@genome-spy/core 0.18.0 → 0.19.1

package/dist/schema.json

@@ -4062,10 +4062,6 @@
           "description": "The exponent of the `pow` scale.",
           "type": "number"
         },
-        "fp64": {
-          "description": "Use emulated 64bit floating points on the GPU to increase precision.\n\nEmulation has a performance cost when compared to the native 32bit processing, but the effect is negligible in the most cases.\n\n__Default value:__ `true` for `\"locus\"` scale, `false` for others.",
-          "type": "boolean"
-        },
         "interpolate": {
           "anyOf": [
             {

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "BSD-2-Clause",
-  "version": "0.18.0",
+  "version": "0.19.1",
   "main": "dist/index.js",
   "module": "src/index.js",
   "exports": {
@@ -28,6 +28,7 @@
     "dev": "node dev-server.js",
     "build": "vite build && npm run build:schema",
     "prepublishOnly": "npm run build",
+    "test:vitest": "vitest run",
     "test:tsc": "tsc -p tsconfig.json",
     "checkSpec": "tsc --allowJs --checkJs --strict --noEmit --moduleResolution node --target es6 src/spec/root.d.ts",
     "build:schema": "mkdir -p dist && ts-json-schema-generator --path 'src/spec/*.ts' --type RootSpec > dist/schema.json"
@@ -52,5 +53,5 @@
     "vega-scale": "^7.1.1",
     "vega-util": "^1.16.0"
   },
-  "gitHead": "ae445fc90ed7640ad9c3b39e81560d81126ebbeb"
+  "gitHead": "ca14d08659918a002fb330ffcd325e9c1e122a8c"
 }

package/src/data/collector.js

@@ -27,7 +27,7 @@ export default class Collector extends FlowNode {
         /** @type {(function(Collector):void)[]} */
         this.observers = [];
 
-        /** @type {Map<any | any[], Data>} */
+        /** @type {Map<any | any[], Data>} TODO: proper type for key */
         this.facetBatches = undefined;
 
         this._init();
@@ -59,8 +59,6 @@ export default class Collector extends FlowNode {
      * @param {import("./flowBatch").FlowBatch} flowBatch
      */
     beginBatch(flowBatch) {
-        // TODO: Propagate batches to children(?)
-
         if (isFacetBatch(flowBatch)) {
             this._data = [];
             this.facetBatches.set(asArray(flowBatch.facetId), this._data);
@@ -103,7 +101,14 @@ export default class Collector extends FlowNode {
         }
 
         if (this.children.length) {
-            for (const data of this.facetBatches.values()) {
+            for (const [key, data] of this.facetBatches.entries()) {
+                if (key) {
+                    /** @type {import("./flowBatch").FacetBatch} */
+                    const facetBatch = { type: "facet", facetId: key };
+                    for (const child of this.children) {
+                        child.beginBatch(facetBatch);
+                    }
+                }
                 for (const datum of data) {
                     this._propagate(datum);
                 }

package/src/data/collector.test.js

@@ -1,3 +1,5 @@
+import { expect, test } from "vitest";
+
 import Collector from "./collector";
 
 const data = [1, 5, 2, 4, 3].map((x) => ({ x }));

package/src/data/dataFlow.test.js

@@ -1,3 +1,5 @@
+import { describe, test } from "vitest";
+
 describe("DataFlow", () => {
     test.todo("TODO");
 });

package/src/data/flow.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import FilterTransform from "./transforms/filter";
 import FormulaTransform from "./transforms/formula";
 import Collector from "./collector";

package/src/data/flowNode.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import FlowNode from "./flowNode";
 import { validateLinks } from "./flowOptimizer";
 

package/src/data/flowOptimizer.js

@@ -1,3 +1,4 @@
+import Collector from "./collector";
 import { BEHAVIOR_CLONES } from "./flowNode";
 import CloneTransform from "./transforms/clone";
 
