@genome-spy/core 0.75.0 → 0.77.0

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/lazy/bigWigSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"bigWigSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/bigWigSource.js"],"names":[],"mappings":"AAQA;;GAEG;AACH;IAOI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,UAAU,QAC1C,OAAO,uBAAuB,EAAE,OAAO,EAoCjD;IArBG,mDAYC;IA+DL;;;;OAIG;IACH,wBAFW,MAAM,EAAE,iBAqBlB;IAED;;;OAGG;IAEH,uBAJW,MAAM,EAAE,kBACR,MAAM,iBA2BhB;;CACJ;qCAhKoC,+BAA+B"}
+{"version":3,"file":"bigWigSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/bigWigSource.js"],"names":[],"mappings":"AAQA;;GAEG;AACH;IAOI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,UAAU,QAC1C,OAAO,uBAAuB,EAAE,OAAO,EAoCjD;IArBG,mDAYC;IA+DL;;;;OAIG;IACH,wBAFW,MAAM,EAAE,iBAqBlB;IAED;;;OAGG;IAEH,uBAJW,MAAM,EAAE,kBACR,MAAM,iBAkChB;;CACJ;qCAvKoC,+BAA+B"}

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

@@ -142,23 +142,30 @@ export default class BigWigSource extends SingleAxisWindowedSource {
     async loadInterval(interval, reductionLevel) {
         const scale =
             1 / 2 / reductionLevel / withoutExprRef(this.params.pixelsPerBin);
-        const featureChunks = await this.discretizeAndLoad(
-            interval,
-            (d, signal) =>
+        const featureChunks = await this.discretizeAndLoad(interval, {
+            load: (d, signal) =>
                 this.#bbi
                     .getFeatures(d.chrom, d.startPos, d.endPos, {
                         scale,
                         signal,
                     })
-                    .then((features) =>
-                        features.map((f) => ({
-                            chrom: d.chrom,
-                            start: f.start,
-                            end: f.end,
-                            score: f.score,
-                        }))
+                    .then((features) => mapFeatures(d.chrom, features)),
+            loadBatch: (intervals, signal) =>
+                this.#bbi
+                    .getFeaturesMulti(
+                        intervals.map((d) => ({
+                            refName: d.chrom,
+                            start: d.startPos,
+                            end: d.endPos,
+                        })),
+                        { scale, signal }
                     )
-        );
+                    .then((featureChunks) =>
+                        featureChunks.map((features, i) =>
+                            mapFeatures(intervals[i].chrom, features)
+                        )
+                    ),
+        });
 
         if (featureChunks) {
             this.publishData(featureChunks);
@@ -176,6 +183,19 @@ function isBigWigSource(params) {
 
 registerBuiltInLazyDataSource(isBigWigSource, BigWigSource);
 
+/**
+ * @param {string} chrom
+ * @param {import("@gmod/bbi").Feature[]} features
+ */
+function mapFeatures(chrom, features) {
+    return features.map((f) => ({
+        chrom,
+        start: f.start,
+        end: f.end,
+        score: f.score,
+    }));
+}
+
 /**
  * @param {number[]} domain
  * @param {number} widthInPixels view width in pixels

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/singleAxisWindowedSource.d.ts

