m

dist/index.js

@@ -124,12 +124,15 @@ runName, libName, outputDir, onData, options) {
             '-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)
-                throw 'Error discordant reads can be found only in paired reads';
-            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) {
+                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);

index.ts

@@ -85,11 +85,14 @@ const asyncBwaMem = (
       ]
 
       if(options?.output_discordant) {
-        if(!isPairedEnd) throw 'Error discordant reads can be found only in paired reads'
-        const discordantFile = path.join(outputDir, `bwa_mem_discordants_on_${refName}.sam`)
-        console.log('Discordant reads file path: ', discordantFile);
-        samblasterCmd = [...samblasterCmd, '-d', discordantFile]
-        retObj = {...retObj, discordantFile}
+        if(!isPairedEnd) {
+          console.log('Discordant reads can be found only in paired reads, skipping')
+        } else {
+          const discordantFile = path.join(outputDir, `bwa_mem_discordants_on_${refName}.sam`)
+          console.log('Discordant reads file path: ', discordantFile);
+          samblasterCmd = [...samblasterCmd, '-d', discordantFile]
+          retObj = {...retObj, discordantFile}
+        }
       }
 
       if (!isPairedEnd) {