@@ -31,6 +32,11 @@ export function validateLinks(node, parent = undefined) {
  * @param {FlowNode} node
  */
 export function removeRedundantCloneTransforms(node, cloneRequired = false) {
+    if (node instanceof Collector) {
+        // If an object is modified downstream of Collector, it must be cloned
+        cloneRequired = true;
+    }
+
     if (node instanceof CloneTransform) {
         if (cloneRequired) {
             cloneRequired = false;

package/src/data/flowOptimizer.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import FlowNode, { BEHAVIOR_CLONES } from "./flowNode";
 import { removeRedundantCloneTransforms, validateLinks } from "./flowOptimizer";
 import CloneTransform from "./transforms/clone";

package/src/data/formats/fasta.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import fasta from "./fasta";
 
 test("fasta", () => {

package/src/data/sources/inlineSource.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import Collector from "../collector";
 import InlineSource from "./inlineSource";
 

package/src/data/sources/sequenceSource.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import Collector from "../collector";
 import SequenceSource from "./sequenceSource";
 

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

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import CloneTransform from "./clone";
 

package/src/data/transforms/coverage.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import CoverageTransform from "./coverage";
 import { processData } from "../flowTestUtils";
 

package/src/data/transforms/filter.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import FilterTransform from "./filter";
 

package/src/data/transforms/flattenDelimited.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import FlattenDelimitedTransform from "./flattenDelimited";
 

package/src/data/transforms/flattenSequence.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import FlattenSequenceTransform from "./flattenSequence";
 

package/src/data/transforms/formula.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import FormulaTransform from "./formula";
 

package/src/data/transforms/identifier.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { range } from "d3-array";
 import { processData } from "../flowTestUtils";
 import IdentifierTransform, { BLOCK_SIZE, DEFAULT_AS } from "./identifier";

package/src/data/transforms/pileup.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import PileupTransform from "./pileup";
 import { processData } from "../flowTestUtils";
 

package/src/data/transforms/project.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import ProjectTransform from "./project";
 

package/src/data/transforms/regexExtract.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 
 import RegexExtractTransform from "./regexExtract";

package/src/data/transforms/regexFold.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import RegexFoldTransform from "./regexFold";
 

package/src/data/transforms/sample.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import SampleTransform from "./sample";
 import { extent } from "d3-array";
 import { createChain } from "../../view/flowBuilder";

package/src/data/transforms/stack.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import StackTransform from "./stack";
 

package/src/encoder/accessor.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import AccessorFactory from "./accessor";
 
 const af = new AccessorFactory();

package/src/encoder/encoder.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import AccessorFactory from "./accessor";
 import { scale as vegaScale } from "vega-scale";
 

package/src/genome/genome.js

@@ -257,15 +257,27 @@ export default class Genome {
     parseInterval(str) {
         // TODO: consider changing [0-9XY] to support other species besides humans
         const matches = str.match(
-            /^(chr[0-9A-Z]+):([0-9,]+)-(?:(chr[0-9A-Z]+):)?([0-9,]+)$/
+            /^(chr[0-9A-Z]+)(?::([0-9,]+)(?:-(?:(chr[0-9A-Z]+):)?([0-9,]+))?)?$/
         );
 
         if (matches) {
             const startChr = matches[1];
+
+            if (matches.slice(2).every((x) => x === undefined)) {
+                const chrom = this.getChromosome(startChr);
+                if (chrom) {
+                    return [chrom.continuousStart, chrom.continuousEnd];
+                }
+                return;
+            }
+
             const endChr = matches[3] || startChr;
 
             const startIndex = parseInt(matches[2].replace(/,/g, ""));
-            const endIndex = parseInt(matches[4].replace(/,/g, ""));
+            const endIndex =
+                matches[4] !== undefined
+                    ? parseInt(matches[4].replace(/,/g, ""))
+                    : startIndex;
 
             return [
                 this.toContinuous(startChr, startIndex - 1),

package/src/genome/genome.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import Genome from "./genome";
 
