@jbrowse/plugin-bed 3.6.5 → 4.0.0

package/dist/GuessAdapter/index.js

@@ -1,68 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = GuessAdapterF;
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-function GuessAdapterF(pluginManager) {
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const fileName = (0, tracks_1.getFileName)(file);
-            const indexName = index && (0, tracks_1.getFileName)(index);
-            if ((0, util_1.testAdapter)(fileName, /\.bedpe(\.gz)?$/i, adapterHint, 'BedpeAdapter')) {
-                return {
-                    type: 'BedpeAdapter',
-                    bedpeLocation: file,
-                };
-            }
-            else if ((0, util_1.testAdapter)(fileName, /\.bb$/i, adapterHint, 'BigBedAdapter') ||
-                (0, util_1.testAdapter)(fileName, /\.bigBed?$/i, adapterHint, 'BigBedAdapter')) {
-                return {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: file,
-                };
-            }
-            else if ((0, util_1.testAdapter)(fileName, /\.bed$/i, adapterHint, 'BedAdapter')) {
-                return {
-                    type: 'BedAdapter',
-                    bedLocation: file,
-                };
-            }
-            else if ((0, util_1.testAdapter)(fileName, /\.bg$/i, adapterHint, 'BedGraphAdapter')) {
-                return {
-                    type: 'BedGraphAdapter',
-                    bedGraphLocation: file,
-                };
-            }
-            else if ((0, util_1.testAdapter)(fileName, /\.bg(\.gz)?$/i, adapterHint, 'BedGraphTabixAdapter')) {
-                return {
-                    type: 'BedGraphTabixAdapter',
-                    bedGraphGzLocation: file,
-                    index: {
-                        location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
-                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
-                    },
-                };
-            }
-            else if ((0, util_1.testAdapter)(fileName, /\.bed\.gz$/i, adapterHint, 'BedTabixAdapter')) {
-                return {
-                    type: 'BedTabixAdapter',
-                    bedGzLocation: file,
-                    index: {
-                        location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
-                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
-                    },
-                };
-            }
-            else {
-                return adapterGuesser(file, index, adapterHint);
-            }
-        };
-    });
-    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => (adapterName) => {
-        return ({
-            BedpeAdapter: 'VariantTrack',
-            BedGraphAdapter: 'QuantitativeTrack',
-            BedGraphTabixAdapter: 'QuantitativeTrack',
-        }[adapterName] || trackTypeGuesser(adapterName));
-    });
-}

package/dist/generateBedMethylFeature.d.ts

@@ -1,31 +0,0 @@
-export declare function isBedMethylFeature({ splitLine, start, end, }: {
-    splitLine: string[];
-    start: number;
-    end: number;
-}): boolean;
-export declare function generateBedMethylFeature({ splitLine, uniqueId, refName, start, end, }: {
-    splitLine: string[];
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-}): {
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-    code: string | undefined;
-    score: number;
-    strand: string | undefined;
-    color: string | undefined;
-    source: string | undefined;
-    n_valid_cov: string | undefined;
-    fraction_modified: string | undefined;
-    n_mod: string | undefined;
-    n_canonical: string | undefined;
-    n_other_mod: string | undefined;
-    n_delete: string | undefined;
-    n_fail: string | undefined;
-    n_diff: string | undefined;
-    n_nocall: string | undefined;
-};

package/dist/generateBedMethylFeature.js

@@ -1,32 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.isBedMethylFeature = isBedMethylFeature;
-exports.generateBedMethylFeature = generateBedMethylFeature;
-function isBedMethylFeature({ splitLine, start, end, }) {
-    return (+(splitLine[6] || 0) === start &&
-        +(splitLine[7] || 0) === end &&
-        [9, 10, 11, 12, 13, 14, 15, 16, 17].every(r => splitLine[r] && !Number.isNaN(+splitLine[r])));
-}
-function generateBedMethylFeature({ splitLine, uniqueId, refName, start, end, }) {
-    const [, , , code, , strand, , , color, n_valid_cov, fraction_modified, n_mod, n_canonical, n_other_mod, n_delete, n_fail, n_diff, n_nocall,] = splitLine;
-    return {
-        uniqueId,
-        refName,
-        start,
-        end,
-        code,
-        score: +fraction_modified || 0,
-        strand,
-        color,
-        source: code,
-        n_valid_cov,
-        fraction_modified,
-        n_mod,
-        n_canonical,
-        n_other_mod,
-        n_delete,
-        n_fail,
-        n_diff,
-        n_nocall,
-    };
-}

