m

dist/index.js

@@ -77,90 +77,90 @@ var asyncBwaMem = function (refPath, reads,
 // R1        : string | Array<string>,
 // R2        : string | Array<string>,
 runName, libName, outputDir, onData, options) {
-    var defaultOptions = {
-        output_discordant: true,
-        output_splitted: true,
-        output_unmapped: true
-    };
-    if (typeof options === 'undefined') {
-        options = defaultOptions;
-    }
-    else {
-        options = __assign(__assign({}, defaultOptions), options);
-    }
-    var refName = path_1.default.parse(refPath).name;
-    var bwa = 'bwa';
-    var samblaster = 'samblaster';
-    var samtools = 'samtools';
-    var sambamba = 'sambamba';
-    var readsIn;
-    var isPairedEnd = false;
-    if (Array.isArray(reads)) {
-        isPairedEnd = true;
-        console.log('Assuming paired end reads');
-        var R1 = reads[0], R2 = reads[1];
-        var R1_arr = Array.isArray(R1) ? R1.join(' ') : R1;
-        var R2_arr = Array.isArray(R2) ? R2.join(' ') : R2;
-        var R1_kitty = R1_arr.slice(-2) === 'gz' ? 'zcat' : 'cat';
-        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, "'");
-        readsIn = R1_in + ' ' + R2_in;
-    }
-    else {
-        readsIn = reads;
-    }
-    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"));
-    var retObj = { bamSorted: bamSorted };
-    if (options === null || options === void 0 ? void 0 : options.remove_mapped) {
-        bam = '/dev/null';
-        delete retObj.bamSorted;
-    }
-    var threads = String((0, os_1.cpus)().length);
-    var samblasterCmd = [];
-    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');
-        // 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) {
-            if (!isPairedEnd) {
-                console.log('Discordant reads can be found only in paired reads, skipping');
-            }
-            else {
-                var 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) {
-            var 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 });
-        }
-        console.log(options);
-        if (options === null || options === void 0 ? void 0 : options.output_unmapped) {
-            var 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 });
-        }
-    }
     return new Promise(function (resolve, reject) { return __awaiter(void 0, void 0, void 0, function () {
-        var code, code_sort, err_1;
+        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 = [];
+                    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');
+                        // 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) {
+                            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 });
+                        }
+                        console.log(options);
+                        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:

index.ts

@@ -26,101 +26,102 @@ const asyncBwaMem = (
     onData    : Function,
     options?  : any,
   ) => {
-    const defaultOptions = {
-      output_discordant: true,
-      output_splitted: true,
-      output_unmapped: true
-    }
-
-    if (typeof options === 'undefined') {
-      options = defaultOptions
-    } else {
-      options = {...defaultOptions, ...options}
-    }
-
-    const refName = path.parse(refPath).name
+    
   
-    const bwa        = 'bwa'
-    const samblaster = 'samblaster'
-    const samtools   = 'samtools'
-    const sambamba   = 'sambamba'
-
-    let readsIn: string
-    let isPairedEnd = false
-
-    if (Array.isArray(reads) ) {
-      isPairedEnd = true
-      console.log('Assuming paired end reads');
+    return new Promise<string[]>(async (resolve, reject) => {
+      try {
+        const defaultOptions = {
+          output_discordant: true,
+          output_splitted: true,
+          output_unmapped: true
+        }
+    
+        if (typeof options === 'undefined') {
+          options = defaultOptions
+        } else {
+          options = {...defaultOptions, ...options}
+        }
+    
+        const refName = path.parse(refPath).name
       
-      const [R1, R2] = reads
-      const R1_arr = Array.isArray(R1) ? R1.join(' ') : R1
-      const R2_arr = Array.isArray(R2) ? R2.join(' ') : R2
+        const bwa        = 'bwa'
+        const samblaster = 'samblaster'
+        const samtools   = 'samtools'
+        const sambamba   = 'sambamba'
     
-      const R1_kitty = R1_arr.slice(-2) === 'gz' ? 'zcat' : 'cat'
-      const R2_kitty = R2_arr.slice(-2) === 'gz' ? 'zcat' : 'cat'
+        let readsIn: string
+        let isPairedEnd = false
     