 describe("Human genome, chromosome names prefixed with 'chr'", () => {
@@ -150,3 +151,38 @@ describe("C. elegans genome, chromosome names prefixed with 'chr'", () => {
         expect(g.toContinuous("III", 10)).toEqual(30351865);
     });
 });
+
+describe("Parse interval strings", () => {
+    const chromosomes = [
+        { name: "chr1", size: 1000 },
+        { name: "chr2", size: 2000 },
+        { name: "chr3", size: 3000 },
+        { name: "chrX", size: 4000 },
+    ];
+
+    const g = new Genome({ name: "random", contigs: chromosomes });
+
+    test("Parses a single chromosome, returns an interval spanning the chromosome", () => {
+        expect(g.parseInterval("chr2")).toEqual([1000, 3000]);
+    });
+
+    test("Returns undefined on unknown chromosome", () => {
+        expect(g.parseInterval("chrZ")).toBeUndefined();
+    });
+
+    test("Parses a single coordinate without a thousand separator", () => {
+        expect(g.parseInterval("chr2:1500")).toEqual([2499, 2500]);
+    });
+
+    test("Parses a single coordinate with a thousand separator", () => {
+        expect(g.parseInterval("chr2:1,500")).toEqual([2499, 2500]);
+    });
+
+    test("Parses an interval within a single chromosome", () => {
+        expect(g.parseInterval("chr2:1,500-1,700")).toEqual([2499, 2700]);
+    });
+
+    test("Parses an interval spanning multiple chromosomes", () => {
+        expect(g.parseInterval("chr2:1,500-chr3:1,500")).toEqual([2499, 4500]);
+    });
+});

package/src/genome/scaleIndex.js

@@ -24,7 +24,7 @@ export default function scaleIndex() {
     let numberingOffset = 0;
 
     const scaleFunction = (/** @type {number} */ x) =>
-        ((x - domain[0]) / domainSpan) * rangeSpan + range[0];
+        ((x + align - domain[0]) / domainSpan) * rangeSpan + range[0];
 
     /**
      * In principle, the domain consists of integer indices. However,
@@ -34,7 +34,8 @@ export default function scaleIndex() {
      */
     const scale = /** @type {any} */ (scaleFunction);
 
-    scale.invert = (y) => ((y - range[0]) / rangeSpan) * domainSpan + domain[0];
+    scale.invert = (y) =>
+        ((y - range[0]) / rangeSpan) * domainSpan + domain[0] - align;
 
     // @ts-expect-error
     scale.domain = function (_) {

package/src/genome/scaleIndex.test.js

@@ -1,23 +1,40 @@
+import { expect, test } from "vitest";
 import scaleIndex from "./scaleIndex";
 
 test("Scale with defaults works as expected", () => {
     const scale = scaleIndex();
 
-    expect(scale(-1)).toEqual(-1);
-    expect(scale(0)).toEqual(0);
-    expect(scale(1)).toEqual(1);
-    expect(scale(2)).toEqual(2);
+    // Align is 0.5 by default
+    expect(scale(-1)).toEqual(-0.5);
+    expect(scale(0)).toEqual(0.5);
+    expect(scale(1)).toEqual(1.5);
+    expect(scale(2)).toEqual(2.5);
 });
 
 test("Scale scales correctly with custom domain and range", () => {
-    const scale = scaleIndex().domain([0, 10]).range([100, 200]);
+    const scale = scaleIndex().domain([0, 10]).range([100, 200]).align(0.0);
 
     expect(scale(0)).toEqual(100);
     expect(scale(10)).toEqual(200);
 });
 
 test("Invert works as expected", () => {
-    const scale = scaleIndex().domain([0, 10]).range([100, 200]);
+    const scale = scaleIndex().domain([0, 10]).range([100, 200]).align(0.0);
+
+    expect(scale.invert(scale(0))).toEqual(0);
+    expect(scale.invert(scale(5))).toEqual(5);
+    expect(scale.invert(scale(10))).toEqual(10);
+});
+
+test("Scale scales correctly with custom domain, range, and align", () => {
+    const scale = scaleIndex().domain([0, 10]).range([100, 200]).align(0.5);
+
+    expect(scale(0)).toEqual(105);
+    expect(scale(10)).toEqual(205);
+});
+
+test("Invert works as expected with align", () => {
+    const scale = scaleIndex().domain([0, 10]).range([100, 200]).align(0.5);
 
     expect(scale.invert(scale(0))).toEqual(0);
     expect(scale.invert(scale(5))).toEqual(5);

package/src/genome/scaleLocus.test.js

@@ -1,3 +1,4 @@
+import { test } from "vitest";
 import scaleLocus from "./scaleLocus";
 
 test.todo("Write some tests!");

package/src/gl/dataToVertices.js

@@ -1,12 +1,15 @@
 import { InternMap } from "internmap";
 import { format } from "d3-format";
 import { isString } from "vega-util";
-import { fp64ify } from "./includes/fp64-utils";
 import ArrayBuilder from "./arrayBuilder";
 import { SDF_PADDING } from "../fonts/bmFontMetrics";
 import { peek } from "../utils/arrayUtils";
 import createBinningRangeIndexer from "../utils/binnedRangeIndex";
 import { isValueDef } from "../encoder/encoder";
+import {
+    isHighPrecisionScale,
+    splitHighPrecision,
+} from "../scale/glslScaleGenerator";
 