package/dist/generateRepeatMaskerFeature.d.ts

@@ -1,51 +0,0 @@
-export declare function isRepeatMaskerDescriptionField(desc?: string): desc is string;
-export declare function generateRepeatMaskerFeature({ uniqueId, refName, start, end, description, ...rest }: {
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-    description: string;
-    [key: string]: unknown;
-}): {
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-    bitsw_score: string | undefined;
-    percent_div: string | undefined;
-    percent_del: string | undefined;
-    percent_ins: string | undefined;
-    query_chr: string | undefined;
-    query_begin: string | undefined;
-    query_end: string | undefined;
-    query_remaining: string | undefined;
-    orientation: string | undefined;
-    matching_repeat_name: string | undefined;
-    matching_repeat_class: string | undefined;
-    matching_repeat_begin: string | undefined;
-    matching_repeat_end: string | undefined;
-    matching_repeat_remaining: string | undefined;
-    repeat_id: string | undefined;
-    description?: undefined;
-} | {
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-    description: undefined;
-    bitsw_score?: undefined;
-    percent_div?: undefined;
-    percent_del?: undefined;
-    percent_ins?: undefined;
-    query_chr?: undefined;
-    query_begin?: undefined;
-    query_end?: undefined;
-    query_remaining?: undefined;
-    orientation?: undefined;
-    matching_repeat_name?: undefined;
-    matching_repeat_class?: undefined;
-    matching_repeat_begin?: undefined;
-    matching_repeat_end?: undefined;
-    matching_repeat_remaining?: undefined;
-    repeat_id?: undefined;
-};

package/dist/generateRepeatMaskerFeature.js

@@ -1,42 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.isRepeatMaskerDescriptionField = isRepeatMaskerDescriptionField;
-exports.generateRepeatMaskerFeature = generateRepeatMaskerFeature;
-function isRepeatMaskerDescriptionField(desc) {
-    const ret = desc === null || desc === void 0 ? void 0 : desc.trim().split(' ');
-    return [0, 1, 2, 3, 5, 6].every(s => (ret === null || ret === void 0 ? void 0 : ret[s]) !== undefined ? !Number.isNaN(+ret[s]) : false);
-}
-function makeRepeatTrackDescription(description) {
-    if (isRepeatMaskerDescriptionField(description)) {
-        const [bitsw_score, percent_div, percent_del, percent_ins, query_chr, query_begin, query_end, query_remaining, orientation, matching_repeat_name, matching_repeat_class, matching_repeat_begin, matching_repeat_end, matching_repeat_remaining, repeat_id,] = description.trim().split(' ');
-        return {
-            bitsw_score,
-            percent_div,
-            percent_del,
-            percent_ins,
-            query_chr,
-            query_begin,
-            query_end,
-            query_remaining,
-            orientation,
-            matching_repeat_name,
-            matching_repeat_class,
-            matching_repeat_begin,
-            matching_repeat_end,
-            matching_repeat_remaining,
-            repeat_id,
-        };
-    }
-    return { description };
-}
-function generateRepeatMaskerFeature({ uniqueId, refName, start, end, description, ...rest }) {
-    const { subfeatures, ...rest2 } = rest;
-    return {
-        ...rest2,
-        ...makeRepeatTrackDescription(description),
-        uniqueId,
-        refName,
-        start,
-        end,
-    };
-}

package/dist/generateUcscTranscript.d.ts

@@ -1,20 +0,0 @@
-import type { TranscriptFeat } from './types';
-export declare function isUcscTranscript({ thickStart, blockCount, strand, }: {
-    thickStart?: number;
-    blockCount?: number;
-    strand?: number;
-}): boolean | 0 | undefined;
-export declare function generateUcscTranscript(data: TranscriptFeat): {
-    uniqueId: string;
-    strand: number;
-    type: string;
-    refName: string;
-    subfeatures: {
-        type: string;
-        start: number;
-        end: number;
-        refName: string;
-    }[];
-    start: number;
-    end: number;
-};

