@jbrowse/plugin-alignments 3.7.0 → 4.0.0

package/dist/CramAdapter/CramTestAdapters.js

@@ -1,85 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.SequenceAdapter = exports.FetchableSmallFasta = void 0;
-exports.parseSmallFasta = parseSmallFasta;
-const configuration_1 = require("@jbrowse/core/configuration");
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-const rxjs_1 = require("rxjs");
-function parseSmallFasta(text) {
-    return text
-        .split('>')
-        .filter(t => /\S/.test(t))
-        .map(entryText => {
-        const [defLine, ...seqLines] = entryText.split(/\n|\r\n|\r/);
-        const [id, ...descriptionLines] = defLine.split(' ');
-        const description = descriptionLines.join(' ');
-        const sequence = seqLines.join('').replaceAll(/\s/g, '');
-        return {
-            id: id,
-            description,
-            sequence,
-        };
-    });
-}
-class FetchableSmallFasta {
-    constructor(filehandle) {
-        this.data = filehandle.readFile().then(buffer => {
-            const decoder = new TextDecoder('utf8');
-            const text = decoder.decode(buffer);
-            return parseSmallFasta(text);
-        });
-    }
-    async fetch(id, start, end) {
-        const data = await this.data;
-        const entry = data[id];
-        const length = end - start + 1;
-        if (!entry) {
-            throw new Error(`no sequence with id ${id} exists`);
-        }
-        return entry.sequence.slice(start, start + length);
-    }
-    async getSequenceList() {
-        const data = await this.data;
-        return data.map(entry => entry.id);
-    }
-}
-exports.FetchableSmallFasta = FetchableSmallFasta;
-class SequenceAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    constructor(filehandle) {
-        super((0, configuration_1.ConfigurationSchema)('empty', {}).create());
-        this.refNames = [];
-        this.fasta = new FetchableSmallFasta(filehandle);
-    }
-    async getRefNames() {
-        return this.refNames;
-    }
-    getFeatures({ refName, start, end, }) {
-        return new rxjs_1.Observable(observer => {
-            this.fasta
-                .getSequenceList()
-                .then(refNames => {
-                this.refNames = refNames;
-            })
-                .then(() => this.fasta.fetch(this.refNames.indexOf(refName), start, end))
-                .then(ret => {
-                observer.next(new simpleFeature_1.default({
-                    uniqueId: `${refName}-${start}-${end}`,
-                    refName,
-                    seq: ret,
-                    start,
-                    end,
-                }));
-                observer.complete();
-            })
-                .catch((e) => {
-                observer.error(e);
-            });
-            return { unsubscribe: () => { } };
-        });
-    }
-}
-exports.SequenceAdapter = SequenceAdapter;

package/dist/CramAdapter/configSchema.d.ts

@@ -1,27 +0,0 @@
-declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    fetchSizeLimit: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    cramLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    craiLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    sequenceAdapter: {
-        type: string;
-        description: string;
-        defaultValue: null;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default configSchema;

package/dist/CramAdapter/configSchema.js

@@ -1,48 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const configSchema = (0, configuration_1.ConfigurationSchema)('CramAdapter', {
-    fetchSizeLimit: {
-        type: 'number',
-        description: 'size in bytes over which to display a warning to the user that too much data will be fetched',
-        defaultValue: 3000000,
-    },
-    cramLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/my.cram',
-            locationType: 'UriLocation',
-        },
-    },
-    craiLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/my.cram.crai',
-            locationType: 'UriLocation',
-        },
-    },
-    sequenceAdapter: {
-        type: 'frozen',
-        description: 'sequence data adapter',
-        defaultValue: null,
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                cramLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-                craiLocation: {
-                    uri: `${snap.uri}.crai`,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = configSchema;

package/dist/CramAdapter/index.d.ts

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

package/dist/CramAdapter/index.js

@@ -1,51 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = CramAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function CramAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => {
-        return new AdapterType_1.default({
-            name: 'CramAdapter',
-            displayName: 'CRAM adapter',
-            configSchema: configSchema_1.default,
-            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./CramAdapter'))).then(r => r.default),
-        });
-    });
-}

