE,MAAM,CAAA;SAAC;MACnF;IAEhB,kCAAkC;IAClC,SADW,OAAY,IAAI,CAAC,EAAE,CACb;IAEjB,qCAAqC;IACrC,cADW,QAAU,GAAG,KAAE,IAAI,CAAC,EAAE,CACX;IAEtB,oBAAoB;IAGxB;;;;OAIG;IACH,wBAHW,MAAM,YACN,iBAAiB,QAc3B;IAED;;;;;;OAMG;IACH,6BALW,MAAM,iBACN,MAAM,mBACN,MAAM,EAAE,UACE,MAAM,GAAC,MAAM,EAAE,SA8EnC;IAED,gBA0BC;IAED;;;OAGG;IACH,uBAFW,MAAM,QA6BhB;IAED;;;OAGG;IACH,qBAFW,MAAM,QAKhB;CACJ;;;;;;;;;cAvMkB,MAAM,KAAE,GAAG;;;;qBACpB,MAAM,EAAE;oBACR,MAAM"}
+{"version":3,"file":"arrayBuilder.d.ts","sourceRoot":"","sources":["../../../src/gl/arrayBuilder.js"],"names":[],"mappings":"AASA;;;;;;;;GAQG;AACH;IAKI;;;OAGG;IACH,kBAFW,MAAM,EAehB;IAZG,aAAgB;IAEhB,mJAAmJ;IACnJ;YADmB,MAAM,GAAE;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;MAC9H;IAEhB,kCAAkC;IAClC,SADW,OAAY,IAAI,CAAC,EAAE,CACb;IAEjB,qCAAqC;IACrC,cADW,QAAU,GAAG,KAAE,IAAI,CAAC,EAAE,CACX;IAEtB,oBAAoB;IAGxB,kBAOC;IAED;;;;OAIG;IACH,wBAHW,MAAM,YACN,iBAAiB,QAe3B;IAED;;;;;;;OAOG;IACH,6BANW,MAAM,iBACN,MAAM,oBACN,kBAAkB,GAAG,iBAAiB,GAAG,kBAAkB,GAAG,iBAAiB,GAAG,mBAAmB,mBACrG,MAAM,EAAE,UACE,MAAM,GAAC,MAAM,EAAE,SAoFnC;IAED,gBAEC;IAED;;OAEG;IACH,uBAFW,MAAM,QAIhB;IAuDD;;;OAGG;IACH,qBAFW,MAAM,QAKhB;;CACJ;;;;;;;;;cA9NkB,MAAM,KAAE,GAAG;;;;qBACpB,MAAM,EAAE;oBACR,MAAM;;;;sBACN,kBAAkB,GAAG,iBAAiB,GAAG,kBAAkB,GAAG,iBAAiB,GAAG,mBAAmB"}

package/dist/src/gl/arrayBuilder.js

@@ -14,10 +14,13 @@ const UNROLL_LIMIT = 10000;
  * @prop {function(object):any} f The converter
  * @prop {number[]} [arrayReference] An optimization for fp64 mainly
  * @prop {number} [numComponents]
+ * @prop {typeof Uint16Array | typeof Int16Array | typeof Uint32Array | typeof Int32Array | typeof Float32Array} [targetArrayType] Defaults to Float32Array
  */
 export default class ArrayBuilder {
     // TODO: Support strided layout. May yield better performance or not. No consensus in literature.
 
+    #configured = false;
+
     /**
      *
      * @param {number} size Size if known, uses TypedArray
@@ -25,7 +28,7 @@ export default class ArrayBuilder {
     constructor(size) {
         this.size = size;
 
-        /** @type {Object.<string, {data: number[] | Float32Array, numComponents: number, divisor?: number}>} */
+        /** @type {Object.<string, {data: Uint16Array | Int16Array | Uint32Array | Int32Array | Float32Array, numComponents: number, divisor?: number}>} */
         this.arrays = {};
 
         /** @type {(function():void)[]} */
@@ -37,6 +40,15 @@ export default class ArrayBuilder {
         this.vertexCount = 0;
     }
 
