@genome-spy/core 0.74.0 → 0.76.0

package/dist/src/config/defaults/markDefaults.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"markDefaults.d.ts","sourceRoot":"","sources":["../../../../src/config/defaults/markDefaults.js"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,4BADW,OAAO,sBAAsB,EAAE,UAAU,CAKlD;AAEF,yDAAyD;AACzD,kCADW,OAAO,sBAAsB,EAAE,WAAW,CAkBnD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CAYlD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CAWlD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CAUlD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CAiClD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CAmBlD"}
+{"version":3,"file":"markDefaults.d.ts","sourceRoot":"","sources":["../../../../src/config/defaults/markDefaults.js"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,4BADW,OAAO,sBAAsB,EAAE,UAAU,CAMlD;AAEF,yDAAyD;AACzD,kCADW,OAAO,sBAAsB,EAAE,WAAW,CAgBnD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CAUlD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CASlD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CAQlD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CA+BlD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CAiBlD"}

package/dist/src/config/defaults/markDefaults.js

@@ -3,15 +3,14 @@ export const MARK_DEFAULTS = {
     xOffset: 0,
     yOffset: 0,
     minBufferSize: 0,
+    opacity: 1.0,
 };
 
 /** @type {import("../../spec/config.js").PointConfig} */
 export const POINT_MARK_DEFAULTS = {
     x: 0.5,
     y: 0.5,
-    color: "#4c78a8",
     filled: true,
-    opacity: 1.0,
     size: 100.0,
     semanticScore: 0.0,
     shape: "circle",
@@ -30,8 +29,6 @@ export const RECT_MARK_DEFAULTS = {
     x2: undefined,
     y2: undefined,
     filled: true,
-    color: "#4c78a8",
-    opacity: 1.0,
     strokeWidth: 3,
     cornerRadius: 0.0,
     minWidth: 0.5,
@@ -44,8 +41,6 @@ export const RULE_MARK_DEFAULTS = {
     x2: undefined,
     y2: undefined,
     size: 1,
-    color: "black",
-    opacity: 1.0,
     minLength: 0.0,
     strokeDash: null,
     strokeDashOffset: 0,
@@ -54,8 +49,6 @@ export const RULE_MARK_DEFAULTS = {
 
 /** @type {import("../../spec/config.js").TickConfig} */
 export const TICK_MARK_DEFAULTS = {
-    color: "black",
-    opacity: 1.0,
     minLength: 0.0,
     strokeDash: null,
     strokeDashOffset: 0,
@@ -72,8 +65,6 @@ export const TEXT_MARK_DEFAULTS = {
     y2: undefined,
     text: "",
     size: 11.0,
-    color: "black",
-    opacity: 1.0,
     font: undefined,
     fontStyle: undefined,
     fontWeight: undefined,
@@ -106,8 +97,6 @@ export const LINK_MARK_DEFAULTS = {
     y: 0.0,
     y2: undefined,
     size: 1.0,
-    color: "black",
-    opacity: 1.0,
     segments: 101,
     arcHeightFactor: 1.0,
     minArcHeight: 1.5,

package/dist/src/config/defaults/scaleDefaults.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"scaleDefaults.d.ts","sourceRoot":"","sources":["../../../../src/config/defaults/scaleDefaults.js"],"names":[],"mappings":"AAAA,yDAAyD;AACzD,6BADW,OAAO,sBAAsB,EAAE,WAAW,CAUnD;AAEF,yDAAyD;AACzD,6BADW,OAAO,sBAAsB,EAAE,WAAW,CAKnD"}
+{"version":3,"file":"scaleDefaults.d.ts","sourceRoot":"","sources":["../../../../src/config/defaults/scaleDefaults.js"],"names":[],"mappings":"AAAA,yDAAyD;AACzD,6BADW,OAAO,sBAAsB,EAAE,WAAW,CAUnD;AAEF,yDAAyD;AACzD,6BADW,OAAO,sBAAsB,EAAE,WAAW,CAMnD"}

package/dist/src/config/defaults/scaleDefaults.js

@@ -15,4 +15,5 @@ export const RANGE_DEFAULTS = {
     shape: ["circle", "square", "triangle-up", "cross", "diamond"],
     size: [0, 400],
     angle: [0, 360],
+    heatmap: "yellowgreenblue",
 };

