@jbrowse/plugin-alignments 3.6.5 → 4.0.0

package/dist/MismatchParser/getNextRefPos.js

@@ -1,38 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getNextRefPos = getNextRefPos;
-function getNextRefPos(cigarOps, positions) {
-    let readPos = 0;
-    let refPos = 0;
-    let currPos = 0;
-    const ret = [];
-    for (let i = 0; i < cigarOps.length && currPos < positions.length; i += 2) {
-        const len = +cigarOps[i];
-        const op = cigarOps[i + 1];
-        if (op === 'S' || op === 'I') {
-            for (let i = 0; i < len && currPos < positions.length; i++) {
-                if (positions[currPos] === readPos + i) {
-                    currPos++;
-                }
-            }
-            readPos += len;
-        }
-        else if (op === 'D' || op === 'N') {
-            refPos += len;
-        }
-        else if (op === 'M' || op === 'X' || op === '=') {
-            for (let i = 0; i < len && currPos < positions.length; i++) {
-                if (positions[currPos] === readPos + i) {
-                    ret.push({
-                        ref: refPos + i,
-                        idx: currPos,
-                    });
-                    currPos++;
-                }
-            }
-            readPos += len;
-            refPos += len;
-        }
-    }
-    return ret;
-}

package/dist/MismatchParser/index.d.ts

@@ -1,27 +0,0 @@
-import type { Mismatch } from '../shared/types';
-import type { Feature } from '@jbrowse/core/util';
-export declare function parseCigar(s?: string): string[];
-export declare function getMismatches(cigar?: string, md?: string, seq?: string, ref?: string, qual?: Uint8Array): Mismatch[];
-export declare function getOrientedCigar(flip: boolean, cigar: string[]): string[];
-export declare function getOrientedMismatches(flip: boolean, cigar: string): Mismatch[];
-export declare function getLengthOnRef(cigar: string): number;
-export declare function getLength(cigar: string): number;
-export declare function getLengthSansClipping(cigar: string): number;
-export declare function getClip(cigar: string, strand: number): number;
-export declare function getTag(feature: Feature, tag: string): any;
-export declare function featurizeSA(SA: string | undefined, id: string, strand: number, readName: string, normalize?: boolean): {
-    refName: string;
-    start: number;
-    end: number;
-    seqLength: number;
-    clipPos: number;
-    CIGAR: string;
-    strand: number;
-    uniqueId: string;
-    mate: {
-        start: number;
-        end: number;
-        refName: string;
-    };
-}[];
-export { getNextRefPos } from './getNextRefPos';

