Add command-line option to assume contigs are already oriented

[fedarko]

From the comments of #10:
"adding a command-line option to collate.py that, for a GFA/LastGraph/etc file, assumes that contigs are already oriented (and thus doesn't create implied negative nodes/edges). Since MetaCarvel can produce GFA output, implementing something like this would be worthwhile.

(We'd also probably have to adjust the JS code for the viewer interface to -- instead of just treating ASM_FILETYPE === "GML" as the basis for graphs with oriented contigs -- getting some corresponding bool from the db re: the contigs being oriented or unoriented, and operating accordingly.)"

This is actually causing problems with certain GFA files, so need to do this.

[fedarko]

This issue was moved to marbl/MetagenomeScope#67