package/dist/src/config/markConfig.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"markConfig.d.ts","sourceRoot":"","sources":["../../../src/config/markConfig.js"],"names":[],"mappings":"AAGA;;;;;GAKG;AACH,kDALW,OAAO,mBAAmB,EAAE,eAAe,EAAE,YAC7C,OAAO,iBAAiB,EAAE,QAAQ,SAClC,MAAM,GAAG,MAAM,EAAE,GAAG,SAAS,GAC3B,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,CAmB/B"}
+{"version":3,"file":"markConfig.d.ts","sourceRoot":"","sources":["../../../src/config/markConfig.js"],"names":[],"mappings":"AAGA;;;;;GAKG;AACH,kDALW,OAAO,mBAAmB,EAAE,eAAe,EAAE,YAC7C,OAAO,iBAAiB,EAAE,QAAQ,SAClC,MAAM,GAAG,MAAM,EAAE,GAAG,SAAS,GAC3B,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,CA2B/B"}

package/dist/src/config/markConfig.js

@@ -12,16 +12,24 @@ export function getConfiguredMarkDefaults(scopes, markType, style) {
     // part of style resolution, and explicit mark.style entries augment it.
     const styles = [markType, ...normalizeStyle(style)];
 
-    return mergeConfigScopes(
-        scopes.flatMap((scope) => [
-            /** @type {Record<string, any> | undefined} */ (scope.mark),
-            /** @type {Record<string, any> | undefined} */ (scope[markType]),
-            ...styles.map(
+    const genericBuckets = scopes.map(
+        (scope) => /** @type {Record<string, any> | undefined} */ (scope.mark)
+    );
+    const markTypeBuckets = scopes.map(
+        (scope) =>
+            /** @type {Record<string, any> | undefined} */ (scope[markType])
+    );
+
+    return mergeConfigScopes([
+        ...genericBuckets,
+        ...markTypeBuckets,
+        ...scopes.flatMap((scope) =>
+            styles.map(
                 (styleName) =>
                     /** @type {Record<string, any> | undefined} */ (
                         scope.style?.[styleName]
                     )
-            ),
-        ])
-    );
+            )
+        ),
+    ]);
 }

package/dist/src/config/themes.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"themes.d.ts","sourceRoot":"","sources":["../../../src/config/themes.js"],"names":[],"mappings":"AA+QA;;;GAGG;AACH,gDAHW,OAAO,mBAAmB,EAAE,gBAAgB,GAC1C,MAAM,GAAG,SAAS,CAI9B;AAED;;;GAGG;AACH,iDAHW,OAAO,mBAAmB,EAAE,gBAAgB,GAAG,OAAO,mBAAmB,EAAE,gBAAgB,EAAE,GAAG,SAAS,GACvG,OAAO,mBAAmB,EAAE,eAAe,GAAG,SAAS,CAWnE;AA1BD;;GAEG;AACH,iCAFU,OAAO,mBAAmB,EAAE,gBAAgB,CAER"}
+{"version":3,"file":"themes.d.ts","sourceRoot":"","sources":["../../../src/config/themes.js"],"names":[],"mappings":"AA4RA;;;GAGG;AACH,gDAHW,OAAO,mBAAmB,EAAE,gBAAgB,GAC1C,MAAM,GAAG,SAAS,CAI9B;AAED;;;GAGG;AACH,iDAHW,OAAO,mBAAmB,EAAE,gBAAgB,GAAG,OAAO,mBAAmB,EAAE,gBAAgB,EAAE,GAAG,SAAS,GACvG,OAAO,mBAAmB,EAAE,eAAe,GAAG,SAAS,CAWnE;AA1BD;;GAEG;AACH,iCAFU,OAAO,mBAAmB,EAAE,gBAAgB,CAER"}

package/dist/src/config/themes.js

@@ -39,7 +39,7 @@ const VEGALITE_THEME = {
         quantitativeColorScheme: "blues",
     },
     range: {
-        heatmap: "viridis",
+        heatmap: "yellowgreenblue",
         ramp: "blues",
         diverging: "blueorange",
     },
@@ -59,7 +59,20 @@ const VEGALITE_THEME = {
  * @type {Record<import("../spec/config.js").BuiltInThemeName, import("../spec/config.js").GenomeSpyConfig & { background?: string}>}
  */
 const BUILT_IN_THEME_DEFINITIONS = {
-    genomespy: {},
+    genomespy: {
+        mark: {
+            color: "#4c78a8",
+        },
+        rule: {
+            color: "black",
+        },
+        text: {
+            color: "black",
+        },
+        link: {
+            color: "black",
+        },
+    },
     vegalite: VEGALITE_THEME,
     quartz: mergeConfigScopes([
         VEGALITE_THEME,

