added Bowtie2 compliant cmdline options for input/output files
added Bowtie2 compliant cmdline options for input/output files

kimrutherford/nvbio,kimrutherford/nvbio,kimrutherford/nvbio,NVlabs/nvbio,NVlabs/nvbio,NVlabs/nvbio,kimrutherford/nvbio,NVlabs/nvbio