+    configure() {
+        if (this.#configured) {
+            throw new Error("Already configured!");
+        }
+        this.#configurePushAll();
+        this.#configureUpdateFromDatum();
+        this.#configured = true;
+    }
+
     /**
      *
      * @param {string} attribute
@@ -46,6 +58,7 @@ export default class ArrayBuilder {
         const updater = this.createUpdater(
             ATTRIBUTE_PREFIX + attribute,
             metadata.numComponents || 1,
+            metadata.targetArrayType ?? Float32Array,
             metadata.arrayReference
         );
         const f = metadata.f;
@@ -60,10 +73,16 @@ export default class ArrayBuilder {
      *
      * @param {string} attributeName
      * @param {number} numComponents
+     * @param {typeof Uint16Array | typeof Int16Array | typeof Uint32Array | typeof Int32Array | typeof Float32Array} [targetArrayType]
      * @param {number[]} [arrayReference]
      * @return {function(number|number[])}
      */
-    createUpdater(attributeName, numComponents, arrayReference) {
+    createUpdater(
+        attributeName,
+        numComponents,
+        targetArrayType = Float32Array,
+        arrayReference = undefined
+    ) {
         if (!isNumber(this.size)) {
             throw new Error("The number of vertices must be defined!");
         }
@@ -73,7 +92,8 @@ export default class ArrayBuilder {
         let updater;
         let i = 0;
 
-        const array = new Float32Array(this.size * numComponents);
+        // eslint-disable-next-line new-cap
+        const array = new targetArrayType(this.size * numComponents);
 
         this.arrays[attributeName] = {
             data: array,
@@ -142,6 +162,17 @@ export default class ArrayBuilder {
     }
 
     pushAll() {
+        throw new Error("Call configure() first!");
+    }
+
+    /**
+     * @param {object} datum
+     */
+    updateFromDatum(datum) {
+        throw new Error("Call configure() first!");
+    }
+
+    #configurePushAll() {
         if (this.size > UNROLL_LIMIT) {
             const preps = this.pushers
                 .map((_v, i) => `const p${i} = that.pushers[${i}];`)
@@ -165,15 +196,9 @@ ${pushs}
                 this.vertexCount++;
             };
         }
-
-        this.pushAll();
     }
 
-    /**
-     *
-     * @param {object} datum
-     */
-    updateFromDatum(datum) {
+    #configureUpdateFromDatum() {
         if (this.size > UNROLL_LIMIT) {
             const preps = this.dataUpdaters
                 .map((_v, i) => `const u${i} = that.dataUpdaters[${i}];`)
@@ -192,14 +217,12 @@ ${updates}
 };`
             )(this);
         } else {
-            this.updateFromDatum = (datum) => {
+            this.updateFromDatum = (/** @type {object} */ datum) => {
                 for (let i = 0; i < this.dataUpdaters.length; i++) {
                     this.dataUpdaters[i](datum);
                 }
             };
         }
-
-        this.updateFromDatum(datum);
     }
 
     /**

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

@@ -63,9 +63,9 @@ export class GeometryBuilder {
         getIndex: () => import("../utils/binnedIndex.js").Lookup;
     };
     toArrays(): {
-        /** @type {Record<string, {data: number[] | Float32Array, numComponents: number, divisor?: number}>} */
+        /** @type {Record<string, {data: Uint16Array | Int16Array | Uint32Array | Int32Array | Float32Array, numComponents: number, divisor?: number}>} */
         arrays: Record<string, {
-            data: number[] | Float32Array;
+            data: Uint16Array | Int16Array | Uint32Array | Int32Array | Float32Array;
             numComponents: number;
             divisor?: number;
         }>;
@@ -89,6 +89,7 @@ export class RectVertexBuilder extends GeometryBuilder {
         attributes: string[];
         numItems?: number;
     });
+    pushAllSixTimes: any;
 }
 export class RuleVertexBuilder extends GeometryBuilder {
     /**