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

@@ -8,10 +8,12 @@
  */
 export function getFormat(params: import("../../spec/data.js").DataSource, urls?: string | string[]): {
     type?: "csv" | "tsv";
+    columns?: string[];
     parse?: import("../../spec/data.js").Parse | null;
 } | {
     type?: "dsv";
     delimiter: string;
+    columns?: string[];
     parse?: import("../../spec/data.js").Parse | null;
 } | {
     type?: "json";
@@ -28,6 +30,29 @@ export function getFormat(params: import("../../spec/data.js").DataSource, urls?
     type: string;
     parse?: import("../../spec/data.js").Parse | null;
 };
+/**
+ * Vega's DSV readers support synthetic header rows via `format.header`.
+ * GenomeSpy exposes the user-facing option as `format.columns`.
+ *
+ * @param {import("../../spec/data.js").DataFormat} format
+ */
+export function toVegaLoaderFormat(format: import("../../spec/data.js").DataFormat): {
+    type?: "csv" | "tsv";
+    columns?: string[];
+    parse?: import("../../spec/data.js").Parse | null;
+} | {
+    type?: "dsv";
+    delimiter: string;
+    columns?: string[];
+    parse?: import("../../spec/data.js").Parse | null;
+} | {
+    type?: "json";
+    property?: string;
+    parse?: import("../../spec/data.js").Parse | null;
+} | {
+    type: string;
+    parse?: import("../../spec/data.js").Parse | null;
+};
 /**
  * @param {string} type
  * @returns {string}

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

@@ -1 +1 @@
-{"version":3,"file":"dataUtils.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/dataUtils.js"],"names":[],"mappings":"AAMA;;;;;;;GAOG;AACH,kCAJW,OAAO,oBAAoB,EAAE,UAAU,SAEvC,MAAM,GAAG,MAAM,EAAE;;;;;;;;;;;;;;;;;;;;;EAsB3B;AAED;;;GAGG;AACH,mCAHW,MAAM,GACJ,MAAM,CAIlB;AAED;;GAEG;AACH,wCAFW,MAAM,GAAG,MAAM,EAAE,UA2B3B;AAED;;GAEG;AACH,sCAFW,MAAM,WAWhB;AAkBD;;;GAGG;AACH,4CAHW,OAAO,oBAAoB,EAAE,UAAU,GACtC,UAAU,IAAI,OAAO,oBAAoB,EAAE,aAAa,CAInE;AAED;;;GAGG;AACH,4CAHW,OAAO,oBAAoB,EAAE,UAAU,GACtC,UAAU,IAAI,OAAO,oBAAoB,EAAE,aAAa,CAInE;AAED;;;GAGG;AACH,6CAHW,OAAO,oBAAoB,EAAE,UAAU,GACtC,UAAU,IAAI,OAAO,oBAAoB,EAAE,cAAc,CAIpE;AAED;;;;GAIG;AACH,sCAHW,OAAO,oBAAoB,EAAE,UAAU,GACtC,UAAU,IAAI,OAAO,oBAAoB,EAAE,OAAO,CAI7D;AAED;;GAEG;AACH,wCAFW,MAAM,GAAG,SAAS,WAI5B;AA/CM,+BAAgC,GAAG,QAI3B,OAAO,uBAAuB,EAAE,MAAM;;UAGtB,OAAO,gBAAgB,EAAE,KAAK,qCANR"}
+{"version":3,"file":"dataUtils.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/dataUtils.js"],"names":[],"mappings":"AAMA;;;;;;;GAOG;AACH,kCAJW,OAAO,oBAAoB,EAAE,UAAU,SAEvC,MAAM,GAAG,MAAM,EAAE;;;;;;;;;;;;;;;;;;;;;;;EAsB3B;AAED;;;;;GAKG;AACH,2CAFW,OAAO,oBAAoB,EAAE,UAAU;;;;;;;;;;;;;;;;EAiBjD;AAED;;;GAGG;AACH,mCAHW,MAAM,GACJ,MAAM,CAIlB;AAED;;GAEG;AACH,wCAFW,MAAM,GAAG,MAAM,EAAE,UA2B3B;AAED;;GAEG;AACH,sCAFW,MAAM,WAWhB;AAkBD;;;GAGG;AACH,4CAHW,OAAO,oBAAoB,EAAE,UAAU,GACtC,UAAU,IAAI,OAAO,oBAAoB,EAAE,aAAa,CAInE;AAED;;;GAGG;AACH,4CAHW,OAAO,oBAAoB,EAAE,UAAU,GACtC,UAAU,IAAI,OAAO,oBAAoB,EAAE,aAAa,CAInE;AAED;;;GAGG;AACH,6CAHW,OAAO,oBAAoB,EAAE,UAAU,GACtC,UAAU,IAAI,OAAO,oBAAoB,EAAE,cAAc,CAIpE;AAED;;;;GAIG;AACH,sCAHW,OAAO,oBAAoB,EAAE,UAAU,GACtC,UAAU,IAAI,OAAO,oBAAoB,EAAE,OAAO,CAI7D;AAED;;GAEG;AACH,wCAFW,MAAM,GAAG,SAAS,WAI5B;AA/CM,+BAAgC,GAAG,QAI3B,OAAO,uBAAuB,EAAE,MAAM;;UAGtB,OAAO,gBAAgB,EAAE,KAAK,qCANR"}