 /**
  * @typedef {object} RangeEntry Represents a location of a vertex subset
@@ -55,7 +58,7 @@ export class GeometryBuilder {
             const accessor = ce.accessor;
 
             const doubleArray = [0, 0];
-            const fp64 = ce.scale.fp64;
+            const hp = isHighPrecisionScale(ce.scale.type);
 
             const indexer = ce.indexer;
 
@@ -68,14 +71,14 @@ export class GeometryBuilder {
              */
             const f = indexer
                 ? (d) => indexer(accessor(d))
-                : fp64
-                ? (d) => fp64ify(accessor(d), doubleArray)
+                : hp
+                ? (d) => splitHighPrecision(accessor(d), doubleArray)
                 : accessor;
 
             this.variableBuilder.addConverter(channel, {
                 f,
-                numComponents: fp64 ? 2 : 1,
-                arrayReference: fp64 ? doubleArray : undefined,
+                numComponents: hp ? 2 : 1,
+                arrayReference: hp ? doubleArray : undefined,
             });
         }
 

package/src/gl/includes/common.glsl

@@ -1,12 +1,12 @@
 #define PI 3.141593
 
 /** Offset in "unit" units */
-uniform vec2 uViewOffset;
+uniform mediump vec2 uViewOffset;
 
-uniform vec2 uViewScale;
+uniform mediump vec2 uViewScale;
 
 /** Size of the logical viewport in pixels, i.e., the view */
-uniform vec2 uViewportSize;
+uniform mediump vec2 uViewportSize;
 
 uniform lowp float uDevicePixelRatio;
 

package/src/gl/includes/scales.glsl

@@ -1,3 +1,5 @@
+const float inf = 1.0 / 0.0;
+
 // Utils ------------
 
 vec3 getDiscreteColor(sampler2D s, int index) {
@@ -67,15 +69,44 @@ float scaleBand(float value, vec2 domainExtent, vec2 range,
     // TODO: reverse
     float start = range[0];
     float stop = range[1];
+    float rangeSpan = stop - start;
 
     float n = domainExtent[1] - domainExtent[0];
 
+    // This fix departs from Vega and d3: https://github.com/vega/vega/issues/3357#issuecomment-1063253596
     paddingInner = int(n) > 1 ? paddingInner : 0.0;
 
     // Adapted from: https://github.com/d3/d3-scale/blob/master/src/band.js
-    float step = (stop - start) / max(1.0, n - paddingInner + paddingOuter * 2.0);
-    start += (stop - start - step * (n - paddingInner)) * align;
+    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;
 }
+
+// High precision variant of scaleBand for index/locus scales
+float scaleBandHp(vec2 value, vec3 domainExtent, vec2 range,
+                 float paddingInner, float paddingOuter,
+                 float align, float band) {
+
+    // TODO: reverse
+    float start = range[0];
+    float stop = range[1];
+    float rangeSpan = stop - start;
+
+    vec2 domainStart = domainExtent.xy;
+    float n = domainExtent[2];
+
+    // The following computation is identical for every vertex. Could be done on the JS side.
+    float step = rangeSpan / max(1.0, n - paddingInner + paddingOuter * 2.0);
+    start += (rangeSpan - step * (n - paddingInner)) * align;
+    float bandwidth = step * (1.0 - paddingInner);
+
+    // Using max to prevent the shader compiler from wrecking the precision.
+    // Othwewise the compiler could optimize the sum of the four terms into
+    // some equivalent form that does premature rounding.
+    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));
+}

package/src/gl/point.vertex.glsl

@@ -1,5 +1,3 @@
-precision mediump float;
-
 /**
  * The stroke should only grow inwards, e.g, the diameter/outline is not affected by the stroke width.
  * Thus, a point that has a zero size has no visible stroke. This allows strokes to be used with

package/src/gl/rule.vertex.glsl

@@ -12,7 +12,7 @@ in float side;
 /** Minimum rule length in pixels */
 uniform float uMinLength;
 
