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ultimatesource / denovogear

A program to detect denovo-variants using next-generation sequencing data.
http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html
GNU General Public License v3.0
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Add functionality to output graph to file #269

Open anderspitman opened 6 years ago

anderspitman commented 6 years ago

Uses boost to write in GraphML format.

dng-jenkins commented 6 years ago

Can one of the admins verify this patch?

anderspitman commented 6 years ago

@reedacartwright this outputs a ped_graph.graphml file. Opening with gephi, manually dragging the nodes, and adjusting a couple simple settings I was able to pretty quickly achieve the following: screenshot_155357

Am I dumping the graph at the right place currently? Also, I'm guessing we'll want to have this behind a flag of some sort, and probably allow the user to specify the output path. Do you have any preferences on how I set that up?

reedacartwright commented 6 years ago

Jenkins, okay to test.

reedacartwright commented 6 years ago

This pull request needs to contain a dng-graph program and an associated task similar to how the dng-loglike program works. I don't want dng-call to spit out a graphml file every time it runs.

anderspitman commented 6 years ago

That should be pretty straight-forward. Do we only care about the final version of the graph though? Having the dump inside the Construct method like it is now gives us the flexibility of outputting it at different stages, or even multiple stages.