package/dist/MismatchParser/index.js

@@ -1,145 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getNextRefPos = void 0;
-exports.parseCigar = parseCigar;
-exports.getMismatches = getMismatches;
-exports.getOrientedCigar = getOrientedCigar;
-exports.getOrientedMismatches = getOrientedMismatches;
-exports.getLengthOnRef = getLengthOnRef;
-exports.getLength = getLength;
-exports.getLengthSansClipping = getLengthSansClipping;
-exports.getClip = getClip;
-exports.getTag = getTag;
-exports.featurizeSA = featurizeSA;
-const cigarToMismatches_1 = require("./cigarToMismatches");
-const mdToMismatches_1 = require("./mdToMismatches");
-const startClip = new RegExp(/(\d+)[SH]$/);
-const endClip = new RegExp(/^(\d+)([SH])/);
-function parseCigar(s = '') {
-    let currLen = '';
-    let len;
-    let op;
-    const ret = [];
-    for (let i = 0, l = s.length; i < l; i++) {
-        const c = s[i];
-        if (c >= '0' && c <= '9') {
-            currLen = currLen + c;
-        }
-        else {
-            len = currLen;
-            op = c;
-            currLen = '';
-            ret.push(len, op);
-        }
-    }
-    return ret;
-}
-function getMismatches(cigar, md, seq, ref, qual) {
-    let mismatches = [];
-    const ops = parseCigar(cigar);
-    if (cigar) {
-        mismatches = mismatches.concat((0, cigarToMismatches_1.cigarToMismatches)(ops, seq, ref, qual));
-    }
-    if (md && seq) {
-        mismatches = mismatches.concat((0, mdToMismatches_1.mdToMismatches)(md, ops, mismatches, seq, qual));
-    }
-    return mismatches;
-}
-function getOrientedCigar(flip, cigar) {
-    if (flip) {
-        const ret = [];
-        for (let i = 0; i < cigar.length; i += 2) {
-            const len = cigar[i];
-            let op = cigar[i + 1];
-            if (op === 'D') {
-                op = 'I';
-            }
-            else if (op === 'I') {
-                op = 'D';
-            }
-            ret.push(len, op);
-        }
-        return ret;
-    }
-    return cigar;
-}
-function getOrientedMismatches(flip, cigar) {
-    const p = parseCigar(cigar);
-    return (0, cigarToMismatches_1.cigarToMismatches)(flip ? getOrientedCigar(flip, p) : p);
-}
-function getLengthOnRef(cigar) {
-    const cigarOps = parseCigar(cigar);
-    let lengthOnRef = 0;
-    for (let i = 0; i < cigarOps.length; i += 2) {
-        const len = +cigarOps[i];
-        const op = cigarOps[i + 1];
-        if (op !== 'H' && op !== 'S' && op !== 'I') {
-            lengthOnRef += len;
-        }
-    }
-    return lengthOnRef;
-}
-function getLength(cigar) {
-    const cigarOps = parseCigar(cigar);
-    let length = 0;
-    for (let i = 0; i < cigarOps.length; i += 2) {
-        const len = +cigarOps[i];
-        const op = cigarOps[i + 1];
-        if (op !== 'D' && op !== 'N') {
-            length += len;
-        }
-    }
-    return length;
-}
-function getLengthSansClipping(cigar) {
-    const cigarOps = parseCigar(cigar);
-    let length = 0;
-    for (let i = 0; i < cigarOps.length; i += 2) {
-        const len = +cigarOps[i];
-        const op = cigarOps[i + 1];
-        if (op !== 'H' && op !== 'S' && op !== 'D' && op !== 'N') {
-            length += len;
-        }
-    }
-    return length;
-}
-function getClip(cigar, strand) {
-    return strand === -1
-        ? +(startClip.exec(cigar) || [])[1] || 0
-        : +(endClip.exec(cigar) || [])[1] || 0;
-}
-function getTag(feature, tag) {
-    return feature.get('tags')[tag];
-}
-function featurizeSA(SA, id, strand, readName, normalize) {
-    return ((SA === null || SA === void 0 ? void 0 : SA.split(';').filter(aln => !!aln).map((aln, index) => {
-        const ret = aln.split(',');
-        const saRef = ret[0];
-        const saStart = ret[1];
-        const saStrand = ret[2];
-        const saCigar = ret[3];
-        const saLengthOnRef = getLengthOnRef(saCigar);
-        const saLength = getLength(saCigar);
-        const saLengthSansClipping = getLengthSansClipping(saCigar);
-        const saStrandNormalized = saStrand === '-' ? -1 : 1;
-        const saClipPos = getClip(saCigar, (normalize ? strand : 1) * saStrandNormalized);
-        const saRealStart = +saStart - 1;
-        return {
-            refName: saRef,
-            start: saRealStart,
-            end: saRealStart + saLengthOnRef,
-            seqLength: saLength,
-            clipPos: saClipPos,
-            CIGAR: saCigar,
-            strand: (normalize ? strand : 1) * saStrandNormalized,
-            uniqueId: `${id}_SA${index}`,
-            mate: {
-                start: saClipPos,
-                end: saClipPos + saLengthSansClipping,
-                refName: readName,
-            },
-        };
-    })) || []);
-}
-var getNextRefPos_1 = require("./getNextRefPos");
-Object.defineProperty(exports, "getNextRefPos", { enumerable: true, get: function () { return getNextRefPos_1.getNextRefPos; } });

package/dist/MismatchParser/mdToMismatches.d.ts

@@ -1,2 +0,0 @@
-import type { Mismatch } from '../shared/types';
-export declare function mdToMismatches(mdstring: string, ops: string[], cigarMismatches: Mismatch[], seq: string, qual?: Uint8Array): Mismatch[];