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

@@ -1 +1 @@
-{"version":3,"file":"dataToVertices.d.ts","sourceRoot":"","sources":["../../../src/gl/dataToVertices.js"],"names":[],"mappings":"AAeA;;;;;GAKG;AACH;IACI;;;OAGG;IAEH;;;;;;OAMG;IACH;;qBAJW,MAAM,EAAE;sBACR,MAAM;OAuEhB;IAnEG,gEAAwB;IAGxB;;MAKC;IAQD,0BAAoC;IAEpC,8BAAoD;IA6CpD,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,QA+DhB;IAED;;;;;OAKG;IACH,mBAFW,OAAO,qBAAqB,EAAE,KAAK,QAI7C;IA/DO;;;MAAyB;IAiEjC;QAEQ,uGAAuG;gBAA5F,OAAO,MAAM,EAAE;YAAC,IAAI,EAAE,MAAM,EAAE,GAAG,YAAY,CAAC;YAAC,aAAa,EAAE,MAAM,CAAC;YAAC,OAAO,CAAC,EAAE,MAAM,CAAA;SAAC,CAAC;QAEnG,8BAA8B;;QAE9B,8CAA8C;;;MAIrD;CACJ;AAED;IACI;;;;;;OAMG;IACH;;oBAHW,MAAM,EAAE;mBACR,MAAM;OAQhB;CAkCJ;AAED;IACI;;;;;;;;;OASG;IACH;;oBANW,MAAM,EAAE;gCACR,MAAM;uBAEN,MAAM,EAAE;mBACR,MAAM;OAsBhB;IANG,uBAAgC;IAEhC,8BAA8D;IAE9D,6CAA+D;IAC/D,4CAA6D;CA2CpE;AAED;IACI;;;;;;OAMG;IACH;;oBAHW,MAAM,EAAE;mBACR,MAAM;OAQhB;CACJ;AAED;IACI;;;;;OAKG;IACH;;oBAHW,MAAM,EAAE;mBACR,MAAM;OAQhB;CAYJ;AAED;IACI;;;;;;;;;OASG;IACH;;oBANW,MAAM,EAAE;qBACR,OAAO,2BAA2B,EAAE,aAAa;oBACjD,OAAO,MAAM,EAAE,GAAG,CAAC;wBACnB,MAAM;sBACN,OAAO;OA4CjB;IA7BG,4DAA2B;IAC3B,2DAA0B;IAE1B,gCAA4B;IAQ5B,qCAAqC;IACrC,sBADmB,GAAG,KAAK,MAAM,CAMf;IAElB,oDAGC;IACD,qDAGC;IAED,8CAAiE;CA8IxE;;;;;;;;YAzkBS,MAAM;;;;WACN,MAAM;YACN,OAAO,yBAAyB,EAAE,MAAM;;yBAhBzB,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;OA6EhB;IAzEG,gEAAwB;IAGxB;;MAKC;IAQD,0BAAoC;IAEpC,8BAAoD;IAmDpD,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,QA+DhB;IAED;;;;;OAKG;IACH,mBAFW,OAAO,qBAAqB,EAAE,KAAK,QAI7C;IA/DO;;;MAAyB;IAiEjC;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;OA8CjB;IA/BG,4DAA2B;IAC3B,2DAA0B;IAE1B,gCAA4B;IAQ5B,qCAAqC;IACrC,sBADmB,GAAG,KAAK,MAAM,CAMf;IAElB,oDAGC;IACD,qDAGC;IAED,8CAAiE;CAgJxE;;;;;;;;YAvmBS,MAAM;;;;WACN,MAAM;YACN,OAAO,yBAAyB,EAAE,MAAM;;yBAjBzB,mBAAmB"}

package/dist/src/gl/dataToVertices.js

@@ -8,10 +8,11 @@ import { isValueDef } from "../encoder/encoder.js";
 import {
     dedupeEncodingFields,
     isHighPrecisionScale,
+    isLargeGenome,
     makeAttributeName,
-    splitHighPrecision,
+    splitLargeHighPrecision,
 } from "./glslScaleGenerator.js";
-import { isContinuous } from "vega-scale";
+import { isContinuous, isDiscrete } from "vega-scale";
 
 /**
  * @typedef {object} RangeEntry Represents a location of a vertex subset
@@ -67,8 +68,9 @@ export class GeometryBuilder {
 
             const accessor = ce.accessor;
 
-            const doubleArray = [0, 0];
             const hp = isHighPrecisionScale(ce.scale.type);
+            const largeHp = hp && isLargeGenome(ce.scale.domain());
+            const largeHpArray = [0, 0];
 
             const indexer = ce.indexer;
 
