Add command-line option to assume that contigs are unoriented

[fedarko]

From @fedarko on August 2, 2017 1:36

At present, this would only be necessary for GML files, I think?

Anyway, this would -- for GML files -- result in us ignoring the orientation of nodes and creating duplicate nodes for each (e.g. a node with id 1 would result in two nodes being created, a forward-oriented node with id 1 and a reverse-oriented node with id -1). Similarly, edges would also result in two edges being created; A -> B also implies -B -> -A.

Copied from original issue: fedarko/MetagenomeScope#251

[fedarko]

Made a bit of progress on this. Since I'd like to work on other collate-specific changes for now, I'm storing the affected .py files here so I can do a git reset and make different changes. These changes (+ more) can be integrated later.
gml_unoriented_code.zip