@jbrowse/plugin-variants 4.0.4 → 4.1.3

package/esm/PlinkLDAdapter/PlinkLDTabixAdapter.js

@@ -0,0 +1,156 @@
+import { TabixIndexedFile } from '@gmod/tabix';
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { updateStatus } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+export default class PlinkLDTabixAdapter extends BaseAdapter {
+    configured;
+    async configurePre(_opts) {
+        const ldLocation = this.getConf('ldLocation');
+        const location = this.getConf(['index', 'location']);
+        const indexType = this.getConf(['index', 'indexType']);
+        const filehandle = openLocation(ldLocation, this.pluginManager);
+        const isCSI = indexType === 'CSI';
+        const ld = new TabixIndexedFile({
+            filehandle,
+            csiFilehandle: isCSI
+                ? openLocation(location, this.pluginManager)
+                : undefined,
+            tbiFilehandle: !isCSI
+                ? openLocation(location, this.pluginManager)
+                : undefined,
+            chunkCacheSize: 50 * 2 ** 20,
+        });
+        const headerLine = await ld.getHeader();
+        const header = this.parseHeader(headerLine);
+        return { ld, header };
+    }
+    parseHeader(headerLine) {
+        const columns = headerLine.trim().split(/\s+/);
+        const findIdx = (names) => {
+            for (const name of names) {
+                const idx = columns.indexOf(name);
+                if (idx !== -1) {
+                    return idx;
+                }
+            }
+            return -1;
+        };
+        const chrAIdx = findIdx(['CHR_A', 'CHR1']);
+        const bpAIdx = findIdx(['BP_A', 'BP1', 'POS_A', 'POS1']);
+        const snpAIdx = findIdx(['SNP_A', 'SNP1', 'ID_A', 'ID1']);
+        const chrBIdx = findIdx(['CHR_B', 'CHR2']);
+        const bpBIdx = findIdx(['BP_B', 'BP2', 'POS_B', 'POS2']);
+        const snpBIdx = findIdx(['SNP_B', 'SNP2', 'ID_B', 'ID2']);
+        const r2Idx = findIdx(['R2', 'R^2', 'RSQ']);
+        const dprimeIdx = findIdx(['DP', 'DPRIME', "D'"]);
+        const mafAIdx = findIdx(['MAF_A', 'MAF1']);
+        const mafBIdx = findIdx(['MAF_B', 'MAF2']);
+        if (chrAIdx === -1 || bpAIdx === -1 || chrBIdx === -1 || bpBIdx === -1) {
+            throw new Error(`Invalid PLINK LD header. Expected columns CHR_A, BP_A, CHR_B, BP_B. Got: ${columns.join(', ')}`);
+        }
+        if (r2Idx === -1 && dprimeIdx === -1) {
+            throw new Error(`Invalid PLINK LD header. Expected at least R2 or DP column. Got: ${columns.join(', ')}`);
+        }
+        return {
+            columns,
+            hasR2: r2Idx !== -1,
+            hasDprime: dprimeIdx !== -1,
+            hasMafA: mafAIdx !== -1,
+            hasMafB: mafBIdx !== -1,
+            chrAIdx,
+            bpAIdx,
+            snpAIdx,
+            chrBIdx,
+            bpBIdx,
+            snpBIdx,
+            r2Idx,
+            dprimeIdx,
+            mafAIdx,
+            mafBIdx,
+        };
+    }
+    async configurePre2() {
+        if (!this.configured) {
+            this.configured = this.configurePre().catch((e) => {
+                this.configured = undefined;
+                throw e;
+            });
+        }
+        return this.configured;
+    }
+    async configure(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        return updateStatus('Downloading index', statusCallback, () => this.configurePre2());
+    }
+    async getRefNames(opts = {}) {
+        const { ld } = await this.configure(opts);
+        return ld.getReferenceSequenceNames(opts);
+    }
+    async getHeader(opts) {
+        const { header } = await this.configure(opts);
+        return header;
+    }
+    async getLDRecords(query, opts = {}) {
+        const { refName, start, end } = query;
+        const { ld, header } = await this.configure(opts);
+        const records = [];
+        await ld.getLines(refName, start, end, {
+            lineCallback: (line) => {
+                const record = this.parseLine(line, header);
+                if (record) {
+                    records.push(record);
+                }
+            },
+            ...opts,
+        });
+        return records;
+    }
+    async getLDRecordsInRegion(query, opts = {}) {
+        const { refName, start, end } = query;
+        const records = await this.getLDRecords(query, opts);
+        return records.filter(r => r.chrB === refName &&
+            r.bpB >= start &&
+            r.bpB <= end &&
+            r.chrA === refName &&
+            r.bpA >= start &&
+            r.bpA <= end);
+    }
+    parseLine(line, header) {
+        const fields = line.trim().split(/\s+/);
+        const chrA = fields[header.chrAIdx];
+        const bpA = Number.parseInt(fields[header.bpAIdx] ?? '', 10);
+        const snpA = header.snpAIdx >= 0 ? fields[header.snpAIdx] : `${chrA}:${bpA}`;
+        const chrB = fields[header.chrBIdx];
+        const bpB = Number.parseInt(fields[header.bpBIdx] ?? '', 10);
+        const snpB = header.snpBIdx >= 0 ? fields[header.snpBIdx] : `${chrB}:${bpB}`;
+        if (!chrA || !chrB || Number.isNaN(bpA) || Number.isNaN(bpB)) {
+            return null;
+        }
+        const r2 = header.r2Idx >= 0
+            ? Number.parseFloat(fields[header.r2Idx] ?? '')
+            : undefined;
+        const dprime = header.dprimeIdx >= 0
+            ? Number.parseFloat(fields[header.dprimeIdx] ?? '')
+            : undefined;
+        const mafA = header.mafAIdx >= 0
+            ? Number.parseFloat(fields[header.mafAIdx] ?? '')
+            : undefined;
+        const mafB = header.mafBIdx >= 0
+            ? Number.parseFloat(fields[header.mafBIdx] ?? '')
+            : undefined;
+        return {
+            chrA,
+            bpA,
+            snpA: snpA ?? `${chrA}:${bpA}`,
+            chrB,
+            bpB,
+            snpB: snpB ?? `${chrB}:${bpB}`,
+            r2: r2 ?? 0,
+            dprime,
+            mafA,
+            mafB,
+        };
+    }
+    freeResources() {
+    }
+}