@@ -81,8 +83,8 @@ export class GeometryBuilder {
              */
             const f = indexer
                 ? (d) => indexer(accessor(d))
-                : hp
-                ? (d) => splitHighPrecision(accessor(d), doubleArray)
+                : largeHp
+                ? (d) => splitLargeHighPrecision(accessor(d), largeHpArray)
                 : accessor;
 
             const attributeName = sharedChannels
@@ -91,8 +93,13 @@ export class GeometryBuilder {
 
             this.variableBuilder.addConverter(attributeName, {
                 f,
-                numComponents: hp ? 2 : 1,
-                arrayReference: hp ? doubleArray : undefined,
+                numComponents: largeHp ? 2 : 1,
+                arrayReference: largeHp ? largeHpArray : undefined,
+                targetArrayType: isDiscrete(ce.scale.type)
+                    ? Uint16Array
+                    : hp
+                    ? Uint32Array
+                    : Float32Array,
             });
         }
 
@@ -226,7 +233,7 @@ export class GeometryBuilder {
 
     toArrays() {
         return {
-            /** @type {Record<string, {data: number[] | Float32Array, numComponents: number, divisor?: number}>} */
+            /** @type {Record<string, {data: Uint16Array | Int16Array | Uint32Array | Int32Array | Float32Array, numComponents: number, divisor?: number}>} */
             arrays: this.variableBuilder.arrays,
             /** Number of vertices used */
             vertexCount: this.variableBuilder.vertexCount,
@@ -251,6 +258,29 @@ export class RectVertexBuilder extends GeometryBuilder {
             attributes,
             numVertices: numItems * 6,
         });
+        this.variableBuilder.configure();
+
+        const pushAll = this.variableBuilder.pushAll;
+
+        this.pushAllSixTimes =
+            // TODO: Don't do this stupid comparison. Instead, reuse the previous GeometryBuilder.
+            numItems > 500
+                ? // Make a new function instance where the JS engine can inline
+                  // all pushAll calls to avoid the function call overhead.
+                  new Function(
+                      "pushAll",
+                      `return function unrolledPushAllSixTimes() {
+  pushAll(); pushAll(); pushAll(); pushAll(); pushAll(); pushAll();
+};`
+                  )(pushAll)
+                : function pushAllSixTimes() {
+                      pushAll();
+                      pushAll();
+                      pushAll();
+                      pushAll();
+                      pushAll();
+                      pushAll();
+                  };
     }
 
     /**
@@ -273,12 +303,7 @@ export class RectVertexBuilder extends GeometryBuilder {
 
             // Six vertices per rect. The vertex shader is using gl_VertexID to
             // determine the vertex position within the rect.
-            this.variableBuilder.pushAll();
-            this.variableBuilder.pushAll();
-            this.variableBuilder.pushAll();
-            this.variableBuilder.pushAll();
-            this.variableBuilder.pushAll();
-            this.variableBuilder.pushAll();
+            this.pushAllSixTimes();
 
             this.addToXIndex(d);
         }
@@ -318,6 +343,8 @@ export class RuleVertexBuilder extends GeometryBuilder {
 
         this.updateSide = this.variableBuilder.createUpdater("side", 1);
         this.updatePos = this.variableBuilder.createUpdater("pos", 1);
+
+        this.variableBuilder.configure();
     }
 
     /* eslint-disable complexity */
@@ -376,6 +403,7 @@ export class PointVertexBuilder extends GeometryBuilder {
             attributes,
             numVertices: numItems,
         });
+        this.variableBuilder.configure();
     }
 }
 
@@ -392,6 +420,7 @@ export class LinkVertexBuilder extends GeometryBuilder {
             attributes,
             numVertices: numItems,
         });
+        this.variableBuilder.configure();
     }
 
     toArrays() {
@@ -459,6 +488,8 @@ export class TextVertexBuilder extends GeometryBuilder {
         );
 
         this.updateWidth = this.variableBuilder.createUpdater("width", 1);
+
+        this.variableBuilder.configure();
     }
 