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

@@ -34,6 +34,29 @@ export function getFormat(params, urls = []) {
     return format;
 }
 
+/**
+ * Vega's DSV readers support synthetic header rows via `format.header`.
+ * GenomeSpy exposes the user-facing option as `format.columns`.
+ *
+ * @param {import("../../spec/data.js").DataFormat} format
+ */
+export function toVegaLoaderFormat(format) {
+    const readFormat = { ...format };
+
+    if (
+        (isCsvDataFormat(readFormat) || isDsvDataFormat(readFormat)) &&
+        readFormat.columns &&
+        !("header" in readFormat)
+    ) {
+        // @ts-ignore Vega loader supports `header`, but the public data format
+        // type intentionally exposes the GenomeSpy-level `columns` property
+        // instead.
+        readFormat.header = readFormat.columns;
+    }
+
+    return readFormat;
+}
+
 /**
  * @param {string} type
  * @returns {string}

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

@@ -1,5 +1,5 @@
 import { read } from "vega-loader";
-import { getFormat, makeWrapper } from "./dataUtils.js";
+import { getFormat, makeWrapper, toVegaLoaderFormat } from "./dataUtils.js";
 import DataSource from "./dataSource.js";
 
 /**
@@ -79,7 +79,7 @@ export default class InlineSource extends DataSource {
             data = [values];
         } else if (typeof values == "string") {
             // It's a string that needs to be parsed
-            data = read(values, getFormat(this.params));
+            data = read(values, toVegaLoaderFormat(getFormat(this.params)));
         } else {
             throw new Error(
                 '"values" in data configuration is not an array, object, or a string!'

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

@@ -1,8 +1,8 @@
-import "./axisTickSource.js";
-import "./axisGenomeSource.js";
+import "./registerCoreLazySources.js";
 import "./indexedFastaSource.js";
 import "./bigWigSource.js";
 import "./bigBedSource.js";
 import "./bamSource.js";
+import "./tabixTsvSource.js";
 import "./gff3Source.js";
 import "./vcfSource.js";

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

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

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

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

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

@@ -0,0 +1,2 @@
+import "./axisTickSource.js";
+import "./axisGenomeSource.js";

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

@@ -14,6 +14,13 @@ export default class TabixSource<T> extends SingleAxisWindowedSource {
      * @protected
      */
     protected _handleHeader(header: string): Promise<void>;
+    /**
+     * Read a prefix of the Tabix file and decode it as text.
+     *
+     * @returns {Promise<string>}
+     * @protected
+     */
+    protected _readFilePrefix(): Promise<string>;
     /**
      * @abstract
      * @protected

