gjospin/Amphora-2 — Issue #75: refactor modules into "subcommands"
Author: koadman
Created: 2012-02-13 21:26:14+00:00
State: open

Right now the software has a frontend script that parses arguments. That script needs to know all the arguments that can go to submodules (e.g. the fast screening, marker alignment, read placement). I propose a refactor so that submodules parse their own command lines. This will improve modularity, and give greater flexibility for command syntax. This approach is similar to what git and many other programs use. Submodules can thus have a consistent interface, possibly deriving from a common parent object.