use Genome::Sys->create_directories instead of mkdir
new file format for files sorted by chromosome and start position

allow retrieval of whole line based on those keys

retrieval has to happen in sort order
use Genome::File::OrderedPosition
remove templating comments
improved the way the header is retrieved
minor code cleanup
support string chromosome values
use OrderedPosition for the variant file
edit test messages for clarity
don't parse the first line on initialization
Throw an error if there is an empty line in the file to process
remove the old way of processing the input variants file
remove the lsf_resource param

after the refactor this module works with the default LSF memory requirements
test to ensure that the initialization doesn't read in the first line
extract _job_group_spec
extract _default_job_group
refactor test to use _default_job_group instead of duplicating
refactor _job_group_spec for conciseness
extract _server_dispatch
extract _job_dispatch