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@@ -21,7 +21,7 @@ const asyncBwaMem = (
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R2 : string | Array<string>,
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runName : string,
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libName : string,
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- output_dir: string,
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+ outputDir: string,
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onData : Function,
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options? : any,
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) => {
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@@ -44,11 +44,11 @@ const asyncBwaMem = (
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const R1_in = `'< ${R1_kitty} ${R1_arr}'`
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const R2_in = `'< ${R2_kitty} ${R2_arr}'`
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- const discordantFile = path.join(output_dir, `bwa_mem_discordants_on_${refName}.sam`)
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- const splitterFile = path.join(output_dir, `bwa_mem_splitters_on_${refName}.sam`)
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- const unmappedFile = path.join(output_dir, `bwa_mem_unmapped_on_${refName}.fq`)
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- const bam = path.join(output_dir, `bwa_mem_properly_on_${refName}.bam`)
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- const bamSorted = path.join(output_dir, `bwa_mem_properly_on_${refName}.sorted.bam`)
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+ const discordantFile = path.join(outputDir, `bwa_mem_discordants_on_${refName}.sam`)
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+ const splitterFile = path.join(outputDir, `bwa_mem_splitters_on_${refName}.sam`)
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+ const unmappedFile = path.join(outputDir, `bwa_mem_unmapped_on_${refName}.fq`)
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+ const bam = path.join(outputDir, `bwa_mem_properly_on_${refName}.bam`)
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+ const bamSorted = path.join(outputDir, `bwa_mem_properly_on_${refName}.sorted.bam`)
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return new Promise<string[]>(async (resolve, reject) => {
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try {
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