aligner/dist/index.js

"use strict";
var __assign = (this && this.__assign) || function () {
    __assign = Object.assign || function(t) {
        for (var s, i = 1, n = arguments.length; i < n; i++) {
            s = arguments[i];
            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
                t[p] = s[p];
        }
        return t;
    };
    return __assign.apply(this, arguments);
};
var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
    return new (P || (P = Promise))(function (resolve, reject) {
        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
        step((generator = generator.apply(thisArg, _arguments || [])).next());
    });
};
var __generator = (this && this.__generator) || function (thisArg, body) {
    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
    function verb(n) { return function (v) { return step([n, v]); }; }
    function step(op) {
        if (f) throw new TypeError("Generator is already executing.");
        while (_) try {
            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
            if (y = 0, t) op = [op[0] & 2, t.value];
            switch (op[0]) {
                case 0: case 1: t = op; break;
                case 4: _.label++; return { value: op[1], done: false };
                case 5: _.label++; y = op[1]; op = [0]; continue;
                case 7: op = _.ops.pop(); _.trys.pop(); continue;
                default:
                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
                    if (t[2]) _.ops.pop();
                    _.trys.pop(); continue;
            }
            op = body.call(thisArg, _);
        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
    }
};
var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
        if (ar || !(i in from)) {
            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
            ar[i] = from[i];
        }
    }
    return to.concat(ar || Array.prototype.slice.call(from));
};
var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
exports.makeReference = exports.writeSequence = exports.asyncBwaMem = void 0;
var child_process_1 = require("child_process");
var os_1 = require("os");
var fs_1 = __importDefault(require("fs"));
var path_1 = __importDefault(require("path"));
var async_exec = function (prog, args, onData) {
    return new Promise(function (resolve, reject) {
        var child = (0, child_process_1.spawn)(prog, args, { shell: true });
        child.stdout.on('data', function (data) { return onData(data.toString().trim()); });
        child.stderr.on('data', function (data) { return onData(data.toString().trim()); });
        child.on('error', function (err) { return reject(err); });
        child.on('exit', function (code) { return resolve(code); });
    });
};
var invReplace = function (regex, string, by) {
    if (by === void 0) { by = '_'; }
    return string.split('').map(function (letter) { return letter.match(regex) ? letter : by; }).join('');
};
var writeSequence = function (sequenceName, sequence, filePath, lineN) {
    if (lineN === void 0) { lineN = 80; }
    return __awaiter(void 0, void 0, void 0, function () {
        return __generator(this, function (_a) {
            return [2 /*return*/, new Promise(function (resolve, reject) { return __awaiter(void 0, void 0, void 0, function () {
                    var r, regex_sam_restriction, nSeqName, error_1;
                    var _a;
                    return __generator(this, function (_b) {
                        switch (_b.label) {
                            case 0:
                                _b.trys.push([0, 2, , 3]);
                                r = new RegExp(".{1," + lineN + "}", "g");
                                regex_sam_restriction = /[>0-9A-Za-z!#$%&+\./:;?@^_|~-]|[\n\t]/g;
                                nSeqName = invReplace(regex_sam_restriction, sequenceName);
                                return [4 /*yield*/, fs_1.default.promises.writeFile(filePath, '>' + nSeqName + '\n' + ((_a = sequence.match(r)) === null || _a === void 0 ? void 0 : _a.join('\n').toUpperCase()))];
                            case 1:
                                _b.sent();
                                resolve(true);
                                return [3 /*break*/, 3];
                            case 2:
                                error_1 = _b.sent();
                                console.log(error_1);
                                reject(false);
                                return [3 /*break*/, 3];
                            case 3: return [2 /*return*/];
                        }
                    });
                }); })];
        });
    });
};
exports.writeSequence = writeSequence;
var makeReference = function (sequenceName, sequence, filePath, lineN) {
    if (lineN === void 0) { lineN = 80; }
    return __awaiter(void 0, void 0, void 0, function () {
        return __generator(this, function (_a) {
            switch (_a.label) {
                case 0: return [4 /*yield*/, writeSequence(sequenceName, sequence, filePath, lineN)];
                case 1:
                    if (!_a.sent()) return [3 /*break*/, 3];
                    return [4 /*yield*/, async_exec('bwa', ['index', filePath], function () { return console.log; })];
                case 2:
                    _a.sent();
                    _a.label = 3;
                case 3: return [2 /*return*/];
            }
        });
    });
};
exports.makeReference = makeReference;
var asyncBwaMem = function (refPath, reads, 
// R1        : string | Array<string>,
// R2        : string | Array<string>,
runName, libName, outputDir, onData, options) {
    return new Promise(function (resolve, reject) { return __awaiter(void 0, void 0, void 0, function () {
        var defaultOptions, refName, bwa, samblaster, samtools, sambamba, readsIn, isPairedEnd, R1, R2, R1_arr, R2_arr, R1_kitty, R2_kitty, R1_in, R2_in, bam, bamSorted, retObj, threads, samblasterCmd, discordantFile, splitterFile, unmappedFile, code, code_sort, err_1;
        return __generator(this, function (_a) {
            switch (_a.label) {
                case 0:
                    _a.trys.push([0, 6, , 7]);
                    defaultOptions = {
                        output_discordant: true,
                        output_splitted: true,
                        output_unmapped: true
                    };
                    if (typeof options === 'undefined') {
                        options = defaultOptions;
                    }
                    else {
                        options = __assign(__assign({}, defaultOptions), options);