package/dist/CramAdapter/readFeaturesToCIGAR.d.ts

@@ -1,9 +0,0 @@
-import type { Mismatch } from '../shared/types';
-import type { CramRecord } from '@gmod/cram';
-type ReadFeatures = CramRecord['readFeatures'];
-export declare function readFeaturesToMismatches(readFeatures: ReadFeatures, start: number, qual?: number[] | null): Mismatch[];
-export declare function readFeaturesToCIGAR(readFeatures: ReadFeatures, alignmentStart: number, readLen: number, refRegion?: {
-    seq: string;
-    start: number;
-}): string;
-export {};

package/dist/CramAdapter/readFeaturesToCIGAR.js

@@ -1,212 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.readFeaturesToMismatches = readFeaturesToMismatches;
-exports.readFeaturesToCIGAR = readFeaturesToCIGAR;
-function readFeaturesToMismatches(readFeatures = [], start, qual) {
-    const mismatches = new Array(readFeatures.length);
-    let j = 0;
-    let insLen = 0;
-    let refPos = 0;
-    let sublen = 0;
-    let lastPos = start;
-    for (const ret of readFeatures) {
-        const { refPos: p, code, pos, data, sub, ref } = ret;
-        sublen = refPos - lastPos;
-        lastPos = refPos;
-        if (sublen && insLen > 0) {
-            mismatches[j++] = {
-                start: refPos,
-                type: 'insertion',
-                base: `${insLen}`,
-                insertedBases: data,
-                length: 0,
-            };
-            insLen = 0;
-        }
-        refPos = p - 1 - start;
-        if (code === 'X') {
-            mismatches[j++] = {
-                start: refPos,
-                length: 1,
-                base: sub,
-                qual: qual === null || qual === void 0 ? void 0 : qual[pos - 1],
-                altbase: ref === null || ref === void 0 ? void 0 : ref.toUpperCase(),
-                type: 'mismatch',
-            };
-        }
-        else if (code === 'I') {
-            mismatches[j++] = {
-                start: refPos,
-                type: 'insertion',
-                base: `${data.length}`,
-                length: 0,
-            };
-        }
-        else if (code === 'N') {
-            mismatches[j++] = {
-                type: 'skip',
-                length: data,
-                start: refPos,
-                base: 'N',
-            };
-        }
-        else if (code === 'S') {
-            const len = data.length;
-            mismatches[j++] = {
-                start: refPos,
-                type: 'softclip',
-                base: `S${len}`,
-                cliplen: len,
-                length: 1,
-            };
-        }
-        else if (code === 'P') {
-        }
-        else if (code === 'H') {
-            const len = data;
-            mismatches[j++] = {
-                start: refPos,
-                type: 'hardclip',
-                base: `H${len}`,
-                cliplen: len,
-                length: 1,
-            };
-        }
-        else if (code === 'D') {
-            mismatches[j++] = {
-                type: 'deletion',
-                length: data,
-                start: refPos,
-                base: '*',
-            };
-        }
-        else if (code === 'b') {
-        }
-        else if (code === 'q') {
-        }
-        else if (code === 'B') {
-        }
-        else if (code === 'i') {
-            insLen++;
-        }
-        else if (code === 'Q') {
-        }
-    }
-    if (sublen && insLen > 0) {
-        mismatches[j++] = {
-            start: refPos,
-            type: 'insertion',
-            base: `${insLen}`,
-            length: 0,
-        };
-        insLen = 0;
-    }
-    return mismatches.slice(0, j);
-}
-function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
-    let seq = '';
-    let cigar = '';
-    let op = 'M';
-    let oplen = 0;
-    if (!refRegion) {
-        return '';
-    }
-    const ref = refRegion.seq;
-    const refStart = refRegion.start;
-    let lastPos = alignmentStart;
-    let sublen = 0;
-    let insLen = 0;
-    if (readFeatures !== undefined) {
-        for (const { code, refPos, sub, data } of readFeatures) {
-            sublen = refPos - lastPos;
-            seq += ref.slice(lastPos - refStart, refPos - refStart);
-            lastPos = refPos;
-            if (insLen > 0 && sublen) {
-                cigar += `${insLen}I`;
-                insLen = 0;
-            }
-            if (oplen && op !== 'M') {
-                cigar += `${oplen}${op}`;
-                oplen = 0;
-            }
-            if (sublen) {
-                op = 'M';
-                oplen += sublen;
-            }
-            if (code === 'b') {
-                const ret = data.split(',');
-                const added = String.fromCharCode(...ret);
-                seq += added;
-                lastPos += added.length;
-                oplen += added.length;
-            }
-            else if (code === 'B') {
-                seq += sub;
-                lastPos++;
-                oplen++;
-            }
-            else if (code === 'X') {
-                seq += sub;
-                lastPos++;
-                oplen++;
-            }
-            else if (code === 'D' || code === 'N') {
-                lastPos += data;
-                if (oplen) {
-                    cigar += `${oplen}${op}`;
-                }
-                cigar += data + code;
-                oplen = 0;
-            }
-            else if (code === 'I' || code === 'S') {
-                seq += data;
-                if (oplen) {
-                    cigar += `${oplen}${op}`;
-                }
-                cigar += data.length + code;
-                oplen = 0;
-            }
-            else if (code === 'i') {
-                if (oplen) {
-                    cigar += `${oplen}${op}`;
-                }
-                insLen++;
-                seq += data;
-                oplen = 0;
-            }
-            else if (code === 'P') {
-                if (oplen) {
-                    cigar += `${oplen}${op}`;
-                }
-                cigar += `${data}P`;
-            }
-            else if (code === 'H') {
-                if (oplen) {
-                    cigar += `${oplen}${op}`;
-                }
-                cigar += `${data}H`;
-                oplen = 0;
-            }
-        }
-    }
-    else {
-        sublen = readLen - seq.length;
-    }
-    if (seq.length !== readLen) {
-        sublen = readLen - seq.length;
-        seq += ref.slice(lastPos - refStart, lastPos - refStart + sublen);
-        if (oplen && op !== 'M') {
-            cigar += `${oplen}${op}`;
-            oplen = 0;
-        }
-        op = 'M';
-        oplen += sublen;
-    }
-    if (sublen && insLen > 0) {
-        cigar += `${insLen}I`;
-    }
-    if (oplen) {
-        cigar += `${oplen}${op}`;
-    }
-    return cigar;
-}

