Support using IDs instead of labels as key for AGP files

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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Support using IDs instead of labels as key for AGP files #227

Closed fedarko closed 7 years ago

fedarko commented 7 years ago

This should be the default behavior for LastGraph/GFA files, since they don't have labels.

Once implemented, this functionality can be specified in the README.

fedarko commented 7 years ago

Sample AGP file describing a single scaffold in cc 2 of the Velvet E. coli assembly graph:

scaffold_1  1   4033    0   W   17  1   4033    +
scaffold_1  4034    4060    1   W   -35 1   27  -
scaffold_1  4061    5819    2   W   -63 1   1759    -
scaffold_1  5820    5822    3   W   259 1   3   +

After making this I think I have a better grasp on constructing AGP files (should help with programmatically doing that in #242).

fedarko commented 7 years ago

Did some more testing with invalid AGP files on both GML (labels as node keys) and non-GML (IDs as node keys) files, everything seems to be working alright. Closing.