@jbrowse/plugin-bed 2.16.1 → 2.18.0

package/dist/generateBedMethylFeature.d.ts

@@ -0,0 +1,31 @@
+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

@@ -0,0 +1,30 @@
+"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;
+}
+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

@@ -0,0 +1,51 @@
+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

@@ -0,0 +1,41 @@
+"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 }) {
+    return {
+        ...rest,
+        ...makeRepeatTrackDescription(description),
+        uniqueId,
+        refName,
+        start,
+        end,
+    };
+}

package/dist/generateUcscTranscript.d.ts

@@ -0,0 +1,15 @@
+import type { MinimalFeature, 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: MinimalFeature[];
+    start: number;
+    end: number;
+};

package/dist/generateUcscTranscript.js

@@ -0,0 +1,95 @@
+"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);
+    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',
+                start: thickStart,
+                end,
+                refName,
+            });
+        }
+        else if (thickStart <= start && thickEnd >= end) {
+            subfeatures.push({
+                type: 'CDS',
+                start,
+                end,
+                refName,
+            });
+        }
+        else if (thickStart > start && thickStart < end && thickEnd < end) {
+            subfeatures.push({
+                type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
+                start,
+                end: thickStart,
+                refName,
+            }, {
+                type: 'CDS',
+                start: thickStart,
+                end: thickEnd,
+                refName,
+            }, {
+                type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
+                start: thickEnd,
+                end,
+                refName,
+            });
+        }
+        else if (thickStart <= start && thickEnd > start && thickEnd < end) {
+            subfeatures.push({
+                type: 'CDS',
+                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,
+    };
+}

package/dist/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class BedPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -4,11 +4,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const BigBedAdapter_1 = __importDefault(require("./BigBedAdapter"));
-const BedpeAdapter_1 = __importDefault(require("./BedpeAdapter"));
-const BedTabixAdapter_1 = __importDefault(require("./BedTabixAdapter"));
-const BedAdapter_1 = __importDefault(require("./BedAdapter"));
 const tracks_1 = require("@jbrowse/core/util/tracks");
+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"));
 class BedPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
@@ -19,6 +21,8 @@ class BedPlugin extends Plugin_1.default {
         (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);
         pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
             return (file, index, adapterHint) => {
                 const regexGuess = /\.(bb|bigbed)$/i;

package/dist/types.d.ts

@@ -0,0 +1,18 @@
+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

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

package/dist/util.d.ts

@@ -1,48 +1,203 @@
-import BED from '@gmod/bed';
-import { SimpleFeature } from '@jbrowse/core/util';
-export interface MinimalFeature {
+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;
-    [key: string]: unknown;
-}
-export interface TranscriptFeat extends MinimalFeature {
-    thickStart: number;
-    thickEnd: number;
-    blockCount: number;
-    blockSizes: number[];
-    chromStarts: number[];
+    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;
-    strand?: number;
-    subfeatures: MinimalFeature[];
-}
-export declare function ucscProcessedTranscript(feature: TranscriptFeat): TranscriptFeat | {
+    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: MinimalFeature[];
+    subfeatures: import("./types").MinimalFeature[];
+    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 makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }: {
-    blockCount: number;
+export declare function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, }: {
+    splitLine: string[];
+    refName: string;
     start: number;
+    end: number;
+    parser: BED;
     uniqueId: string;
-    refName: string;
-    chromStarts?: number[];
-    blockSizes: number[];
-    blockStarts?: number[];
+    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;
-}[];
-export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: BED, uniqueId: string, names?: string[]): SimpleFeature;
-export declare function isUcscProcessedTranscript(f: {
-    thickStart?: number;
-    blockCount?: number;
-    strand?: number;
-}): boolean | 0 | undefined;
+    refName: string;
+    subfeatures: import("./types").MinimalFeature[];
+    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;