package/dist/CramAdapter/readFeaturesToMismatches.d.ts

@@ -1,5 +0,0 @@
-import type { Mismatch } from '../shared/types';
-import type { CramRecord } from '@gmod/cram';
-type ReadFeatures = CramRecord['readFeatures'];
-export declare function readFeaturesToMismatches(readFeatures: ReadFeatures, start: number, qual?: number[] | null): Mismatch[];
-export {};

package/dist/CramAdapter/readFeaturesToMismatches.js

@@ -1,106 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.readFeaturesToMismatches = readFeaturesToMismatches;
-function readFeaturesToMismatches(readFeatures = [], start, qual) {
-    const mismatches = new Array(readFeatures.length);
-    let j = 0;
-    let refPos = 0;
-    let sublen = 0;
-    let lastPos = start;
-    let insertedBases = '';
-    for (const ret of readFeatures) {
-        const { refPos: p, code, pos, data, sub, ref } = ret;
-        sublen = refPos - lastPos;
-        lastPos = refPos;
-        if (sublen && insertedBases.length > 0) {
-            mismatches[j++] = {
-                start: refPos,
-                type: 'insertion',
-                base: `${insertedBases.length}`,
-                insertedBases,
-                length: 0,
-            };
-            insertedBases = '';
-        }
-        refPos = p - 1 - start;
-        if (code === 'X') {
-            mismatches[j++] = {
-                start: refPos,
-                length: 1,
-                base: sub,
-                qual: qual === null || qual === void 0 ? void 0 : qual[pos - 1],
-                altbase: ref === null || ref === void 0 ? void 0 : ref.toUpperCase(),
-                type: 'mismatch',
-            };
-        }
-        else if (code === 'I') {
-            mismatches[j++] = {
-                start: refPos,
-                type: 'insertion',
-                base: `${data.length}`,
-                insertedBases: data,
-                length: 0,
-            };
-        }
-        else if (code === 'N') {
-            mismatches[j++] = {
-                type: 'skip',
-                length: data,
-                start: refPos,
-                base: 'N',
-            };
-        }
-        else if (code === 'S') {
-            const len = data.length;
-            mismatches[j++] = {
-                start: refPos,
-                type: 'softclip',
-                base: `S${len}`,
-                cliplen: len,
-                length: 1,
-            };
-        }
-        else if (code === 'P') {
-        }
-        else if (code === 'H') {
-            const len = data;
-            mismatches[j++] = {
-                start: refPos,
-                type: 'hardclip',
-                base: `H${len}`,
-                cliplen: len,
-                length: 1,
-            };
-        }
-        else if (code === 'D') {
-            mismatches[j++] = {
-                type: 'deletion',
-                length: data,
-                start: refPos,
-                base: '*',
-            };
-        }
-        else if (code === 'b') {
-        }
-        else if (code === 'q') {
-        }
-        else if (code === 'B') {
-        }
-        else if (code === 'i') {
-            insertedBases += data;
-        }
-        else if (code === 'Q') {
-        }
-    }
-    if (sublen && insertedBases.length > 0) {
-        mismatches[j++] = {
-            start: refPos,
-            type: 'insertion',
-            base: `${insertedBases.length}`,
-            insertedBases,
-            length: 0,
-        };
-        insertedBases = '';
-    }
-    return mismatches.slice(0, j);
-}