@@ -1,3 +1,13 @@
+/**
+ * @template T
+ * @typedef {(discreteInterval: import("@genome-spy/core/genome/genome.js").DiscreteChromosomeInterval, signal: AbortSignal) => Promise<T>} DiscreteIntervalLoader
+ */
+/**
+ * @template T
+ * @typedef {object} DiscreteIntervalLoaders
+ * @prop {DiscreteIntervalLoader<T>} load
+ * @prop {(discreteIntervals: import("@genome-spy/core/genome/genome.js").DiscreteChromosomeInterval[], signal: AbortSignal) => Promise<T[]>} [loadBatch]
+ */
 /**
  * Divides the domain into windows and loads the data for one or two consecutive windows
  * that cover the visible interval.
@@ -36,15 +46,16 @@ export default class SingleAxisWindowedSource extends SingleAxisLazySource {
     protected reloadLastDomain(): void;
     /**
      * Splits the interval into discrete chromosomal intervals – one for each chromosome –
-     * and loads the data for each of them. Handles abort signals and errors.
+     * and loads the data using a batched loader when available. Handles abort signals
+     * and errors.
      *
      * @param {number[]} interval
-     * @param {(discreteInteval: import("@genome-spy/core/genome/genome.js").DiscreteChromosomeInterval, signal: AbortSignal) => Promise<T>} loader
+     * @param {DiscreteIntervalLoader<T> | DiscreteIntervalLoaders<T>} loader
      * @return {Promise<T[]>}
      * @template T
      * @protected
      */
-    protected discretizeAndLoad<T>(interval: number[], loader: (discreteInteval: import("@genome-spy/core/genome/genome.js").DiscreteChromosomeInterval, signal: AbortSignal) => Promise<T>): Promise<T[]>;
+    protected discretizeAndLoad<T>(interval: number[], loader: DiscreteIntervalLoader<T> | DiscreteIntervalLoaders<T>): Promise<T[]>;
     /**
      *
      * @param {number[]} interval Domain
@@ -55,5 +66,10 @@ export default class SingleAxisWindowedSource extends SingleAxisLazySource {
     protected callIfWindowsChanged(interval: number[], windowSize: number, callback: (arg0: number[]) => void): void;
     #private;
 }
+export type DiscreteIntervalLoader<T> = (discreteInterval: import("@genome-spy/core/genome/genome.js").DiscreteChromosomeInterval, signal: AbortSignal) => Promise<T>;
+export type DiscreteIntervalLoaders<T> = {
+    load: DiscreteIntervalLoader<T>;
+    loadBatch?: (discreteIntervals: import("@genome-spy/core/genome/genome.js").DiscreteChromosomeInterval[], signal: AbortSignal) => Promise<T[]>;
+};
 import SingleAxisLazySource from "./singleAxisLazySource.js";
 //# sourceMappingURL=singleAxisWindowedSource.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"singleAxisWindowedSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/singleAxisWindowedSource.js"],"names":[],"mappings":"AAIA;;;;;GAKG;AACH;IAWI;;;OAGG;IACH,kBAHU;QAAC,UAAU,CAAC,EAAE,MAAM,GAAG,OAAO,4BAA4B,EAAE,OAAO,CAAA;KAAC,CAGvE;IAEP;;;OAGG;IACH,0CAHW,OAAO,uBAAuB,EAAE,aAAa,QAqBvD;IAED;;;;OAIG;IACH,wBAFW,MAAM,EAAE,QAqBlB;IAeD;;;;;OAKG;IACH,iCAHW,MAAM,EAAE,iBAKlB;IArBD;;OAEG;IACH,mCAQC;IAyBD;;;;;;;;;OASG;IACH,4BAHa,CAAC,YAHH,MAAM,EAAE,UACR,CAAC,eAAe,EAAE,OAAO,mCAAmC,EAAE,0BAA0B,EAAE,MAAM,EAAE,WAAW,KAAK,OAAO,CAAC,CAAC,CAAC,GAC3H,OAAO,CAAC,CAAC,EAAE,CAAC,CAyCvB;IAED;;;;;;OAMG;IACH,yCALW,MAAM,EAAE,cACR,MAAM,YACN,CAAS,IAAQ,EAAR,MAAM,EAAE,KAAE,IAAI,QAyBjC;;CACJ;iCA9LgC,2BAA2B"}
+{"version":3,"file":"singleAxisWindowedSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/singleAxisWindowedSource.js"],"names":[],"mappings":"AAIA;;;GAGG;AAEH;;;;;GAKG;AAEH;;;;;GAKG;AACH;IAWI;;;OAGG;IACH,kBAHU;QAAC,UAAU,CAAC,EAAE,MAAM,GAAG,OAAO,4BAA4B,EAAE,OAAO,CAAA;KAAC,CAGvE;IAEP;;;OAGG;IACH,0CAHW,OAAO,uBAAuB,EAAE,aAAa,QAqBvD;IAED;;;;OAIG;IACH,wBAFW,MAAM,EAAE,QAqBlB;IAeD;;;;;OAKG;IACH,iCAHW,MAAM,EAAE,iBAKlB;IArBD;;OAEG;IACH,mCAQC;IAyBD;;;;;;;;;;OAUG;IACH,4BAHa,CAAC,YAHH,MAAM,EAAE,UACR,sBAAsB,CAAC,CAAC,CAAC,GAAG,uBAAuB,CAAC,CAAC,CAAC,GACrD,OAAO,CAAC,CAAC,EAAE,CAAC,CAiDvB;IAED;;;;;;OAMG;IACH,yCALW,MAAM,EAAE,cACR,MAAM,YACN,CAAS,IAAQ,EAAR,MAAM,EAAE,KAAE,IAAI,QAyBjC;;CACJ;mCAhNY,CAAC,IACD,CAAC,gBAAgB,EAAE,OAAO,mCAAmC,EAAE,0BAA0B,EAAE,MAAM,EAAE,WAAW,KAAK,OAAO,CAAC,CAAC,CAAC;oCAI7H,CAAC;UAEJ,sBAAsB,CAAC,CAAC,CAAC;gBACzB,CAAC,iBAAiB,EAAE,OAAO,mCAAmC,EAAE,0BAA0B,EAAE,EAAE,MAAM,EAAE,WAAW,KAAK,OAAO,CAAC,CAAC,EAAE,CAAC;;iCAX3G,2BAA2B"}