package/dist/generateUcscTranscript.js

@@ -1,123 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.isUcscTranscript = isUcscTranscript;
-exports.generateUcscTranscript = generateUcscTranscript;
-function isUcscTranscript({ thickStart, blockCount, strand, }) {
-    return thickStart && blockCount && strand !== 0;
-}
-function generateUcscTranscript(data) {
-    const { strand = 0, chrom: _1, chromStart: _2, chromEnd: _3, chromStarts, blockStarts, blockSizes, uniqueId, ...rest } = data;
-    const { subfeatures: oldSubfeatures, thickStart, thickEnd, blockCount, refName, ...rest2 } = rest;
-    const subfeatures = [];
-    const feats = oldSubfeatures
-        .filter(child => child.type === 'block')
-        .sort((a, b) => a.start - b.start);
-    const { cdsEndStat, cdsStartStat } = rest2;
-    if (cdsStartStat === 'none' && cdsEndStat === 'none') {
-        return {
-            ...rest2,
-            uniqueId,
-            strand,
-            type: 'transcript',
-            refName,
-            subfeatures: feats.map(e => ({
-                ...e,
-                type: 'exon',
-            })),
-        };
-    }
-    else {
-        for (const block of feats) {
-            const start = block.start;
-            const end = block.end;
-            if (thickStart >= end) {
-                subfeatures.push({
-                    type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
-                    start,
-                    end,
-                    refName,
-                });
-            }
-            else if (thickStart > start && thickStart < end && thickEnd >= end) {
-                subfeatures.push({
-                    type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
-                    start,
-                    end: thickStart,
-                    refName,
-                }, {
-                    type: 'CDS',
-                    phase: 0,
-                    start: thickStart,
-                    end,
-                    refName,
-                });
-            }
-            else if (thickStart <= start && thickEnd >= end) {
-                subfeatures.push({
-                    type: 'CDS',
-                    phase: 0,
-                    start,
-                    end,
-                    refName,
-                });
-            }
-            else if (thickStart > start && thickStart < end && thickEnd < end) {
-                subfeatures.push({
-                    type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
-                    start,
-                    end: thickStart,
-                    refName,
-                }, {
-                    type: 'CDS',
-                    phase: 0,
-                    start: thickStart,
-                    end: thickEnd,
-                    refName,
-                }, {
-                    type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
-                    start: thickEnd,
-                    end,
-                    refName,
-                });
-            }
-            else if (thickStart <= start && thickEnd > start && thickEnd < end) {
-                subfeatures.push({
-                    type: 'CDS',
-                    phase: 0,
-                    start,
-                    end: thickEnd,
-                    refName,
-                }, {
-                    type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
-                    start: thickEnd,
-                    end,
-                    refName,
-                });
-            }
-            else if (thickEnd <= start) {
-                subfeatures.push({
-                    type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
-                    start,
-                    end,
-                    refName,
-                });
-            }
-        }
-        return {
-            ...rest2,
-            uniqueId,
-            strand,
-            type: 'mRNA',
-            refName,
-            subfeatures,
-        };
-    }
-    return {
-        ...rest2,
-        uniqueId,
-        strand,
-        type: 'mRNA',
-        refName,
-        subfeatures,
-    };
-}

package/dist/index.d.ts

@@ -1,6 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin';
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default class BedPlugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-}

package/dist/index.js

@@ -1,29 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const BedAdapter_1 = __importDefault(require("./BedAdapter"));
-const BedGraphAdapter_1 = __importDefault(require("./BedGraphAdapter"));
-const BedGraphTabixAdapter_1 = __importDefault(require("./BedGraphTabixAdapter"));
-const BedTabixAdapter_1 = __importDefault(require("./BedTabixAdapter"));
-const BedpeAdapter_1 = __importDefault(require("./BedpeAdapter"));
-const BigBedAdapter_1 = __importDefault(require("./BigBedAdapter"));
-const GuessAdapter_1 = __importDefault(require("./GuessAdapter"));
-class BedPlugin extends Plugin_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'BedPlugin';
-    }
-    install(pluginManager) {
-        (0, BigBedAdapter_1.default)(pluginManager);
-        (0, BedAdapter_1.default)(pluginManager);
-        (0, BedpeAdapter_1.default)(pluginManager);
-        (0, BedTabixAdapter_1.default)(pluginManager);
-        (0, BedGraphAdapter_1.default)(pluginManager);
-        (0, BedGraphTabixAdapter_1.default)(pluginManager);
-        (0, GuessAdapter_1.default)(pluginManager);
-    }
-}
-exports.default = BedPlugin;

package/dist/types.d.ts

@@ -1,18 +0,0 @@
-export interface MinimalFeature {
-    type: string;
-    start: number;
-    end: number;
-    refName: string;
-    [key: string]: unknown;
-}
-export interface TranscriptFeat extends MinimalFeature {
-    uniqueId: string;
-    thickStart: number;
-    thickEnd: number;
-    blockCount: number;
-    blockSizes: number[];
-    chromStarts: number[];
-    refName: string;
-    strand?: number;
-    subfeatures: MinimalFeature[];
-}

package/dist/types.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/dist/util.d.ts

