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@@ -92,6 +92,10 @@ const asyncBwaMem = (
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retObj = {...retObj, discordantFile}
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}
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+ if (!isPairedEnd) {
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+ samblasterCmd = [...samblasterCmd, '--ignoreUnmated']
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+ }
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+
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if(options?.output_splitted) {
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const splitterFile = path.join(outputDir, `bwa_mem_splitters_on_${refName}.sam`)
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console.log('Splitted reads file path: ', splitterFile);
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