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

@@ -1 +1 @@
-{"version":3,"file":"tabixSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/tabixSource.js"],"names":[],"mappings":"AAOA;;;GAGG;AACH,iCAHa,CAAC;IAOV;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,SAAS,QACzC,OAAO,uBAAuB,EAAE,OAAO,EAyCjD;IAzBG,kDAgBC;IA0FL;;;OAGG;IACH,gCAHW,MAAM,iBAKhB;IAED;;;;;OAKG;IACH,gCAHW,MAAM,EAAE,GACN,CAAC,EAAE,CAKf;;CACJ;qCAxJoC,+BAA+B"}
+{"version":3,"file":"tabixSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/tabixSource.js"],"names":[],"mappings":"AAQA;;;GAGG;AACH,iCAHa,CAAC;IAOV;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,SAAS,QACzC,OAAO,uBAAuB,EAAE,OAAO,EAyCjD;IAzBG,kDAgBC;IA0FL;;;OAGG;IACH,gCAHW,MAAM,iBAKhB;IAED;;;;;OAKG;IACH,6BAHa,OAAO,CAAC,MAAM,CAAC,CAY3B;IAED;;;;;OAKG;IACH,gCAHW,MAAM,EAAE,GACN,CAAC,EAAE,CAKf;;CACJ;qCAzKoC,+BAA+B"}

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

@@ -1,3 +1,4 @@
+import { unzip } from "@gmod/bgzf-filehandle";
 import {
     activateExprRefProps,
     withoutExprRef,
@@ -145,6 +146,23 @@ export default class TabixSource extends SingleAxisWindowedSource {
         //
     }
 
+    /**
+     * Read a prefix of the Tabix file and decode it as text.
+     *
+     * @returns {Promise<string>}
+     * @protected
+     */
+    async _readFilePrefix() {
+        const { maxBlockSize } = await this.#tbiIndex.getMetadata();
+        const tbiIndex = /** @type {any} */ (this.#tbiIndex);
+        const compressedPrefix = await tbiIndex.filehandle.read(
+            maxBlockSize,
+            0
+        );
+        const bytes = await unzip(compressedPrefix);
+        return new TextDecoder("utf-8").decode(bytes);
+    }
+
     /**
      * @abstract
      * @protected

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

@@ -0,0 +1,37 @@
+/**
+ * Extract a TSV header from a tabix file header.
+ *
+ * Tabix headers commonly end with a commented column line such as
+ * `#chrom\tstart\tend\tvalue`.
+ *
+ * @param {string} header
+ * @returns {string[] | undefined}
+ */
+export function extractTabixTsvColumns(header: string): string[] | undefined;
+/**
+ * Extract a TSV header from the first line of a plain tabix file prefix.
+ *
+ * This is used when the file does not have a commented header line, but the
+ * first physical line still contains column names.
+ *
+ * @param {string} text
+ * @returns {string[] | undefined}
+ */
+export function extractTabixTsvColumnsFromFirstLine(text: string): string[] | undefined;
+/**
+ * Parse tabix TSV records into plain objects.
+ *
+ * @param {string[]} lines
+ * @param {string[]} columns
+ * @param {import("../../../spec/data.js").Parse | null | undefined} [parse]
+ */
+export function parseTabixTsvLines(lines: string[], columns: string[], parse?: import("../../../spec/data.js").Parse | null | undefined): Record<string, any>[];
+/**
+ * @extends {TabixSource<Record<string, any>>}
+ */
+export default class TabixTsvSource extends TabixSource<Record<string, any>> {
+    constructor(params: import("../../../spec/data.js").TabixData, view: import("../../../view/view.js").default);
+    #private;
+}
+import TabixSource from "./tabixSource.js";
+//# sourceMappingURL=tabixTsvSource.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"tabixTsvSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/tabixTsvSource.js"],"names":[],"mappings":"AAMA;;;;;;;;GAQG;AACH,+CAHW,MAAM,GACJ,MAAM,EAAE,GAAG,SAAS,CAsBhC;AAED;;;;;;;;GAQG;AACH,0DAHW,MAAM,GACJ,MAAM,EAAE,GAAG,SAAS,CAkBhC;AAED;;;;;;GAMG;AACH,0CAJW,MAAM,EAAE,WACR,MAAM,EAAE,UACR,OAAO,uBAAuB,EAAE,KAAK,GAAG,IAAI,GAAG,SAAS,yBAgClE;AAED;;GAEG;AACH;;;CA8CC;wBApJuB,kBAAkB"}