package/dist/GuessAlignmentsTypes/index.js

@@ -1,41 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = GuessAlignmentsTypesF;
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-function GuessAlignmentsTypesF(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, /\.bam$/i, adapterHint, 'BamAdapter')) {
-                return {
-                    type: 'BamAdapter',
-                    bamLocation: file,
-                    index: {
-                        location: index || (0, tracks_1.makeIndex)(file, '.bai'),
-                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'BAI'),
-                    },
-                };
-            }
-            else if ((0, util_1.testAdapter)(fileName, /\.cram$/i, adapterHint, 'CramAdapter')) {
-                return {
-                    type: 'CramAdapter',
-                    cramLocation: file,
-                    craiLocation: index || (0, tracks_1.makeIndex)(file, '.crai'),
-                };
-            }
-            else {
-                return adapterGuesser(file, index, adapterHint);
-            }
-        };
-    });
-    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
-        return (adapterName) => {
-            if (adapterName === 'BamAdapter' || adapterName === 'CramAdapter') {
-                return 'AlignmentsTrack';
-            }
-            return trackTypeGuesser(adapterName);
-        };
-    });
-}

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.d.ts

@@ -1,12 +0,0 @@
-import BamAdapter from '../BamAdapter/BamAdapter';
-import type { BamFile } from '@gmod/bam';
-import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-export default class HtsgetBamAdapter extends BamAdapter {
-    protected configurePre(): Promise<{
-        bam: BamFile;
-        sequenceAdapter: BaseFeatureDataAdapter;
-    } | {
-        bam: BamFile;
-        sequenceAdapter?: undefined;
-    }>;
-}

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js

@@ -1,27 +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 bam_1 = require("@gmod/bam");
-const BamAdapter_1 = __importDefault(require("../BamAdapter/BamAdapter"));
-class HtsgetBamAdapter extends BamAdapter_1.default {
-    async configurePre() {
-        const htsgetBase = this.getConf('htsgetBase');
-        const htsgetTrackId = this.getConf('htsgetTrackId');
-        const bam = new bam_1.HtsgetFile({
-            baseUrl: htsgetBase,
-            trackId: htsgetTrackId,
-        });
-        const adapterConfig = this.getConf('sequenceAdapter');
-        if (adapterConfig && this.getSubAdapter) {
-            const adapter = await this.getSubAdapter(adapterConfig);
-            return {
-                bam,
-                sequenceAdapter: adapter.dataAdapter,
-            };
-        }
-        return { bam };
-    }
-}
-exports.default = HtsgetBamAdapter;

package/dist/HtsgetBamAdapter/configSchema.d.ts

@@ -1,18 +0,0 @@
-declare const HtsgetBamAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    htsgetBase: {
-        type: string;
-        description: string;
-        defaultValue: string;
-    };
-    htsgetTrackId: {
-        type: string;
-        description: string;
-        defaultValue: string;
-    };
-    sequenceAdapter: {
-        type: string;
-        description: string;
-        defaultValue: null;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default HtsgetBamAdapter;

package/dist/HtsgetBamAdapter/configSchema.js

@@ -1,22 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const HtsgetBamAdapter = (0, configuration_1.ConfigurationSchema)('HtsgetBamAdapter', {
-    htsgetBase: {
-        type: 'string',
-        description: 'the base URL to fetch from',
-        defaultValue: '',
-    },
-    htsgetTrackId: {
-        type: 'string',
-        description: 'the trackId, which is appended to the base URL',
-        defaultValue: '',
-    },
-    sequenceAdapter: {
-        type: 'frozen',
-        description: 'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
-        defaultValue: null,
-    },
-}, { explicitlyTyped: true });
-exports.default = HtsgetBamAdapter;

package/dist/HtsgetBamAdapter/index.d.ts

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