     /**

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

@@ -18,15 +18,27 @@ export function generateScaleGlsl(channel: Channel, scale: any, channelDef: impo
     domainUniform: string;
 };
 /**
+ * True if scale needs more than 24 bits (float32) of precision.
  *
  * @param {string} type
  */
 export function isHighPrecisionScale(type: string): boolean;
+/**
+ * True if Uint32 cannot represent the domain.
+ *
+ * @param {number[]} domain
+ */
+export function isLargeGenome(domain: number[]): boolean;
 /**
  * @param {number} x Must be an integer
  * @param {number[]} [arr]
  */
 export function splitHighPrecision(x: number, arr?: number[]): number[];
+/**
+ * @param {number} x Must be an integer
+ * @param {number[]} [arr]
+ */
+export function splitLargeHighPrecision(x: number, arr?: number[]): number[];
 /**
  * @param {number[]} domain
  */

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

@@ -1 +1 @@
-{"version":3,"file":"glslScaleGenerator.d.ts","sourceRoot":"","sources":["../../../src/gl/glslScaleGenerator.js"],"names":[],"mappings":";AAmDA;;;;GAIG;AACH,2CAHW,OAAO,SACP,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,GAAG,OAAO,UAsC9C;AAED;;;;;;GAMG;AAEH,2CANW,OAAO,SACP,GAAG,cACH,OAAO,oBAAoB,EAAE,UAAU,+BACvC,OAAO,EAAE;;;;EAmRnB;AA+FD;;;GAGG;AACH,2CAFW,MAAM,WAIhB;AAOD;;;GAGG;AACH,sCAHW,MAAM,QACN,MAAM,EAAE,YAYlB;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;AAzhBD,uCAAwC;AACxC,uCAAwC;AACxC,oCAAqC;AACrC,6CAA8C;AAC9C,kDAAmD;AACnD,oDAAqD;sBAMxC,OAAO,oBAAoB,EAAE,OAAO;;;;8BAsXpC,MAAM,GAAG;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,aAAa,EAAE,MAAM,CAAA;CAAE;;;;uBA8GhD,CAAC,MAAM,EAAE,OAAO,CAAC;0BAjfJ,WAAW"}
+{"version":3,"file":"glslScaleGenerator.d.ts","sourceRoot":"","sources":["../../../src/gl/glslScaleGenerator.js"],"names":[],"mappings":";AAmDA;;;;GAIG;AACH,2CAHW,OAAO,SACP,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,GAAG,OAAO,UAsC9C;AAED;;;;;;GAMG;AAEH,2CANW,OAAO,SACP,GAAG,cACH,OAAO,oBAAoB,EAAE,UAAU,+BACvC,OAAO,EAAE;;;;EA8RnB;AA+FD;;;;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;AA3jBD,uCAAwC;AACxC,uCAAwC;AACxC,oCAAqC;AACrC,6CAA8C;AAC9C,kDAAmD;AACnD,oDAAqD;sBAMxC,OAAO,oBAAoB,EAAE,OAAO;;;;8BAiYpC,MAAM,GAAG;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,aAAa,EAAE,MAAM,CAAA;CAAE;;;;uBAqIhD,CAAC,MAAM,EAAE,OAAO,CAAC;0BAnhBJ,WAAW"}

package/dist/src/gl/glslScaleGenerator.js

@@ -122,8 +122,19 @@ export function generateScaleGlsl(
     const domainUniformName = DOMAIN_PREFIX + primary;
     const rangeName = RANGE_PREFIX + primary;
 
+    // The attribute has discrete values
+    const discrete = isDiscrete(scale.type);
+
     const hp = isHighPrecisionScale(scale.type);
-    const attributeType = hp ? "vec2" : "float";
+    const largeHp = hp && isLargeGenome(scale.domain());
+
+    const attributeType = largeHp
+        ? "uvec2"
+        : hp
+        ? "uint"
+        : discrete
+        ? "uint"
+        : "float";
 
     const domainLength = scale.domain ? scale.domain().length : undefined;
 
@@ -468,6 +479,7 @@ function makeFunctionCall(name, ...args) {
 }
 
 /**
+ * True if scale needs more than 24 bits (float32) of precision.
  *
  * @param {string} type
  */
@@ -475,9 +487,17 @@ export function isHighPrecisionScale(type) {
     return type == "index" || type == "locus";
 }
 
