@jbrowse/plugin-variants 3.3.0 → 3.5.0

package/esm/VariantFeatureWidget/stateModelFactory.d.ts

@@ -3,9 +3,9 @@ import type { Instance } from 'mobx-state-tree';
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    featureData: import("mobx-state-tree").IType<any, any, any>;
+    featureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
     formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -35,15 +35,16 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
     descriptions: import("mobx-state-tree").IType<any, any, any>;
 }, {
     error: unknown;
 } & {
-    setFeatureData(featureData: Record<string, unknown>): void;
+    setFeatureData(featureData: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
     clearFeatureData(): void;
-    setFormattedData(feat: Record<string, unknown>): void;
+    setFormattedData(feat: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
     setExtra(type?: string, trackId?: string, maxDepth?: number): void;
     setError(e: unknown): void;
 } & {
@@ -53,9 +54,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
 } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    featureData: import("mobx-state-tree").IType<any, any, any>;
+    featureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
     formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -85,6 +86,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: "BaseFeatureWidget";
     id: string;
@@ -95,6 +97,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     maxDepth: number | undefined;
     sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
     formattedFields: any;
+    descriptions: Record<string, unknown> | undefined;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/esm/VariantRPC/getGenotypeMatrix.js

@@ -14,11 +14,12 @@ export async function getGenotypeMatrix({ pluginManager, args, }) {
         features: await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe(toArray())),
     });
     for (const { alleleCounts } of mafs) {
-        for (const alt of alleleCounts.keys()) {
+        for (const alt of Object.keys(alleleCounts)) {
             genotypeFactor.add(alt);
         }
     }
     const rows = {};
+    const cacheSplit = {};
     forEachWithStopTokenCheck(mafs, stopToken, ({ feature }) => {
         const genotypes = feature.get('genotypes');
         for (const { name } of sources) {
@@ -26,7 +27,14 @@ export async function getGenotypeMatrix({ pluginManager, args, }) {
                 rows[name] = [];
             }
             const val = genotypes[name];
-            const alleles = val.split(/[/|]/);
+            let alleles;
+            if (cacheSplit[val]) {
+                alleles = cacheSplit[val];
+            }
+            else {
+                alleles = val.split(/[/|]/);
+                cacheSplit[val] = alleles;
+            }
             let genotypeStatus = 0;
             let nonRefCount = 0;
             let uncalledCount = 0;

package/esm/VcfAdapter/VcfAdapter.d.ts

@@ -31,6 +31,5 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
     getSources(): Promise<{
         name: string;
     }[]>;
-    freeResources(): void;
 }
 export {};

package/esm/VcfAdapter/VcfAdapter.js

@@ -135,7 +135,6 @@ class VcfAdapter extends BaseFeatureDataAdapter {
                 .filter(f => s.has(f.name));
         }
     }
-    freeResources() { }
 }
 VcfAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default VcfAdapter;

package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -22,5 +22,4 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     getSources(): Promise<{
         name: string;
     }[]>;
-    freeResources(): void;
 }

package/esm/VcfTabixAdapter/VcfTabixAdapter.js

@@ -108,5 +108,4 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
             return metadataLines.filter(f => vcfSampleSet.has(f.name));
         }
     }
-    freeResources() { }
 }

package/esm/shared/drawAlleleCount.d.ts

@@ -1 +1,2 @@
-export declare function drawColorAlleleCount(alleles: string[], ctx: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, mostFrequentAlt: string, drawReference?: boolean, featureType?: string, featureStrand?: number, alpha?: number): any;
+export declare function getColorAlleleCount(ref: number, alt: number, alt2: number, uncalled: number, total: number, drawReference?: boolean): any;
+export declare function drawColorAlleleCount(c: string, ctx: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, featureType?: string, featureStrand?: number, alpha?: number): void;

package/esm/shared/drawAlleleCount.js

@@ -1,27 +1,8 @@
 import { colord } from '@jbrowse/core/util/colord';
 import { f2 } from './constants';
-function getColorAlleleCount(alleles, mostFrequentAlt, drawReference = true) {
-    const total = alleles.length;
-    let alt = 0;
-    let uncalled = 0;
-    let alt2 = 0;
-    let ref = 0;
-    for (const allele of alleles) {
-        if (allele === mostFrequentAlt) {
-            alt++;
-        }
-        else if (allele === '0') {
-            ref++;
-        }
-        else if (allele === '.') {
-            uncalled++;
-        }
-        else {
-            alt2++;
-        }
-    }
+export function getColorAlleleCount(ref, alt, alt2, uncalled, total, drawReference = true) {
     if (ref === total) {
-        return drawReference ? '#ccc' : undefined;
+        return drawReference ? '#ccc' : '';
     }
     else {
         let a1;
@@ -39,31 +20,27 @@ function getColorAlleleCount(alleles, mostFrequentAlt, drawReference = true) {
         return (a1 === null || a1 === void 0 ? void 0 : a1.toHex()) || 'black';
     }
 }
-export function drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt, drawReference = true, featureType = '', featureStrand, alpha = 1) {
-    const c = getColorAlleleCount(alleles, mostFrequentAlt, drawReference);
-    if (c) {
-        ctx.fillStyle = alpha !== 1 ? colord(c).alpha(alpha).toHex() : c;
-        if (featureType === 'inversion') {
-            if (featureStrand === 1) {
-                ctx.beginPath();
-                ctx.moveTo(x - f2, y - f2);
-                ctx.lineTo(x - f2, y + h + f2);
-                ctx.lineTo(x + w + f2, y + h / 2);
-                ctx.closePath();
-                ctx.fill();
-            }
-            else {
-                ctx.beginPath();
-                ctx.moveTo(x + w + f2, y - f2);
-                ctx.lineTo(x + w + f2, y + h + f2);
-                ctx.lineTo(x - f2, y + h / 2);
-                ctx.closePath();
-                ctx.fill();
-            }
+export function drawColorAlleleCount(c, ctx, x, y, w, h, featureType = '', featureStrand, alpha = 1) {
+    ctx.fillStyle = alpha !== 1 ? colord(c).alpha(alpha).toHex() : c;
+    if (featureType === 'inversion') {
+        if (featureStrand === 1) {
+            ctx.beginPath();
+            ctx.moveTo(x - f2, y - f2);
+            ctx.lineTo(x - f2, y + h + f2);
+            ctx.lineTo(x + w + f2, y + h / 2);
+            ctx.closePath();
+            ctx.fill();
         }
         else {
-            ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+            ctx.beginPath();
+            ctx.moveTo(x + w + f2, y - f2);
+            ctx.lineTo(x + w + f2, y + h + f2);
+            ctx.lineTo(x - f2, y + h / 2);
+            ctx.closePath();
+            ctx.fill();
         }
     }
-    return c;
+    else {
+        ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+    }
 }

