parse command line options
parse command line options

tabbott/diagnose_dups,genome/diagnose_dups,genome/diagnose_dups,fw1121/diagnose_dups,fw1121/diagnose_dups,tabbott/diagnose_dups,fw1121/diagnose_dups,tabbott/diagnose_dups,genome/diagnose_dups,genome/diagnose_dups,genome/diagnose_dups,genome/diagnose_dups,fw1121/diagnose_dups,tabbott/diagnose_dups,fw1121/diagnose_dups,tabbott/diagnose_dups