package/esm/PlinkLDAdapter/configSchema.d.ts

@@ -0,0 +1,10 @@
+declare const PlinkLDAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    ldLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default PlinkLDAdapter;

package/esm/PlinkLDAdapter/configSchema.js

@@ -0,0 +1,25 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+function x() { }
+const PlinkLDAdapter = ConfigurationSchema('PlinkLDAdapter', {
+    ldLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/plink.ld',
+            locationType: 'UriLocation',
+        },
+    },
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                ldLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
+export default PlinkLDAdapter;

package/esm/PlinkLDAdapter/configSchemaTabix.d.ts

@@ -0,0 +1,24 @@
+declare const PlinkLDTabixAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    ldLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    index: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexType: {
+            model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            type: string;
+            defaultValue: string;
+        };
+        location: {
+            type: string;
+            defaultValue: {
+                uri: string;
+                locationType: string;
+            };
+        };
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default PlinkLDTabixAdapter;

package/esm/PlinkLDAdapter/configSchemaTabix.js

@@ -0,0 +1,46 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from '@jbrowse/mobx-state-tree';
+function x() { }
+const PlinkLDTabixAdapter = ConfigurationSchema('PlinkLDTabixAdapter', {
+    ldLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/plink.ld.gz',
+            locationType: 'UriLocation',
+        },
+    },
+    index: ConfigurationSchema('PlinkLDTabixIndex', {
+        indexType: {
+            model: types.enumeration('IndexType', ['TBI', 'CSI']),
+            type: 'stringEnum',
+            defaultValue: 'TBI',
+        },
+        location: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/plink.ld.gz.tbi',
+                locationType: 'UriLocation',
+            },
+        },
+    }),
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                ldLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+                index: {
+                    location: {
+                        uri: `${snap.uri}.tbi`,
+                        baseUri: snap.baseUri,
+                    },
+                },
+            }
+            : snap;
+    },
+});
+export default PlinkLDTabixAdapter;

package/esm/PlinkLDAdapter/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function PlinkLDAdapterF(pluginManager: PluginManager): void;

package/esm/PlinkLDAdapter/index.js

@@ -0,0 +1,25 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from "./configSchema.js";
+import configSchemaTabix from "./configSchemaTabix.js";
+export default function PlinkLDAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'PlinkLDAdapter',
+        displayName: 'PLINK LD adapter',
+        configSchema,
+        adapterMetadata: {
+            category: 'Linkage disequilibrium',
+            description: 'Adapter for pre-computed LD data from PLINK --r2 output (loads into memory)',
+        },
+        getAdapterClass: () => import("./PlinkLDAdapter.js").then(r => r.default),
+    }));
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'PlinkLDTabixAdapter',
+        displayName: 'PLINK LD tabix adapter',
+        configSchema: configSchemaTabix,
+        adapterMetadata: {
+            category: 'Linkage disequilibrium',
+            description: 'Adapter for pre-computed LD data from PLINK --r2 output (tabix-indexed)',
+        },
+        getAdapterClass: () => import("./PlinkLDTabixAdapter.js").then(r => r.default),
+    }));
+}

