add unmapped only and make index if needed

dist/index.js

@@ -153,13 +153,12 @@ runName, libName, outputDir, onData, options) {
                             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 (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); })];

index.ts

@@ -112,15 +112,13 @@ const asyncBwaMem = (
             samblasterCmd = [...samblasterCmd, '-s', splitterFile]
             retObj = {...retObj, splitterFile}
           }
-          console.log(options);
-          
-    
-          if(options?.output_unmapped) {
-            const unmappedFile   = path.join(outputDir, `bwa_mem_unmapped_on_${refName}.fq`)
-            console.log('Unmapped reads file path: ', unmappedFile);
-            samblasterCmd = [...samblasterCmd, '-u', unmappedFile]
-            retObj = {...retObj, unmappedFile}
-          }
+        }
+
+        if(options?.output_unmapped) {
+          const unmappedFile   = path.join(outputDir, `bwa_mem_unmapped_on_${refName}.fq`)
+          console.log('Unmapped reads file path: ', unmappedFile);
+          samblasterCmd = [...samblasterCmd, '-u', unmappedFile]
+          retObj = {...retObj, unmappedFile}
         }
 
         if(!fs.existsSync(refPath+'.amb')) {