package/dist/MismatchParser/mdToMismatches.js

@@ -1,74 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.mdToMismatches = mdToMismatches;
-const mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi);
-function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
-    let curr = { start: 0, base: '', length: 0, type: 'mismatch' };
-    let lastCigar = 0;
-    let lastTemplateOffset = 0;
-    let lastRefOffset = 0;
-    let lastSkipPos = 0;
-    const mismatchRecords = [];
-    const skips = cigarMismatches.filter(cigar => cigar.type === 'skip');
-    function nextRecord() {
-        mismatchRecords.push(curr);
-        curr = {
-            start: curr.start + curr.length,
-            length: 0,
-            base: '',
-            type: 'mismatch',
-        };
-    }
-    function getTemplateCoordLocal(refCoord) {
-        let templateOffset = lastTemplateOffset;
-        let refOffset = lastRefOffset;
-        for (let i = lastCigar; i < ops.length && refOffset <= refCoord; i += 2, lastCigar = i) {
-            const len = +ops[i];
-            const op = ops[i + 1];
-            if (op === 'S' || op === 'I') {
-                templateOffset += len;
-            }
-            else if (op === 'D' || op === 'P' || op === 'N') {
-                refOffset += len;
-            }
-            else if (op !== 'H') {
-                templateOffset += len;
-                refOffset += len;
-            }
-        }
-        lastTemplateOffset = templateOffset;
-        lastRefOffset = refOffset;
-        return templateOffset - (refOffset - refCoord);
-    }
-    const md = mdstring.match(mdRegex) || [];
-    for (const token of md) {
-        const num = +token;
-        if (!Number.isNaN(num)) {
-            curr.start += num;
-        }
-        else if (token.startsWith('^')) {
-            curr.start += token.length - 1;
-        }
-        else {
-            for (let j = 0; j < token.length; j += 1) {
-                curr.length = 1;
-                while (lastSkipPos < skips.length) {
-                    const mismatch = skips[lastSkipPos];
-                    if (curr.start >= mismatch.start) {
-                        curr.start += mismatch.length;
-                        lastSkipPos++;
-                    }
-                    else {
-                        break;
-                    }
-                }
-                const s = getTemplateCoordLocal(curr.start);
-                curr.base = seq[s] || 'X';
-                curr.qual = qual === null || qual === void 0 ? void 0 : qual[s];
-                curr.altbase = token;
-                nextRecord();
-            }
-        }
-    }
-    return mismatchRecords;
-}

package/dist/ModificationParser/consts.d.ts

@@ -1 +0,0 @@
-export declare const modificationRegex: RegExp;

package/dist/ModificationParser/consts.js

@@ -1,4 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.modificationRegex = void 0;
-exports.modificationRegex = new RegExp(/([A-Z])([-+])([a-z]+|[0-9]+)([.?]?)/);

package/dist/ModificationParser/getMethBins.d.ts

@@ -1,7 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-export declare function getMethBins(feature: Feature, cigarOps: string[]): {
-    methBins: number[];
-    hydroxyMethBins: number[];
-    methProbs: number[];
-    hydroxyMethProbs: number[];
-};

package/dist/ModificationParser/getMethBins.js

@@ -1,49 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getMethBins = getMethBins;
-const MismatchParser_1 = require("../MismatchParser");
-const getModPositions_1 = require("./getModPositions");
-const getModProbabilities_1 = require("./getModProbabilities");
-const util_1 = require("../util");
-function getMethBins(feature, cigarOps) {
-    const fstart = feature.get('start');
-    const fend = feature.get('end');
-    const fstrand = feature.get('strand');
-    const flen = fend - fstart;
-    const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
-    const methBins = [];
-    const hydroxyMethBins = [];
-    const methProbs = [];
-    const hydroxyMethProbs = [];
-    const seq = feature.get('seq');
-    if (seq) {
-        const probabilities = (0, getModProbabilities_1.getModProbabilities)(feature);
-        const modifications = (0, getModPositions_1.getModPositions)(mm, seq, fstrand);
-        let probIndex = 0;
-        for (const { type, positions } of modifications) {
-            for (const { ref, idx } of (0, MismatchParser_1.getNextRefPos)(cigarOps, positions)) {
-                if (ref < 0 || ref >= flen) {
-                    continue;
-                }
-                const isReverseStrand = fstrand === -1;
-                const idx2 = probIndex + (isReverseStrand ? positions.length - 1 - idx : idx);
-                const prob = (probabilities === null || probabilities === void 0 ? void 0 : probabilities[idx2]) || 0;
-                if (type === 'm') {
-                    methBins[ref] = 1;
-                    methProbs[ref] = prob;
-                }
-                else if (type === 'h') {
-                    hydroxyMethBins[ref] = 1;
-                    hydroxyMethProbs[ref] = prob;
-                }
-            }
-            probIndex += positions.length;
-        }
-    }
-    return {
-        methBins,
-        hydroxyMethBins,
-        methProbs,
-        hydroxyMethProbs,
-    };
-}