package/esm/PlinkLDAdapter/types.d.ts

@@ -0,0 +1,29 @@
+export interface PlinkLDRecord {
+    chrA: string;
+    bpA: number;
+    snpA: string;
+    chrB: string;
+    bpB: number;
+    snpB: string;
+    r2: number;
+    dprime?: number;
+    mafA?: number;
+    mafB?: number;
+}
+export interface PlinkLDHeader {
+    columns: string[];
+    hasR2: boolean;
+    hasDprime: boolean;
+    hasMafA: boolean;
+    hasMafB: boolean;
+    chrAIdx: number;
+    bpAIdx: number;
+    snpAIdx: number;
+    chrBIdx: number;
+    bpBIdx: number;
+    snpBIdx: number;
+    r2Idx: number;
+    dprimeIdx: number;
+    mafAIdx: number;
+    mafBIdx: number;
+}

package/esm/PlinkLDAdapter/types.js

@@ -0,0 +1 @@
+export {};

package/esm/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.js

@@ -43,7 +43,7 @@ export default function VariantSampleGrid(props) {
     }, [rows, filteredRows, descriptions]);
     return !rows.length ? null : (_jsxs(BaseCard, { ...props, title: "Samples", children: [error ? _jsx(Typography, { color: "error", children: `${error}` }) : null, _jsxs("div", { style: { display: 'flex', alignItems: 'center', gap: 8 }, children: [_jsx(CascadingMenuButton, { menuItems: [
                             {
-                                label: 'Show allele counts ("dosage") instead of exact GT',
+                                label: 'Show allele counts ("dosage")',
                                 helpText: 'This converts a genotype like 1/1 into 1:2 which says there were two occurrences of the ALT allele 1 in the genotype',
                                 type: 'checkbox',
                                 checked: useCounts,

package/esm/VariantRPC/MultiVariantGetFeatureDetails.d.ts

@@ -0,0 +1,14 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+interface GetFeatureArgs {
+    featureId: string;
+    sessionId: string;
+    trackInstanceId: string;
+    rendererType: string;
+}
+export declare class MultiVariantGetFeatureDetails extends RpcMethodType {
+    name: string;
+    execute(args: GetFeatureArgs): Promise<{
+        feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
+    }>;
+}
+export {};

package/esm/VariantRPC/MultiVariantGetFeatureDetails.js

@@ -0,0 +1,15 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+export class MultiVariantGetFeatureDetails extends RpcMethodType {
+    name = 'MultiVariantGetFeatureDetails';
+    async execute(args) {
+        const { featureId, sessionId, trackInstanceId, rendererType } = args;
+        const RendererType = this.pluginManager.getRendererType(rendererType);
+        const feature = RendererType.getFeatureById(featureId, {
+            sessionId,
+            trackInstanceId,
+        });
+        return {
+            feature: feature?.toJSON(),
+        };
+    }
+}

package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.js

@@ -1,11 +1,14 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import { createStopTokenChecker } from '@jbrowse/core/util/stopToken';
 import { getGenotypeMatrix } from "./getGenotypeMatrix.js";
 export class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     name = 'MultiVariantGetGenotypeMatrix';
     async execute(args, rpcDriverClassName) {
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const stopTokenCheck = createStopTokenChecker(deserializedArgs.stopToken);
         return getGenotypeMatrix({
             pluginManager: this.pluginManager,
-            args: await this.deserializeArguments(args, rpcDriverClassName),
+            args: { ...deserializedArgs, stopTokenCheck },
         });
     }
 }

package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -8,6 +8,7 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
     async execute(args, rpcDriverClassName) {
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
         const { lengthCutoffFilter, minorAlleleFrequencyFilter, regions, adapterConfig, stopToken, sessionId, } = deserializedArgs;
+        const stopTokenCheck = createStopTokenChecker(stopToken);
         const { dataAdapter } = await getAdapter(this.pluginManager, sessionId, adapterConfig);
         const rawFeatures = await firstValueFrom(dataAdapter
             .getFeaturesInMultipleRegions(regions, deserializedArgs)
@@ -15,11 +16,10 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
         const sampleInfo = {};
         const genotypesCache = new Map();
         let hasPhased = false;
-        const lastCheck = createStopTokenChecker(stopToken);
         const features = getFeaturesThatPassMinorAlleleFrequencyFilter({
             minorAlleleFrequencyFilter,
             lengthCutoffFilter,
-            lastCheck,
+            stopTokenCheck,
             features: rawFeatures,
             genotypesCache,
         });
@@ -47,7 +47,7 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
                     isPhased: existing?.isPhased || isPhased,
                 };
             }
-            checkStopToken2(lastCheck);
+            checkStopToken2(stopTokenCheck);
         }
         return {
             hasPhased,

