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fedarko / MetagenomeScope

Hierarchical scaffold/assembly graph web visualization tool. As of August 9, 2017, the official repository for this has moved to MarBL! Use that repository instead :)
http://github.com/marbl/MetagenomeScope
GNU General Public License v3.0
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Add command-line option to assume contigs are already oriented #244

Closed fedarko closed 7 years ago

fedarko commented 7 years ago

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 commented 7 years ago

This issue was moved to marbl/metagenomeScope#67