package/esm/shared/minorAlleleFrequencyUtils.d.ts

@@ -1,7 +1,7 @@
 import type { Feature } from '@jbrowse/core/util';
 export declare function findSecondLargestNumber(arr: Iterable<number>): number;
-export declare function calculateAlleleCounts(feat: Feature): Map<any, any>;
-export declare function calculateMinorAlleleFrequency(alleleCounts: Map<string, number>): number;
+export declare function calculateAlleleCounts(feat: Feature): Record<string, number>;
+export declare function calculateMinorAlleleFrequency(alleleCounts: Record<string, number>): number;
 export declare function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, stopToken, }: {
     features: Iterable<Feature>;
     minorAlleleFrequencyFilter: number;
@@ -10,5 +10,5 @@ export declare function getFeaturesThatPassMinorAlleleFrequencyFilter({ features
 }): {
     feature: Feature;
     mostFrequentAlt: string;
-    alleleCounts: Map<string, number>;
+    alleleCounts: Record<string, number>;
 }[];

package/esm/shared/minorAlleleFrequencyUtils.js

@@ -14,24 +14,30 @@ export function findSecondLargestNumber(arr) {
     return secondMax;
 }
 export function calculateAlleleCounts(feat) {
-    const samp = feat.get('genotypes');
-    const alleleCounts = new Map();
-    for (const val of Object.values(samp)) {
-        const alleles = val.split(/[/|]/);
-        for (const allele of alleles) {
-            alleleCounts.set(allele, (alleleCounts.get(allele) || 0) + 1);
+    var _a;
+    const genotypes = feat.get('genotypes');
+    const alleleCounts = { 0: 0, 1: 0, '.': 0 };
+    const cacheSplit = {};
+    const vals = Object.values(genotypes);
+    const len = vals.length;
+    for (let i = 0; i < len; i++) {
+        const genotype = vals[i];
+        const alleles = cacheSplit[genotype] || (cacheSplit[genotype] = genotype.split(/[/|]/));
+        for (let i = 0, len = alleles.length; i < len; i++) {
+            const a = alleles[i];
+            alleleCounts[a] = ((_a = alleleCounts[a]) !== null && _a !== void 0 ? _a : 0) + 1;
         }
     }
     return alleleCounts;
 }
 export function calculateMinorAlleleFrequency(alleleCounts) {
-    return (findSecondLargestNumber(alleleCounts.values()) /
-        (sum(alleleCounts.values()) || 1));
+    return (findSecondLargestNumber(Object.values(alleleCounts)) /
+        (sum(Object.values(alleleCounts)) || 1));
 }
 function getMostFrequentAlt(alleleCounts) {
     let mostFrequentAlt;
     let max = 0;
-    for (const [alt, altCount] of alleleCounts.entries()) {
+    for (const [alt, altCount] of Object.entries(alleleCounts)) {
         if (alt !== '.' && alt !== '0') {
             if (altCount > max) {
                 mostFrequentAlt = alt;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "3.3.0",
+  "version": "3.5.0",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,13 +37,13 @@
   },
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
-    "@gmod/bgzf-filehandle": "^2.0.1",
-    "@gmod/tabix": "^2.0.0",
+    "@gmod/bgzf-filehandle": "^4.0.0",
+    "@gmod/tabix": "^3.0.1",
     "@gmod/vcf": "^6.0.8",
-    "@jbrowse/core": "^3.3.0",
-    "@jbrowse/plugin-circular-view": "^3.3.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.3.0",
-    "@jbrowse/sv-core": "^3.3.0",
+    "@jbrowse/core": "^3.5.0",
+    "@jbrowse/plugin-circular-view": "^3.5.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.5.0",
+    "@jbrowse/sv-core": "^3.5.0",
     "@mui/icons-material": "^7.0.0",
     "@mui/material": "^7.0.0",
     "@mui/x-data-grid": "^8.0.0",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
+  "gitHead": "8a8aa0aab2229dece106a5715a767e649e2fe92b"
 }