@@ -1,213 +0,0 @@
-import type BED from '@gmod/bed';
-export declare function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }: {
-    blockCount: number;
-    start: number;
-    uniqueId: string;
-    refName: string;
-    chromStarts?: number[];
-    blockSizes?: number[];
-    blockStarts?: number[];
-}): {
-    uniqueId: string;
-    start: number;
-    end: number;
-    refName: string;
-    type: string;
-}[];
-export declare function featureData({ line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names, }: {
-    line: string;
-    colRef: number;
-    colStart: number;
-    colEnd: number;
-    scoreColumn: string;
-    parser: BED;
-    uniqueId: string;
-    names?: string[];
-}): {
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-    code: string | undefined;
-    score: number;
-    strand: string | undefined;
-    color: string | undefined;
-    source: string | undefined;
-    n_valid_cov: string | undefined;
-    fraction_modified: string | undefined;
-    n_mod: string | undefined;
-    n_canonical: string | undefined;
-    n_other_mod: string | undefined;
-    n_delete: string | undefined;
-    n_fail: string | undefined;
-    n_diff: string | undefined;
-    n_nocall: string | undefined;
-} | {
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-    bitsw_score: string | undefined;
-    percent_div: string | undefined;
-    percent_del: string | undefined;
-    percent_ins: string | undefined;
-    query_chr: string | undefined;
-    query_begin: string | undefined;
-    query_end: string | undefined;
-    query_remaining: string | undefined;
-    orientation: string | undefined;
-    matching_repeat_name: string | undefined;
-    matching_repeat_class: string | undefined;
-    matching_repeat_begin: string | undefined;
-    matching_repeat_end: string | undefined;
-    matching_repeat_remaining: string | undefined;
-    repeat_id: string | undefined;
-    description?: undefined;
-} | {
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-    description: undefined;
-    bitsw_score?: undefined;
-    percent_div?: undefined;
-    percent_del?: undefined;
-    percent_ins?: undefined;
-    query_chr?: undefined;
-    query_begin?: undefined;
-    query_end?: undefined;
-    query_remaining?: undefined;
-    orientation?: undefined;
-    matching_repeat_name?: undefined;
-    matching_repeat_class?: undefined;
-    matching_repeat_begin?: undefined;
-    matching_repeat_end?: undefined;
-    matching_repeat_remaining?: undefined;
-    repeat_id?: undefined;
-} | {
-    uniqueId: string;
-    strand: number;
-    type: string;
-    refName: string;
-    subfeatures: {
-        type: string;
-        start: number;
-        end: number;
-        refName: string;
-    }[];
-    start: number;
-    end: number;
-} | {
-    uniqueId: string;
-    score: number | undefined;
-    start: number;
-    end: number;
-    strand: any;
-    refName: string;
-    subfeatures: {
-        uniqueId: string;
-        start: number;
-        end: number;
-        refName: string;
-        type: string;
-    }[] | undefined;
-};
-export declare function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, }: {
-    splitLine: string[];
-    refName: string;
-    start: number;
-    end: number;
-    parser: BED;
-    uniqueId: string;
-    scoreColumn: string;
-    names?: string[];
-}): {
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-    code: string | undefined;
-    score: number;
-    strand: string | undefined;
-    color: string | undefined;
-    source: string | undefined;
-    n_valid_cov: string | undefined;
-    fraction_modified: string | undefined;
-    n_mod: string | undefined;
-    n_canonical: string | undefined;
-    n_other_mod: string | undefined;
-    n_delete: string | undefined;
-    n_fail: string | undefined;
-    n_diff: string | undefined;
-    n_nocall: string | undefined;
-} | {
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-    bitsw_score: string | undefined;
-    percent_div: string | undefined;
-    percent_del: string | undefined;
-    percent_ins: string | undefined;
-    query_chr: string | undefined;
-    query_begin: string | undefined;
-    query_end: string | undefined;
-    query_remaining: string | undefined;
-    orientation: string | undefined;
-    matching_repeat_name: string | undefined;
-    matching_repeat_class: string | undefined;
-    matching_repeat_begin: string | undefined;
-    matching_repeat_end: string | undefined;
-    matching_repeat_remaining: string | undefined;
-    repeat_id: string | undefined;
-    description?: undefined;
-} | {
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-    description: undefined;
-    bitsw_score?: undefined;
-    percent_div?: undefined;
-    percent_del?: undefined;
-    percent_ins?: undefined;
-    query_chr?: undefined;
-    query_begin?: undefined;
-    query_end?: undefined;
-    query_remaining?: undefined;
-    orientation?: undefined;
-    matching_repeat_name?: undefined;
-    matching_repeat_class?: undefined;
-    matching_repeat_begin?: undefined;
-    matching_repeat_end?: undefined;
-    matching_repeat_remaining?: undefined;
-    repeat_id?: undefined;
-} | {
-    uniqueId: string;
-    strand: number;
-    type: string;
-    refName: string;
-    subfeatures: {
-        type: string;
-        start: number;
-        end: number;
-        refName: string;
-    }[];
-    start: number;
-    end: number;
-} | {
-    uniqueId: string;
-    score: number | undefined;
-    start: number;
-    end: number;
-    strand: any;
-    refName: string;
-    subfeatures: {
-        uniqueId: string;
-        start: number;
-        end: number;
-        refName: string;
-        type: string;
-    }[] | undefined;
-};
-export declare function arrayify(f?: string | number[]): number[] | undefined;