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

@@ -0,0 +1,163 @@
+import { read } from "vega-loader";
+import { withoutExprRef } from "../../../paramRuntime/paramUtils.js";
+import { toVegaLoaderFormat } from "../dataUtils.js";
+import { registerBuiltInLazyDataSource } from "./lazyDataSourceRegistry.js";
+import TabixSource from "./tabixSource.js";
+
+/**
+ * Extract a TSV header from a tabix file header.
+ *
+ * Tabix headers commonly end with a commented column line such as
+ * `#chrom\tstart\tend\tvalue`.
+ *
+ * @param {string} header
+ * @returns {string[] | undefined}
+ */
+export function extractTabixTsvColumns(header) {
+    const lines = header.split(/\r?\n/);
+
+    for (let i = lines.length - 1; i >= 0; i--) {
+        const line = lines[i].trimEnd().replace(/\r$/, "");
+
+        if (!line || line.startsWith("##")) {
+            continue;
+        }
+
+        if (!line.startsWith("#")) {
+            continue;
+        }
+
+        const columns = line.slice(1).split("\t");
+
+        if (columns.length > 1) {
+            return columns;
+        }
+    }
+}
+
+/**
+ * Extract a TSV header from the first line of a plain tabix file prefix.
+ *
+ * This is used when the file does not have a commented header line, but the
+ * first physical line still contains column names.
+ *
+ * @param {string} text
+ * @returns {string[] | undefined}
+ */
+export function extractTabixTsvColumnsFromFirstLine(text) {
+    const lines = text.split(/\r?\n/);
+
+    const firstLine = lines.find((line) => {
+        const trimmed = line.trimStart();
+        return trimmed !== "" && !trimmed.startsWith("#");
+    });
+
+    if (!firstLine) {
+        return;
+    }
+
+    const columns = firstLine.trimEnd().replace(/\r$/, "").split("\t");
+    if (columns.length > 1) {
+        return columns;
+    }
+}
+
+/**
+ * Parse tabix TSV records into plain objects.
+ *
+ * @param {string[]} lines
+ * @param {string[]} columns
+ * @param {import("../../../spec/data.js").Parse | null | undefined} [parse]
+ */
+export function parseTabixTsvLines(lines, columns, parse) {
+    if (lines.length == 0) {
+        return [];
+    }
+
+    /** @type {any} */
+    const format = {
+        type: "tsv",
+        columns,
+        parse: parse ?? "auto",
+    };
+
+    /** @type {Record<string, any>[]} */
+    const data = read(lines.join("\n"), toVegaLoaderFormat(format));
+
+    const chromField = columns[0];
+    /** @type {unknown} */
+    let prev = null;
+    let stringChrom = "";
+
+    for (const datum of data) {
+        const value = datum[chromField];
+        if (value != prev) {
+            prev = value;
+            stringChrom = String(value);
+        }
+        datum[chromField] = stringChrom;
+    }
+
+    return data;
+}
+
+/**
+ * @extends {TabixSource<Record<string, any>>}
+ */
+export default class TabixTsvSource extends TabixSource {
+    /** @type {string[] | undefined} */
+    #columns;
+
+    get label() {
+        return "tabixSource";
+    }
+
+    /**
+     * @param {string} header
+     */
+    async _handleHeader(header) {
+        const params =
+            /** @type {import("../../../spec/data.js").TabixTsvData} */ (
+                this.params
+            );
+        const columns = withoutExprRef(params.columns);
+        this.#columns = columns ?? extractTabixTsvColumns(header);
+
+        if (!this.#columns?.length) {
+            this.#columns = extractTabixTsvColumnsFromFirstLine(
+                await this._readFilePrefix()
+            );
+        }
+
+        if (!this.#columns?.length) {
+            throw new Error(
+                "No columns available for Tabix TSV source. Provide data.lazy.columns or a tabix header line such as #chrom\\tstart\\tend, or a plain first row such as chrom\\tstart\\tend."
+            );
+        }
+    }
+
+    /**
+     * @param {string[]} lines
+     */
+    _parseFeatures(lines) {
+        const params =
+            /** @type {import("../../../spec/data.js").TabixTsvData} */ (
+                this.params
+            );
+        return parseTabixTsvLines(
+            lines,
+            this.#columns ?? [],
+            withoutExprRef(params.parse)
+        );
+    }
+}
+
+/**
+ * @param {import("../../../spec/data.js").LazyDataParams} params
+ * @returns {params is import("../../../spec/data.js").TabixTsvData}
+ */
+function isTabixTsvSource(params) {
+    return params?.type == "tabix";
+}
+
+registerBuiltInLazyDataSource(isTabixTsvSource, TabixTsvSource);

