fix error when an output file is specified for 'samtools index'
fix error when an output file is specified for 'samtools index'

kundajelab/atac_dnase_pipelines,kundajelab/atac_dnase_pipelines,kundajelab/atac_dnase_pipelines,kundajelab/atac_dnase_pipelines,kundajelab/atac_dnase_pipelines