-// Maximum precise index number is 2^(23 + 11) ~ 17G
-// Higher number increases precision but makes zooming unstable
-const BS = 2 ** 11;
+/**
+ * True if Uint32 cannot represent the domain.
+ *
+ * @param {number[]} domain
+ */
+export function isLargeGenome(domain) {
+    return domain[1] > 2 ** 32;
+}
+
+const LOW_BITS = 12;
+const BS = 2 ** LOW_BITS;
 const BM = BS - 1;
 
 /**
@@ -496,6 +516,20 @@ export function splitHighPrecision(x, arr = []) {
     return arr;
 }
 
+/**
+ * @param {number} x Must be an integer
+ * @param {number[]} [arr]
+ */
+export function splitLargeHighPrecision(x, arr = []) {
+    const lo = x % BS;
+    const hi = (x - lo) / BS;
+
+    arr[0] = hi;
+    arr[1] = lo;
+
+    return arr;
+}
+
 /**
  * @param {number} x
  */

package/dist/src/gl/includes/scales.glsl.js

@@ -1,2 +1,2 @@
-const shader = "uniform highp float uZero;vec3 getDiscreteColor(sampler2D s,int index){return texelFetch(s,ivec2(index % textureSize(s,0).x,0),0).rgb;}vec3 getInterpolatedColor(sampler2D s,float unitValue){return texture(s,vec2(unitValue,0.0)).rgb;}float clampToRange(float value,vec2 range){return clamp(value,min(range[0],range[1]),max(range[0],range[1]));}float scaleIdentity(float value){return value;}float scaleLinear(float value,vec2 domain,vec2 range){float domainSpan=domain[1]-domain[0];float rangeSpan=range[1]-range[0];return(value-domain[0])/domainSpan*rangeSpan+range[0];}float scaleLog(float value,vec2 domain,vec2 range,float base){return scaleLinear(log(value)/log(base),log(domain)/log(base),range);}float symlog(float value,float constant){return sign(value)*log(abs(value/constant)+1.0);}float scaleSymlog(float value,vec2 domain,vec2 range,float constant){return scaleLinear(symlog(value,constant),vec2(symlog(domain[0],constant),symlog(domain[1],constant)),range);}float scalePow(float value,vec2 domain,vec2 range,float exponent){return scaleLinear(pow(abs(value),exponent)*sign(value),pow(abs(domain),vec2(exponent))*sign(domain),range);}float scaleBand(float value,vec2 domainExtent,vec2 range,float paddingInner,float paddingOuter,float align,float band){float start=range[0];float stop=range[1];float rangeSpan=stop-start;float n=domainExtent[1]-domainExtent[0];paddingInner=int(n)>1 ? paddingInner : 0.0;float step=rangeSpan/max(1.0,n-paddingInner+paddingOuter*2.0);start+=(rangeSpan-step*(n-paddingInner))*align;float bandwidth=step*(1.0-paddingInner);return start+(value-domainExtent[0])*step+bandwidth*band;}float scaleBandHp(vec2 value,vec3 domainExtent,vec2 range,float paddingInner,float paddingOuter,float align,float band){float start=range[0];float stop=range[1];float rangeSpan=stop-start;vec2 domainStart=domainExtent.xy;float n=domainExtent[2];float step=rangeSpan/max(1.0,n-paddingInner+paddingOuter*2.0);start+=(rangeSpan-step*(n-paddingInner))*align;float bandwidth=step*(1.0-paddingInner);float inf=1.0/uZero;float hi=max(value[0]-domainStart[0],-inf);float lo=max(value[1]-domainStart[1],-inf);return dot(vec4(start,hi,lo,bandwidth),vec4(1.0,step,step,band));}";
