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if [${regions}]; then |
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if [${regions}]; then |
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INTERVAL="--interval ${regions} --interval_padding ${interval_padding}" |
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INTERVAL="--interval ${regions} --interval_padding ${interval_padding}" |
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else: |
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else |
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INTERVAL="" |
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INTERVAL="" |
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fi |
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fi |
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if [${normal_bam}];then |
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if [${normal_bam}];then |
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INPUT="-i ${tumor_bam} -i ${normal_bam}" |
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INPUT="-i ${tumor_bam} -i ${normal_bam}" |
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SAMPLE="--tumor_sample ${tumor_name} --normal_sample ${normal_name}" |
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SAMPLE="--tumor_sample ${tumor_name} --normal_sample ${normal_name}" |
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else: |
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else |
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INPUT="-i ${tumor_bam}" |
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INPUT="-i ${tumor_bam}" |
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SAMPLE="--tumor_sample ${tumor_name}" |
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SAMPLE="--tumor_sample ${tumor_name}" |
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fi |
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fi |