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

@@ -1 +1 @@
-{"version":3,"file":"urlSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/urlSource.js"],"names":[],"mappings":"AAkJA;;;GAGG;AACH,gCAHW,OAAO,CAAC,OAAO,oBAAoB,EAAE,IAAI,CAAC,GACxC,IAAI,IAAI,OAAO,oBAAoB,EAAE,OAAO,CAIxD;AA5ID;;;GAGG;AACH;IACI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,OAAO,QACpC,OAAO,oBAAoB,EAAE,OAAO,EAc9C;IATG,6CAMC;IAED,gBAAiC;;CAgHxC;uBA9IsB,iBAAiB"}
+{"version":3,"file":"urlSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/urlSource.js"],"names":[],"mappings":"AAuJA;;;GAGG;AACH,gCAHW,OAAO,CAAC,OAAO,oBAAoB,EAAE,IAAI,CAAC,GACxC,IAAI,IAAI,OAAO,oBAAoB,EAAE,OAAO,CAIxD;AA5ID;;;GAGG;AACH;IACI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,OAAO,QACpC,OAAO,oBAAoB,EAAE,OAAO,EAc9C;IATG,6CAMC;IAED,gBAAiC;;CAgHxC;uBA9IsB,iBAAiB"}

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

@@ -1,5 +1,10 @@
 import { read } from "vega-loader";
-import { getFormat, hasGzipExtension, responseType } from "./dataUtils.js";
+import {
+    getFormat,
+    hasGzipExtension,
+    responseType,
+    toVegaLoaderFormat,
+} from "./dataUtils.js";
 import DataSource from "./dataSource.js";
 import {
     activateExprRefProps,
@@ -63,7 +68,7 @@ export default class UrlSource extends DataSource {
         );
 
         const files = /** @type {string[] | {url: string}[]} */ (
-            read(content, format)
+            read(content, toVegaLoaderFormat(format))
         )
             .map((u) => (typeof u === "string" ? u : u.url))
             .map((u) => concatUrl(listUrl, u));
@@ -114,7 +119,7 @@ export default class UrlSource extends DataSource {
         const readAndParse = async (content, url) => {
             try {
                 /** @type {any[] | Promise<any[]>} */
-                const dataOrPromise = read(content, format);
+                const dataOrPromise = read(content, toVegaLoaderFormat(format));
                 const data =
                     dataOrPromise instanceof Promise
                         ? await dataOrPromise

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

@@ -97,12 +97,12 @@ export function isChannelDefWithScale(channelDef: import("../spec/channel.js").C
 /**
  * @param {import("../spec/channel.js").ChannelDef} channelDef
  */
-export function findChannelDefWithScale(channelDef: import("../spec/channel.js").ChannelDef): import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, number> | import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, string> | import("../spec/channel.js").PositionFieldDef | import("../spec/channel.js").ChromPosDef | import("../spec/channel.js").PositionDatumDef | import("../spec/channel.js").Conditional<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>> | import("../spec/channel.js").Conditional<import("../spec/channel.js").MarkPropExprDef<import("../spec/channel.js").Type>>;
+export function findChannelDefWithScale(channelDef: import("../spec/channel.js").ChannelDef): import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, number> | import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, string> | import("../spec/channel.js").PositionFieldDef | import("../spec/channel.js").ChromPosDef | import("../spec/channel.js").PositionDatumDef | import("../spec/channel.js").MarkPropExprDef<import("../spec/channel.js").Type> | import("../spec/channel.js").Conditional<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>>;
 /**
  * @param {import("../view/unitView.js").default} view
  * @param {import("../spec/channel.js").Channel} channel
  */
-export function getChannelDefWithScale(view: import("../view/unitView.js").default, channel: import("../spec/channel.js").Channel): import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, number> | import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, string> | import("../spec/channel.js").PositionFieldDef | import("../spec/channel.js").ChromPosDef | import("../spec/channel.js").PositionDatumDef | import("../spec/channel.js").Conditional<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>> | import("../spec/channel.js").Conditional<import("../spec/channel.js").MarkPropExprDef<import("../spec/channel.js").Type>>;
+export function getChannelDefWithScale(view: import("../view/unitView.js").default, channel: import("../spec/channel.js").Channel): import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, number> | import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, string> | import("../spec/channel.js").PositionFieldDef | import("../spec/channel.js").ChromPosDef | import("../spec/channel.js").PositionDatumDef | import("../spec/channel.js").MarkPropExprDef<import("../spec/channel.js").Type> | import("../spec/channel.js").Conditional<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>>;
 /**
  * @param {import("../spec/channel.js").ChannelDef} channelDef
  * @returns {channelDef is import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type>}