                    }
                    refName = path_1.default.parse(refPath).name;
                    bwa = 'bwa';
                    samblaster = 'samblaster';
                    samtools = 'samtools';
                    sambamba = 'sambamba';
                    readsIn = void 0;
                    isPairedEnd = false;
                    if (Array.isArray(reads)) {
                        isPairedEnd = true;
                        console.log('Assuming paired end reads');
                        R1 = reads[0], R2 = reads[1];
                        R1_arr = Array.isArray(R1) ? R1.join(' ') : R1;
                        R2_arr = Array.isArray(R2) ? R2.join(' ') : R2;
                        R1_kitty = R1_arr.slice(-2) === 'gz' ? 'zcat' : 'cat';
                        R2_kitty = R2_arr.slice(-2) === 'gz' ? 'zcat' : 'cat';
                        R1_in = "'< ".concat(R1_kitty, " ").concat(R1_arr, "'");
                        R2_in = "'< ".concat(R2_kitty, " ").concat(R2_arr, "'");
                        readsIn = R1_in + ' ' + R2_in;
                    }
                    else {
                        readsIn = reads;
                    }
                    bam = path_1.default.join(outputDir, "bwa_mem_properly_on_".concat(refName, ".bam"));
                    bamSorted = path_1.default.join(outputDir, "bwa_mem_properly_on_".concat(refName, ".sorted.bam"));
                    retObj = { bamSorted: bamSorted };
                    if (options === null || options === void 0 ? void 0 : options.remove_mapped) {
                        bam = '/dev/null';
                        delete retObj.bamSorted;
                    }
                    threads = String((0, os_1.cpus)().length);
                    samblasterCmd = [];
                    // https://github.com/GregoryFaust/samblaster
                    samblasterCmd = ['|', samblaster,
                        '--addMateTags',
                        '-a',
                        '-e', // Exclude reads marked as duplicates from discordant, splitter, and/or unmapped
                    ];
                    if ((options === null || options === void 0 ? void 0 : options.output_discordant) || (options === null || options === void 0 ? void 0 : options.output_splitted)) {
                        console.log('Using samblaster');
                        if (options === null || options === void 0 ? void 0 : options.output_discordant) {
                            if (!isPairedEnd) {
                                console.log('Discordant reads can be found only in paired reads, skipping');
                            }
                            else {
                                discordantFile = path_1.default.join(outputDir, "bwa_mem_discordants_on_".concat(refName, ".sam"));
                                console.log('Discordant reads file path: ', discordantFile);
                                samblasterCmd = __spreadArray(__spreadArray([], samblasterCmd, true), ['-d', discordantFile], false);
                                retObj = __assign(__assign({}, retObj), { discordantFile: discordantFile });
                            }
                        }
                        if (!isPairedEnd) {
                            samblasterCmd = __spreadArray(__spreadArray([], samblasterCmd, true), ['--ignoreUnmated'], false);
                        }
                        if (options === null || options === void 0 ? void 0 : options.output_splitted) {
                            splitterFile = path_1.default.join(outputDir, "bwa_mem_splitters_on_".concat(refName, ".sam"));
                            console.log('Splitted reads file path: ', splitterFile);
                            samblasterCmd = __spreadArray(__spreadArray([], samblasterCmd, true), ['-s', splitterFile], false);
                            retObj = __assign(__assign({}, retObj), { splitterFile: splitterFile });
                        }
                    }
                    if (options === null || options === void 0 ? void 0 : options.output_unmapped) {
                        unmappedFile = path_1.default.join(outputDir, "bwa_mem_unmapped_on_".concat(refName, ".fq"));
                        console.log('Unmapped reads file path: ', unmappedFile);
                        samblasterCmd = __spreadArray(__spreadArray([], samblasterCmd, true), ['-u', unmappedFile], false);
                        retObj = __assign(__assign({}, retObj), { unmappedFile: unmappedFile });
                    }
                    if (!!fs_1.default.existsSync(refPath + '.amb')) return [3 /*break*/, 2];
                    return [4 /*yield*/, async_exec(bwa, ['index', refPath], function (message) { return onData('[BWA-INDEX] ' + message); })];
                case 1:
                    _a.sent();
                    _a.label = 2;
                case 2:
                    console.log(options, samblasterCmd);
                    return [4 /*yield*/, async_exec(bwa, __spreadArray(__spreadArray(['mem',
                            '-t', threads,
                            '-R', "\"@RG\\tPL:Illumina\\tID:".concat(+(new Date), "\\tSM:").concat(runName, "\\tLB:").concat(libName, "\""), refPath,
                            readsIn], samblasterCmd, true), ['|',
                            samtools,
                            'view',
                            '-Sb',
                            '-',
                            '>',
                            bam], false), function (message) { return onData('[BWA-MEM] ' + message); })];
                case 3:
                    code = _a.sent();
                    onData('[BWA-MEM][EXIT CODE] ' + code);
                    if (!retObj.bamSorted) return [3 /*break*/, 5];
                    return [4 /*yield*/, async_exec(sambamba, ['sort',
                            '-t', threads,
                            bam
                        ], function (message) { return onData('[SAMBAMBA-SORT] ' + message); })];
                case 4:
                    code_sort = _a.sent();
                    onData('[SAMBAMBA-SORT][EXIT CODE] ' + code_sort);
                    fs_1.default.unlinkSync(bam);
                    _a.label = 5;
                case 5:
                    resolve(retObj);
                    return [3 /*break*/, 7];
                case 6:
                    err_1 = _a.sent();
                    reject(err_1);
                    return [3 /*break*/, 7];
                case 7: return [2 /*return*/];
            }
        });
    }); });
};
exports.asyncBwaMem = asyncBwaMem;