m

dist/index.js

@@ -131,6 +131,9 @@ runName, libName, outputDir, onData, options) {
             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);