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

@@ -2,6 +2,18 @@ import { withoutExprRef } from "../../../paramRuntime/paramUtils.js";
 import { debounce } from "../../../utils/debounce.js";
 import SingleAxisLazySource from "./singleAxisLazySource.js";
 
+/**
+ * @template T
+ * @typedef {(discreteInterval: import("@genome-spy/core/genome/genome.js").DiscreteChromosomeInterval, signal: AbortSignal) => Promise<T>} DiscreteIntervalLoader
+ */
+
+/**
+ * @template T
+ * @typedef {object} DiscreteIntervalLoaders
+ * @prop {DiscreteIntervalLoader<T>} load
+ * @prop {(discreteIntervals: import("@genome-spy/core/genome/genome.js").DiscreteChromosomeInterval[], signal: AbortSignal) => Promise<T[]>} [loadBatch]
+ */
+
 /**
  * Divides the domain into windows and loads the data for one or two consecutive windows
  * that cover the visible interval.
@@ -113,10 +125,11 @@ export default class SingleAxisWindowedSource extends SingleAxisLazySource {
 
     /**
      * Splits the interval into discrete chromosomal intervals – one for each chromosome –
-     * and loads the data for each of them. Handles abort signals and errors.
+     * and loads the data using a batched loader when available. Handles abort signals
+     * and errors.
      *
      * @param {number[]} interval
-     * @param {(discreteInteval: import("@genome-spy/core/genome/genome.js").DiscreteChromosomeInterval, signal: AbortSignal) => Promise<T>} loader
+     * @param {DiscreteIntervalLoader<T> | DiscreteIntervalLoaders<T>} loader
      * @return {Promise<T[]>}
      * @template T
      * @protected
@@ -130,21 +143,29 @@ export default class SingleAxisWindowedSource extends SingleAxisLazySource {
         this.#abortController = new AbortController();
         const signal = this.#abortController.signal;
 
-        // GMOD libraries expect a single chromosome/sequence for each request.
-        // Thus, we split the interval into discrete intervals representing
-        // individual chromosomes and load the data for each of them separately
-        // but in parallel.
+        // Lazy sources load data using chromosome coordinates. The continuous
+        // scale domain must be split before it can be passed to the source.
         const discreteChromosomeIntervals =
             this.genome.continuousToDiscreteChromosomeIntervals(interval);
 
+        const loaders = typeof loader == "function" ? { load: loader } : loader;
+
         try {
-            const resultByChrom = await Promise.all(
-                discreteChromosomeIntervals.map(
-                    async (
-                        /** @type {import("@genome-spy/core/genome/genome.js").DiscreteChromosomeInterval} */ d
-                    ) => loader(d, signal)
-                )
-            );
+            const resultByChrom = loaders.loadBatch
+                ? await loaders.loadBatch(discreteChromosomeIntervals, signal)
+                : await Promise.all(
+                      discreteChromosomeIntervals.map(
+                          async (
+                              /** @type {import("@genome-spy/core/genome/genome.js").DiscreteChromosomeInterval} */ d
+                          ) => loaders.load(d, signal)
+                      )
+                  );
+
+            if (resultByChrom.length !== discreteChromosomeIntervals.length) {
+                throw new Error(
+                    "Batched lazy loader must return one chunk per interval."
+                );
+            }
 
             if (!signal.aborted) {
                 this.setLoadingStatus("complete");