package/dist/ModificationParser/getModPositions.d.ts

@@ -1,6 +0,0 @@
-export declare function getModPositions(mm: string, fseq: string, fstrand: number): {
-    type: string;
-    positions: number[];
-    base: string;
-    strand: string;
-}[];

package/dist/ModificationParser/getModPositions.js

@@ -1,64 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getModPositions = getModPositions;
-const util_1 = require("@jbrowse/core/util");
-const consts_1 = require("./consts");
-function getModPositions(mm, fseq, fstrand) {
-    const seq = fstrand === -1 ? (0, util_1.revcom)(fseq) : fseq;
-    const mods = mm.split(';');
-    const result = [];
-    for (const mod of mods) {
-        if (mod === '') {
-            continue;
-        }
-        const split = mod.split(',');
-        const basemod = split[0];
-        const matches = consts_1.modificationRegex.exec(basemod);
-        if (!matches) {
-            throw new Error(`bad format for MM tag: "${mod}"`);
-        }
-        const [, base, strand, typestr] = matches;
-        const types = typestr.split(/(\d+|.)/);
-        if (strand === '-') {
-            console.warn('unsupported negative strand modifications');
-            result.push({
-                type: 'unsupported',
-                positions: [],
-                base: base,
-                strand: strand,
-            });
-        }
-        for (const type of types) {
-            if (type === '') {
-                continue;
-            }
-            let currPos = 0;
-            const positions = [];
-            for (let i = 1, l = split.length; i < l; i++) {
-                let delta = +split[i];
-                do {
-                    if (base === 'N' || base === seq[currPos]) {
-                        delta--;
-                    }
-                    currPos++;
-                } while (delta >= 0 && currPos < seq.length);
-                if (fstrand === -1) {
-                    const pos = seq.length - currPos;
-                    if (pos >= 0) {
-                        positions.unshift(pos);
-                    }
-                }
-                else {
-                    positions.push(currPos - 1);
-                }
-            }
-            result.push({
-                type,
-                base: base,
-                strand: strand,
-                positions,
-            });
-        }
-    }
-    return result;
-}

package/dist/ModificationParser/getModProbabilities.d.ts

@@ -1,2 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-export declare function getModProbabilities(feature: Feature): number[] | undefined;

package/dist/ModificationParser/getModProbabilities.js

@@ -1,34 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getModProbabilities = getModProbabilities;
-const util_1 = require("../util");
-function getModProbabilities(feature) {
-    const m = (0, util_1.getTagAlt)(feature, 'ML', 'Ml') || [];
-    if (m) {
-        const result = [];
-        if (typeof m === 'string') {
-            const parts = m.split(',');
-            for (let i = 0, l = parts.length; i < l; i++) {
-                result.push(+parts[i] / 255);
-            }
-        }
-        else {
-            for (let i = 0, l = m.length; i < l; i++) {
-                result.push(m[i] / 255);
-            }
-        }
-        return result;
-    }
-    else {
-        const mp = (0, util_1.getTagAlt)(feature, 'MP', 'Mp');
-        if (mp) {
-            const result = [];
-            for (let i = 0, l = mp.length; i < l; i++) {
-                const phred = mp.charCodeAt(i) - 33;
-                result.push(Math.min(1, phred / 50));
-            }
-            return result;
-        }
-        return undefined;
-    }
-}

package/dist/ModificationParser/getModTypes.d.ts

@@ -1,5 +0,0 @@
-export declare function getModTypes(mm: string): {
-    type: string;
-    base: string;
-    strand: string;
-}[];

package/dist/ModificationParser/getModTypes.js

@@ -1,35 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getModTypes = getModTypes;
-const consts_1 = require("./consts");
-function getModTypes(mm) {
-    const result = [];
-    const mods = mm.split(';');
-    for (let i = 0, modsLen = mods.length; i < modsLen; i++) {
-        const mod = mods[i];
-        if (mod === '') {
-            continue;
-        }
-        const basemod = mod.split(',')[0];
-        const matches = consts_1.modificationRegex.exec(basemod);
-        if (!matches) {
-            throw new Error(`bad format for MM tag: "${mod}"`);
-        }
-        const base = matches[1];
-        const strand = matches[2];
-        const typestr = matches[3];
-        const types = typestr.split(/(\d+|.)/);
-        for (let j = 0, typesLen = types.length; j < typesLen; j++) {
-            const type = types[j];
-            if (type === '') {
-                continue;
-            }
-            result.push({
-                type,
-                base,
-                strand,
-            });
-        }
-    }
-    return result;
-}