-uniform float uDashTextureSize;
+uniform mediump float uDashTextureSize;
 uniform lowp int uStrokeCap;
 
 flat out vec4 vColor;

package/src/gl/webGLHelper.js

@@ -8,7 +8,6 @@ import {
     setTextureFromArray,
 } from "twgl.js";
 import { isArray, isString } from "vega-util";
-import { getPlatformShaderDefines } from "./includes/fp64-utils";
 
 import { isDiscrete, isDiscretizing, isInterpolating } from "vega-scale";
 import {
@@ -81,8 +80,6 @@ export default class WebGLHelper {
         // Always use pre-multiplied alpha
         gl.blendFunc(gl.ONE, gl.ONE_MINUS_SRC_ALPHA);
 
-        this._shaderDefines = getPlatformShaderDefines(gl);
-
         this.canvas = canvas;
         this.gl = gl;
 

package/src/marks/mark.js

@@ -8,7 +8,6 @@ import {
     setUniforms,
 } from "twgl.js";
 import { isDiscrete } from "vega-scale";
-import { fp64ify } from "../gl/includes/fp64-utils";
 import createEncoders, {
     isChannelDefWithScale,
     isDatumDef,
@@ -20,11 +19,12 @@ import {
     generateScaleGlsl,
     RANGE_TEXTURE_PREFIX,
     ATTRIBUTE_PREFIX,
+    isHighPrecisionScale,
+    toHighPrecisionDomainUniform,
+    splitHighPrecision,
 } from "../scale/glslScaleGenerator";
-import FP64 from "../gl/includes/fp64-arithmetic.glsl";
 import GLSL_COMMON from "../gl/includes/common.glsl";
 import GLSL_SCALES from "../gl/includes/scales.glsl";
-import GLSL_SCALES_FP64 from "../gl/includes/scales_fp64.glsl";
 import GLSL_SAMPLE_FACET from "../gl/includes/sampleFacet.glsl";
 import GLSL_PICKING_VERTEX from "../gl/includes/picking.vertex.glsl";
 import GLSL_PICKING_FRAGMENT from "../gl/includes/picking.fragment.glsl";
@@ -334,7 +334,10 @@ export default class Mark {
               "};\n\n"
             : "";
 
+        const vertexPrecision = "precision highp float;\n";
+
         const vertexParts = [
+            vertexPrecision,
             ...extraHeaders,
             GLSL_COMMON,
             GLSL_SCALES,
@@ -345,11 +348,6 @@ export default class Mark {
             vertexShader,
         ];
 
-        if (vertexParts.some((code) => /[Ff]p64/.test(code))) {
-            vertexParts.unshift(GLSL_SCALES_FP64);
-            vertexParts.unshift(FP64);
-        }
-
         const fragmentParts = [
             ...extraHeaders,
             GLSL_COMMON,
@@ -413,8 +411,8 @@ export default class Mark {
 
                 const datum = encoder.indexer
                     ? encoder.indexer(channelDef.datum)
-                    : encoder.scale.fp64
-                    ? fp64ify(+channelDef.datum)
+                    : isHighPrecisionScale(encoder.scale.type)
+                    ? splitHighPrecision(+channelDef.datum)
                     : +channelDef.datum;
 
                 setUniforms(this.programInfo, {
@@ -579,8 +577,8 @@ export default class Mark {
                         : scale.domain();
 
                     setter(
-                        scale.fp64
-                            ? domain.map((x) => fp64ify(x)).flat()
+                        isHighPrecisionScale(scale.type)
+                            ? toHighPrecisionDomainUniform(domain)
                             : domain
                     );
                 }
@@ -624,7 +622,6 @@ export default class Mark {
         }
 
         setUniforms(this.programInfo, {
-            ONE: 1.0, // a hack needed by emulated 64 bit floats
             uDevicePixelRatio: this.glHelper.dpr,
             uViewOpacity: this.unitView.getEffectiveOpacity(),
             // TODO: Rendering of the mark should be completely skipped if it doesn't