added in extra test to avoid setting config values to None
Changed the way that phrap options are listed in the configuration file
Changed the assembly wrapper so that both reduction and assembly occur at the same time within a process, reducing runtime
Read from config file if given and output a new config if modified
Paralellize pandaseq
Added in an extra check to make sure that aliases are the same length as the paritig files
Removed some commandline defaults that were corrupting the config file
update the version number 0.2.2
Merge branch 'master' of github.com:ctSkennerton/Amplishot