m

dist/index.d.ts

@@ -1,2 +1,2 @@
-declare const asyncBwaMem: (refPath: string, R1: string | Array<string>, R2: string | Array<string>, runName: string, libName: string, output_dir: string, onData: Function, options?: any) => Promise<string[]>;
-export default asyncBwaMem;
+declare const asyncBwaMem: (refPath: string, R1: string | Array<string>, R2: string | Array<string>, runName: string, libName: string, outputDir: string, onData: Function, options?: any) => Promise<string[]>;
+export { asyncBwaMem };

dist/index.js

@@ -39,7 +39,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+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) {
@@ -51,7 +53,7 @@ var async_exec = function (prog, args, onData) {
         child.on('exit', function (code) { return resolve(code); });
     });
 };
-var asyncBwaMem = function (refPath, R1, R2, runName, libName, output_dir, onData, options) {
+var asyncBwaMem = function (refPath, R1, R2, runName, libName, outputDir, onData, options) {
     if (typeof options === 'undefined')
         options = {};
     var refName = path_1.default.parse(refPath).name;
@@ -65,11 +67,11 @@ var asyncBwaMem = function (refPath, R1, R2, runName, libName, output_dir, onDat
     var R2_kitty = R2_arr.slice(-2) === 'gz' ? 'zcat' : 'cat';
     var R1_in = "'< ".concat(R1_kitty, " ").concat(R1_arr, "'");
     var R2_in = "'< ".concat(R2_kitty, " ").concat(R2_arr, "'");
-    var discordantFile = path_1.default.join(output_dir, "bwa_mem_discordants_on_".concat(refName, ".sam"));
-    var splitterFile = path_1.default.join(output_dir, "bwa_mem_splitters_on_".concat(refName, ".sam"));
-    var unmappedFile = path_1.default.join(output_dir, "bwa_mem_unmapped_on_".concat(refName, ".fq"));
-    var bam = path_1.default.join(output_dir, "bwa_mem_properly_on_".concat(refName, ".bam"));
-    var bamSorted = path_1.default.join(output_dir, "bwa_mem_properly_on_".concat(refName, ".sorted.bam"));
+    var discordantFile = path_1.default.join(outputDir, "bwa_mem_discordants_on_".concat(refName, ".sam"));
+    var splitterFile = path_1.default.join(outputDir, "bwa_mem_splitters_on_".concat(refName, ".sam"));
+    var unmappedFile = path_1.default.join(outputDir, "bwa_mem_unmapped_on_".concat(refName, ".fq"));
+    var bam = path_1.default.join(outputDir, "bwa_mem_properly_on_".concat(refName, ".bam"));
+    var bamSorted = path_1.default.join(outputDir, "bwa_mem_properly_on_".concat(refName, ".sorted.bam"));
     return new Promise(function (resolve, reject) { return __awaiter(void 0, void 0, void 0, function () {
         var code, code_sort, err_1;
         return __generator(this, function (_a) {
@@ -77,7 +79,7 @@ var asyncBwaMem = function (refPath, R1, R2, runName, libName, output_dir, onDat
                 case 0:
                     _a.trys.push([0, 3, , 4]);
                     return [4 /*yield*/, async_exec(bwa, ['mem',
-                            '-t', String(require('os').cpus().length),
+                            '-t', String((0, os_1.cpus)().length),
                             '-R', "\"@RG\\tPL:Illumina\\tID:".concat(+(new Date), "\\tSM:").concat(runName, "\\tLB:").concat(libName, "\""), refPath, R1_in, R2_in,
                             '|',
                             samblaster,
@@ -116,4 +118,4 @@ var asyncBwaMem = function (refPath, R1, R2, runName, libName, output_dir, onDat
         });
     }); });
 };
-exports.default = asyncBwaMem;
+exports.asyncBwaMem = asyncBwaMem;

index.ts

@@ -91,4 +91,4 @@ const asyncBwaMem = (
     })
 }
 
-export default asyncBwaMem 
+export { asyncBwaMem }