package/dist/PileupRPC/base.d.ts

@@ -1,8 +0,0 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import type { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
-export default abstract class PileupBaseRPC extends RpcMethodType {
-    serializeArguments(args: RenderArgs & {
-        stopToken?: string;
-        statusCallback?: (arg: string) => void;
-    }, rpcDriver: string): Promise<Record<string, unknown>>;
-}

package/dist/PileupRPC/base.js

@@ -1,20 +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 RpcMethodType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
-const util_1 = require("@jbrowse/core/util");
-class PileupBaseRPC extends RpcMethodType_1.default {
-    async serializeArguments(args, rpcDriver) {
-        var _a;
-        const { rootModel } = this.pluginManager;
-        const assemblyManager = (_a = rootModel === null || rootModel === void 0 ? void 0 : rootModel.session) === null || _a === void 0 ? void 0 : _a.assemblyManager;
-        if (!assemblyManager) {
-            throw new Error('no assembly manager available');
-        }
-        const renamedArgs = await (0, util_1.renameRegionsIfNeeded)(assemblyManager, args);
-        return super.serializeArguments(renamedArgs, rpcDriver);
-    }
-}
-exports.default = PileupBaseRPC;

package/dist/PileupRPC/index.d.ts

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

package/dist/PileupRPC/index.js

@@ -1,9 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = PileupRPCMethodsF;
-const rpcMethods_1 = require("./rpcMethods");
-function PileupRPCMethodsF(pm) {
-    pm.addRpcMethod(() => new rpcMethods_1.PileupGetGlobalValueForTag(pm));
-    pm.addRpcMethod(() => new rpcMethods_1.PileupGetVisibleModifications(pm));
-    pm.addRpcMethod(() => new rpcMethods_1.PileupGetReducedFeatures(pm));
-}

package/dist/PileupRPC/methods/GetGlobalValueForTag.d.ts

@@ -1,13 +0,0 @@
-import PileupBaseRPC from '../base';
-import type { Region } from '@jbrowse/core/util';
-export default class PileupGetGlobalValueForTag extends PileupBaseRPC {
-    name: string;
-    execute(args: {
-        adapterConfig: Record<string, unknown>;
-        stopToken?: string;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriver: string): Promise<string[]>;
-}

package/dist/PileupRPC/methods/GetGlobalValueForTag.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 dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
-const rxjs_1 = require("rxjs");
-const operators_1 = require("rxjs/operators");
-const base_1 = __importDefault(require("../base"));
-class PileupGetGlobalValueForTag extends base_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'PileupGetGlobalValueForTag';
-    }
-    async execute(args, rpcDriver) {
-        const deserializedArgs = await this.deserializeArguments(args, rpcDriver);
-        const { adapterConfig, sessionId, regions, tag } = deserializedArgs;
-        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
-        const features = dataAdapter.getFeaturesInMultipleRegions(regions, deserializedArgs);
-        const featuresArray = await (0, rxjs_1.firstValueFrom)(features.pipe((0, operators_1.toArray)()));
-        return [
-            ...new Set(featuresArray
-                .map(feature => { var _a; return (_a = feature.get('tags')) === null || _a === void 0 ? void 0 : _a[tag]; })
-                .filter(f => f !== undefined)
-                .map(f => `${f}`)),
-        ];
-    }
-}
-exports.default = PileupGetGlobalValueForTag;

package/dist/PileupRPC/methods/GetReducedFeatures.d.ts

@@ -1,37 +0,0 @@
-import PileupBaseRPC from '../base';
-import type { Region } from '@jbrowse/core/util';
-export default class PileupGetReducedFeatures extends PileupBaseRPC {
-    name: string;
-    execute(args: {
-        adapterConfig: Record<string, unknown>;
-        stopToken?: string;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriver: string): Promise<{
-        chains: {
-            id: string;
-            refName: string;
-            name: any;
-            start: number;
-            strand: any;
-            end: number;
-            flags: any;
-            tlen: any;
-            pair_orientation: any;
-            next_ref: any;
-            next_pos: any;
-            clipPos: number;
-            SA: any;
-        }[][];
-        stats: {
-            upper: number;
-            lower: number;
-            avg: number;
-            sd: number;
-        } | undefined;
-        hasPaired: boolean;
-        containsNoTransferables: boolean;
-    }>;
-}