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

@@ -1 +1 @@
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package/dist/src/genome/scaleLocus.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"scaleLocus.d.ts","sourceRoot":"","sources":["../../../src/genome/scaleLocus.js"],"names":[],"mappings":"AASA,2EA2HC;;AASD;;;;GAIG;AACH,8CAJW,OAAO,aAAa,EAAE,OAAO,GAAG;IAAE,MAAM,CAAC,EAAE,MAAM,OAAO,aAAa,EAAE,OAAO,CAAA;CAAE,GAAG,SAAS,SAC5F,MAAM,GACJ,MAAM,GAAG,OAAO,aAAa,EAAE,gBAAgB,CAK3D;AAED;;;;GAIG;AACH,gDAJW,OAAO,aAAa,EAAE,OAAO,GAAG;IAAE,MAAM,CAAC,EAAE,MAAM,OAAO,aAAa,EAAE,OAAO,CAAA;CAAE,GAAG,SAAS,WAC5F,MAAM,GAAG,OAAO,aAAa,EAAE,gBAAgB,GAC7C,MAAM,CAQlB;AAED;;;;GAIG;AACH,mDAJW,OAAO,aAAa,EAAE,OAAO,GAAG;IAAE,MAAM,CAAC,EAAE,MAAM,OAAO,aAAa,EAAE,OAAO,CAAA;CAAE,GAAG,SAAS,YAC5F,OAAO,kBAAkB,EAAE,YAAY,GAAG,OAAO,kBAAkB,EAAE,aAAa,GAChF,MAAM,EAAE,CAQpB;AAED;;;;GAIG;AACH,iDAJW,OAAO,aAAa,EAAE,OAAO,GAAG;IAAE,MAAM,CAAC,EAAE,MAAM,OAAO,aAAa,EAAE,OAAO,CAAA;CAAE,GAAG,SAAS,YAC5F,OAAO,kBAAkB,EAAE,YAAY,GAAG,OAAO,kBAAkB,EAAE,aAAa,GAChF,OAAO,kBAAkB,EAAE,YAAY,GAAG,OAAO,kBAAkB,EAAE,aAAa,CAO9F;AAED;;;GAGG;AACH,+CAHW,OAAO,aAAa,EAAE,OAAO,GAAG;IAAE,MAAM,CAAC,EAAE,MAAM,OAAO,aAAa,EAAE,OAAO,CAAA;CAAE,GAAG,SAAS,GAC1F,MAAM,EAAE,CAQpB"}

package/dist/src/genome/scaleLocus.js

@@ -5,6 +5,7 @@ import scaleIndex from "./scaleIndex.js";
 import { isChromosomalLocus, isChromosomalLocusInterval } from "./genome.js";
 
 const EXACT_LOCUS_LABEL_STEP_THRESHOLD = 1e6;
+const EXACT_LOCUS_LABEL_THINNING_FACTOR = 0.65;
 
 export default function scaleLocus() {
     /** @type {import("./scaleLocus.js").ScaleLocus} */
@@ -39,13 +40,17 @@ export default function scaleLocus() {
 
         const requestedCount = Math.max(
             1,
-            Math.min(count ?? 10, Math.ceil(domainSpan))
+            Math.min(count ?? 10, Math.floor(domainSpan))
         );
 
         let step = tickStep(domain[0], domain[1], requestedCount);
 
         if (step < EXACT_LOCUS_LABEL_STEP_THRESHOLD) {
-            step = tickStep(domain[0], domain[1], requestedCount * 0.65);
+            step = tickStep(
+                domain[0],
+                domain[1],
+                requestedCount * EXACT_LOCUS_LABEL_THINNING_FACTOR
+            );
         }
 
         step = Math.max(1, step);
@@ -89,7 +94,7 @@ export default function scaleLocus() {
         const step = tickStep(
             domain[0],
             domain[1],
-            Math.max(1, Math.min(count ?? 10, Math.ceil(domainSpan)))
+            Math.max(1, Math.min(count ?? 10, Math.floor(domainSpan)))
         );
         // Use higher display precision for smaller spans
         // TODO: max absolute value should be taken into account too. 2.00M vs 200M