package/esm/VariantRPC/executeClusterGenotypeMatrix.js

@@ -1,14 +1,17 @@
 import { clusterData, toNewick } from '@gmod/hclust';
+import { createStopTokenChecker } from '@jbrowse/core/util/stopToken';
 import { getGenotypeMatrix } from "./getGenotypeMatrix.js";
 import { getPhasedGenotypeMatrix } from "./getPhasedGenotypeMatrix.js";
 export async function executeClusterGenotypeMatrix({ pluginManager, args, }) {
-    const { renderingMode, sampleInfo } = args;
+    const { renderingMode, sampleInfo, stopToken } = args;
+    const stopTokenCheck = createStopTokenChecker(stopToken);
+    const argsWithCheck = { ...args, stopTokenCheck };
     const matrix = renderingMode === 'phased' && sampleInfo
         ? await getPhasedGenotypeMatrix({
             pluginManager,
-            args: { ...args, sampleInfo },
+            args: { ...argsWithCheck, sampleInfo },
         })
-        : await getGenotypeMatrix({ pluginManager, args });
+        : await getGenotypeMatrix({ pluginManager, args: argsWithCheck });
     const sampleLabels = Object.keys(matrix);
     const result = await clusterData({
         data: Object.values(matrix),

package/esm/VariantRPC/getGenotypeMatrix.d.ts

@@ -1,13 +1,12 @@
 import type { Source } from '../shared/types.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
-import type { StopToken } from '@jbrowse/core/util/stopToken';
+import type { LastStopTokenCheck, Region } from '@jbrowse/core/util';
 export declare function getGenotypeMatrix({ pluginManager, args, }: {
     pluginManager: PluginManager;
     args: {
         adapterConfig: AnyConfigurationModel;
-        stopToken?: StopToken;
+        stopTokenCheck?: LastStopTokenCheck;
         sessionId: string;
         headers?: Record<string, string>;
         regions: Region[];

package/esm/VariantRPC/getGenotypeMatrix.js

@@ -1,11 +1,10 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
 import { firstValueFrom, toArray } from 'rxjs';
 import { getFeaturesThatPassMinorAlleleFrequencyFilter } from "../shared/minorAlleleFrequencyUtils.js";
 const SPLITTER = /[/|]/;
 export async function getGenotypeMatrix({ pluginManager, args, }) {
-    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopToken, } = args;
-    const lastCheck = createStopTokenChecker(stopToken);
+    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopTokenCheck, } = args;
     const adapter = await getAdapter(pluginManager, sessionId, adapterConfig);
     const dataAdapter = adapter.dataAdapter;
     const rows = Object.fromEntries(sources.map(s => [s.name, []]));
@@ -13,7 +12,7 @@ export async function getGenotypeMatrix({ pluginManager, args, }) {
     const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter({
         minorAlleleFrequencyFilter,
         lengthCutoffFilter,
-        lastCheck,
+        stopTokenCheck,
         splitCache,
         features: await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe(toArray())),
     });
@@ -42,7 +41,7 @@ export async function getGenotypeMatrix({ pluginManager, args, }) {
                         : 1;
             rows[name].push(genotypeStatus);
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
     return rows;
 }

package/esm/VariantRPC/getLDMatrix.d.ts

@@ -0,0 +1,47 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { LastStopTokenCheck, Region } from '@jbrowse/core/util';
+export type LDMetric = 'r2' | 'dprime';
+export interface FilterStats {
+    totalVariants: number;
+    passedVariants: number;
+    filteredByMaf: number;
+    filteredByLength: number;
+    filteredByMultiallelic: number;
+    filteredByHwe: number;
+    filteredByCallRate: number;
+}
+export interface RecombinationData {
+    values: Float32Array;
+    positions: number[];
+}
+export interface LDMatrixResult {
+    snps: {
+        id: string;
+        refName: string;
+        start: number;
+        end: number;
+    }[];
+    ldValues: Float32Array;
+    metric: LDMetric;
+    filterStats: FilterStats;
+    recombination: RecombinationData;
+}
+export declare function getLDMatrix({ pluginManager, args, }: {
+    pluginManager: PluginManager;
+    args: {
+        adapterConfig: AnyConfigurationModel;
+        stopTokenCheck?: LastStopTokenCheck;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        bpPerPx: number;
+        minorAlleleFrequencyFilter: number;
+        lengthCutoffFilter: number;
+        hweFilterThreshold?: number;
+        callRateFilter?: number;
+        jexlFilters?: string[];
+        ldMetric?: LDMetric;
+        signedLD?: boolean;
+    };
+}): Promise<LDMatrixResult>;