m

dist/index.js

@@ -125,14 +125,14 @@ runName, libName, outputDir, onData, options) {
                     }
                     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');
-                        // 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');

index.ts

@@ -79,18 +79,19 @@ const asyncBwaMem = (
         }
     
         const threads = String(cpus().length)
+
+
     
         let samblasterCmd: Array<string> = []
+        // 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 || 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')