+const shader = "uniform highp float uZero;vec3 getDiscreteColor(sampler2D s,int index){return texelFetch(s,ivec2(index % textureSize(s,0).x,0),0).rgb;}vec3 getInterpolatedColor(sampler2D s,float unitValue){return texture(s,vec2(unitValue,0.0)).rgb;}float clampToRange(float value,vec2 range){return clamp(value,min(range[0],range[1]),max(range[0],range[1]));}float scaleIdentity(float value){return value;}float scaleIdentity(uint value){return float(value);}float scaleLinear(float value,vec2 domain,vec2 range){float domainSpan=domain[1]-domain[0];float rangeSpan=range[1]-range[0];return(value-domain[0])/domainSpan*rangeSpan+range[0];}float scaleLog(float value,vec2 domain,vec2 range,float base){return scaleLinear(log(value)/log(base),log(domain)/log(base),range);}float symlog(float value,float constant){return sign(value)*log(abs(value/constant)+1.0);}float scaleSymlog(float value,vec2 domain,vec2 range,float constant){return scaleLinear(symlog(value,constant),vec2(symlog(domain[0],constant),symlog(domain[1],constant)),range);}float scalePow(float value,vec2 domain,vec2 range,float exponent){return scaleLinear(pow(abs(value),exponent)*sign(value),pow(abs(domain),vec2(exponent))*sign(domain),range);}float scaleBand(uint value,vec2 domainExtent,vec2 range,float paddingInner,float paddingOuter,float align,float band){float start=range[0];float stop=range[1];float rangeSpan=stop-start;float n=domainExtent[1]-domainExtent[0];paddingInner=int(n)>1 ? paddingInner : 0.0;float step=rangeSpan/max(1.0,n-paddingInner+paddingOuter*2.0);start+=(rangeSpan-step*(n-paddingInner))*align;float bandwidth=step*(1.0-paddingInner);return start+(float(value)-domainExtent[0])*step+bandwidth*band;}const int lowBits=12;const float lowDivisor=pow(2.0,float(lowBits));const uint lowMask=uint(lowDivisor-1.0);vec2 splitUint(uint value){uint valueLo=value&lowMask;uint valueHi=value-valueLo;return vec2(float(valueHi),float(valueLo));}/***High precision variant of scaleBand for index/locus scales*/float scaleBandHp(uint value,vec3 domainExtent,vec2 range,float paddingInner,float paddingOuter,float align,float band){float start=range[0];float stop=range[1];float rangeSpan=stop-start;vec2 domainStart=domainExtent.xy;float n=domainExtent[2];float step=rangeSpan/max(1.0,n-paddingInner+paddingOuter*2.0);start+=(rangeSpan-step*(n-paddingInner))*align;float bandwidth=step*(1.0-paddingInner);vec2 splitValue=splitUint(value);float inf=1.0/uZero;float hi=max(splitValue[0]-domainStart[0],-inf);float lo=max(splitValue[1]-domainStart[1],-inf);return dot(vec4(start,hi,lo,bandwidth),vec4(1.0,step,step,band));}/***High precision variant of scaleBand for index/locus scales for large*domains where 32bit uints are not sufficient to represent the domain.*/float scaleBandHp(uvec2 value,vec3 domainExtent,vec2 range,float paddingInner,float paddingOuter,float align,float band){float start=range[0];float stop=range[1];float rangeSpan=stop-start;vec2 domainStart=domainExtent.xy;float n=domainExtent[2];float step=rangeSpan/max(1.0,n-paddingInner+paddingOuter*2.0);start+=(rangeSpan-step*(n-paddingInner))*align;float bandwidth=step*(1.0-paddingInner);vec2 splitValue=vec2(float(value[0])*lowDivisor,float(value[1]));float inf=1.0/uZero;float hi=max(splitValue[0]-domainStart[0],-inf);float lo=max(splitValue[1]-domainStart[1],-inf);return dot(vec4(start,hi,lo,bandwidth),vec4(1.0,step,step,band));}";
 export default shader;

package/dist/src/marks/link.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"link.d.ts","sourceRoot":"","sources":["../../../src/marks/link.js"],"names":[],"mappings":"AAWA;IA+BQ;;;;;OAKG;IACH,yBAEC;IAkGD;;;;;;MAKC;CAoFR;iBAxOgB,WAAW"}
+{"version":3,"file":"link.d.ts","sourceRoot":"","sources":["../../../src/marks/link.js"],"names":[],"mappings":"AAWA;IA+BQ;;;;;OAKG;IACH,yBAEC;IAmGD;;;;;;MAKC;CAoFR;iBAzOgB,WAAW"}