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/transforms/filterScoredLabels.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"filterScoredLabels.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filterScoredLabels.js"],"names":[],"mappings":"AAOA;IAcI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,wBAAwB,QAC1D,OAAO,oBAAoB,EAAE,OAAO,EAkD9C;IA9DD;;;;OAIG;IACH,kDAEC;IAUG,mEAAoB;IAEpB,oBAAoB;IACpB,OADW,GAAG,EAAE,CACD;IAEf,mBAAoC;IAMpC,sDAA8C;IAC9C,oDAAgE;IAChE,wDAAuD;IACvD,sDAAmD;IACnD,mDAA6C;IAC7C,mDAA6C;IAC7C,gCAAgC;IAChC,cADW,CAAS,IAAG,EAAH,GAAG,KAAE,GAAG,CAGd;IACd,gBAAuC;IAEvC,uCAAuC;IACvC,iBADW,GAAG,CAAC,GAAG,EAAE,cAAc,CAAC,CACH;IAEhC,8DAAuD;IAIvD,qBAAuE;IA8B3E,4BAsEC;IAKG,sBAAuB;CAU9B;sBAzKqB,gBAAgB;2BAFX,+BAA+B"}
+{"version":3,"file":"filterScoredLabels.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filterScoredLabels.js"],"names":[],"mappings":"AAOA;IAcI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,wBAAwB,QAC1D,OAAO,oBAAoB,EAAE,OAAO,EAmD9C;IA/DD;;;;OAIG;IACH,kDAEC;IAUG,mEAAoB;IAEpB,oBAAoB;IACpB,OADW,GAAG,EAAE,CACD;IAEf,mBAAoC;IAMpC,sDAA8C;IAC9C,oDAAgE;IAChE,wDAAuD;IACvD,sDAAmD;IACnD,mDAA6C;IAC7C,mDAA6C;IAC7C,gCAAgC;IAChC,cADW,CAAS,IAAG,EAAH,GAAG,KAAE,GAAG,CAGd;IACd,gBAAuC;IAEvC,uCAAuC;IACvC,iBADW,GAAG,CAAC,GAAG,EAAE,cAAc,CAAC,CACH;IAEhC,8DAAuD;IAIvD,qBAAuE;IA+B3E,4BAsEC;IAKG,sBAAuB;CAU9B;sBA1KqB,gBAAgB;2BAFX,+BAA+B"}

package/dist/src/data/transforms/filterScoredLabels.js

@@ -59,8 +59,9 @@ export default class FilterScoredLabelsTransform extends Transform {
         const callback = () => this._filterAndPropagate();
         this.schedule = () => view.context.animator.requestTransition(callback);
 
-        // Propagate when the domain changes
-        const domainListener = () => this.schedule();
+        // Propagate immediately when the domain changes so inertial zoom frames
+        // render with labels computed for the current scale domain.
+        const domainListener = () => this._filterAndPropagate();
         this.resolution.addEventListener("domain", domainListener);
         this.registerDisposer(() =>
             this.resolution.removeEventListener("domain", domainListener)

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

@@ -1 +1 @@
-{"version":3,"file":"embedFactory.d.ts","sourceRoot":"","sources":["../../src/embedFactory.js"],"names":[],"mappings":"AAKA;;;GAGG;AACH,uCAHW,KAAK,SAAS,EAAE,WAAW,EAAE,IAAI,EAAE,OAAO,gBAAgB,EAAE,QAAQ,EAAE,OAAO,CAAC,EAAE,OAAO,qBAAqB,EAAE,YAAY,KAAK,OAAO,gBAAgB,EAAE,OAAO,GAC7J,CAAC,EAAE,EAAE,WAAW,GAAG,MAAM,EAAE,IAAI,EAAE,OAAO,gBAAgB,EAAE,QAAQ,GAAG,MAAM,EAAE,OAAO,CAAC,EAAE,OAAO,qBAAqB,EAAE,YAAY,KAAK,OAAO,CAAC,OAAO,qBAAqB,EAAE,WAAW,CAAC,CAmFpM;AAaD;;;;;GAKG;AACH,8BAFW,MAAM,gBAmBhB"}
+{"version":3,"file":"embedFactory.d.ts","sourceRoot":"","sources":["../../src/embedFactory.js"],"names":[],"mappings":"AAKA;;;GAGG;AACH,uCAHW,KAAK,SAAS,EAAE,WAAW,EAAE,IAAI,EAAE,OAAO,gBAAgB,EAAE,QAAQ,EAAE,OAAO,CAAC,EAAE,OAAO,qBAAqB,EAAE,YAAY,KAAK,OAAO,gBAAgB,EAAE,OAAO,GAC7J,CAAC,EAAE,EAAE,WAAW,GAAG,MAAM,EAAE,IAAI,EAAE,OAAO,gBAAgB,EAAE,QAAQ,GAAG,MAAM,EAAE,OAAO,CAAC,EAAE,OAAO,qBAAqB,EAAE,YAAY,KAAK,OAAO,CAAC,OAAO,qBAAqB,EAAE,WAAW,CAAC,CAqFpM;AAaD;;;;;GAKG;AACH,8BAFW,MAAM,gBAmBhB"}