def get_parser():
main_parser = argparse.ArgumentParser()
main_parser.add_argument('--version',
action='version',
version=version(),
help='display version information and exit')
subparsers = main_parser.add_subparsers(title='modules', dest='which')
global_parser = argparse.ArgumentParser(add_help=False)
settings_parser = Args.settings_args(subparsers.add_parser('settings', help='user definable settings', parents=[global_parser]))
snv_parser = Args.snv_args(subparsers.add_parser('snv', help='run single nucleotide variant association models', parents=[global_parser]))
snvgroup_parser = Args.snvgroup_args(subparsers.add_parser('snvgroup', help='run variant group (ie. gene) based association models', parents=[global_parser]))
meta_parser = Args.meta_args(subparsers.add_parser('meta', help='run meta analysis', parents=[global_parser]))
compile_parser = Args.compile_args(subparsers.add_parser('compile', help='verify and compile results files', parents=[global_parser]))
resubmit_parser = Args.resubmit_args(subparsers.add_parser('resubmit', help='resubmit failed results', parents=[global_parser]))
snvplot_parser = Args.snvplot_args(subparsers.add_parser('snvplot', help='generate qq and manhattan plots for single variant results', parents=[global_parser]))
snvgroupplot_parser = Args.snvgroupplot_args(subparsers.add_parser('snvgroupplot', help='generate qq and manhattan plots for grouped variant results', parents=[global_parser]))
filter_parser = Args.filter_args(subparsers.add_parser('filter', help='filter results / correct single variant results for genomic inflation', parents=[global_parser]))
merge_parser = Args.merge_args(subparsers.add_parser('merge', help='merge and annotate results with external files / snpEff', parents=[global_parser]))
tools_parser = Args.tools_args(subparsers.add_parser('tools', help='run any command line tool with ability to include genomic region automatically', parents=[global_parser]))
return main_parser