-      const R1_in = `'< ${R1_kitty} ${R1_arr}'`
-      const R2_in = `'< ${R2_kitty} ${R2_arr}'`
-      readsIn = R1_in + ' ' + R2_in
-    } else {
-      readsIn = reads
-    }
-
-    let bam       = path.join(outputDir, `bwa_mem_properly_on_${refName}.bam`)
-    let bamSorted = path.join(outputDir, `bwa_mem_properly_on_${refName}.sorted.bam`)
-    let retObj: any = { bamSorted } 
-    if(options?.remove_mapped) {
-      bam = '/dev/null'
-      delete retObj.bamSorted
-    }
-
-    const threads = String(cpus().length)
-
-    let samblasterCmd: Array<string> = []
-    if (options?.output_discordant || options?.output_splitted) {
-      console.log('Using samblaster');
-
-      // https://github.com/GregoryFaust/samblaster
-      samblasterCmd = ['|', samblaster, 
-        '--addMateTags',
-        '-a', // Accept duplicate marks already in input file
-        '-e', // Exclude reads marked as duplicates from discordant, splitter, and/or unmapped
-      ]
-
-      if(options?.output_discordant) {
-        if(!isPairedEnd) {
-          console.log('Discordant reads can be found only in paired reads, skipping')
+        if (Array.isArray(reads) ) {
+          isPairedEnd = true
+          console.log('Assuming paired end reads');
+          
+          const [R1, R2] = reads
+          const R1_arr = Array.isArray(R1) ? R1.join(' ') : R1
+          const R2_arr = Array.isArray(R2) ? R2.join(' ') : R2
+        
+          const R1_kitty = R1_arr.slice(-2) === 'gz' ? 'zcat' : 'cat'
+          const R2_kitty = R2_arr.slice(-2) === 'gz' ? 'zcat' : 'cat'
+        
+          const R1_in = `'< ${R1_kitty} ${R1_arr}'`
+          const R2_in = `'< ${R2_kitty} ${R2_arr}'`
+          readsIn = R1_in + ' ' + R2_in
         } else {
-          const discordantFile = path.join(outputDir, `bwa_mem_discordants_on_${refName}.sam`)
-          console.log('Discordant reads file path: ', discordantFile);
-          samblasterCmd = [...samblasterCmd, '-d', discordantFile]
-          retObj = {...retObj, discordantFile}
+          readsIn = reads
+        }
+    
+        let bam       = path.join(outputDir, `bwa_mem_properly_on_${refName}.bam`)
+        let bamSorted = path.join(outputDir, `bwa_mem_properly_on_${refName}.sorted.bam`)
+        let retObj: any = { bamSorted } 
+        if(options?.remove_mapped) {
+          bam = '/dev/null'
+          delete retObj.bamSorted
+        }
+    
+        const threads = String(cpus().length)
+    
+        let samblasterCmd: Array<string> = []
+        if (options?.output_discordant || options?.output_splitted) {
+          console.log('Using samblaster');
+    
+          // https://github.com/GregoryFaust/samblaster
+          samblasterCmd = ['|', samblaster, 
+            '--addMateTags',
+            '-a', // Accept duplicate marks already in input file
+            '-e', // Exclude reads marked as duplicates from discordant, splitter, and/or unmapped
+          ]
+    
+          if(options?.output_discordant) {
+            if(!isPairedEnd) {
+              console.log('Discordant reads can be found only in paired reads, skipping')
+            } else {
+              const discordantFile = path.join(outputDir, `bwa_mem_discordants_on_${refName}.sam`)
+              console.log('Discordant reads file path: ', discordantFile);
+              samblasterCmd = [...samblasterCmd, '-d', discordantFile]
+              retObj = {...retObj, discordantFile}
+            }
+          }
+    
+          if (!isPairedEnd) {
+            samblasterCmd = [...samblasterCmd, '--ignoreUnmated']
+          }
+    
+          if(options?.output_splitted) {
+            const splitterFile   = path.join(outputDir, `bwa_mem_splitters_on_${refName}.sam`)
+            console.log('Splitted reads file path: ', splitterFile);
+            samblasterCmd = [...samblasterCmd, '-s', splitterFile]
+            retObj = {...retObj, splitterFile}
+          }
+          console.log(options);
+          
+    
+          if(options?.output_unmapped) {
+            const unmappedFile   = path.join(outputDir, `bwa_mem_unmapped_on_${refName}.fq`)
+            console.log('Unmapped reads file path: ', unmappedFile);
+            samblasterCmd = [...samblasterCmd, '-u', unmappedFile]
+            retObj = {...retObj, unmappedFile}
+          }
         }
-      }
-
-      if (!isPairedEnd) {
-        samblasterCmd = [...samblasterCmd, '--ignoreUnmated']
-      }
-
-      if(options?.output_splitted) {
-        const splitterFile   = path.join(outputDir, `bwa_mem_splitters_on_${refName}.sam`)
-        console.log('Splitted reads file path: ', splitterFile);
-        samblasterCmd = [...samblasterCmd, '-s', splitterFile]
-        retObj = {...retObj, splitterFile}
-      }
-      console.log(options);
-      
-
-      if(options?.output_unmapped) {
-        const unmappedFile   = path.join(outputDir, `bwa_mem_unmapped_on_${refName}.fq`)
-        console.log('Unmapped reads file path: ', unmappedFile);
-        samblasterCmd = [...samblasterCmd, '-u', unmappedFile]
-        retObj = {...retObj, unmappedFile}
-      }
-    }
-  
-    return new Promise<string[]>(async (resolve, reject) => {
-      try {
 
         if(!fs.existsSync(refPath+'.amb')) {
           await async_exec(bwa, ['index', refPath], (message: string) => onData('[BWA-INDEX] ' + message))