m

dist/index.js

@@ -165,16 +165,18 @@ runName, libName, outputDir, onData, options) {
                 case 1:
                     _a.sent();
                     _a.label = 2;
-                case 2: 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 2:
+                    console.log(options);
+                    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);

index.ts

@@ -124,6 +124,9 @@ const asyncBwaMem = (
           await async_exec(bwa, ['index', refPath], (message: string) => onData('[BWA-INDEX] ' + message))
         }
 
+        console.log(options);
+        
+
         const code = await async_exec(
         bwa, ['mem',
           '-t', threads,