https://github.com/smondet/plawireg

Play with The Reference Graph
https://github.com/smondet/plawireg

Last synced: 26 days ago
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Play with The Reference Graph

• Host: GitHub
• URL: https://github.com/smondet/plawireg
• Owner: smondet
• License: apache-2.0
• Created: 2015-02-24T19:48:06.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2015-07-11T00:15:10.000Z (over 9 years ago)
• Last Synced: 2023-03-12T03:03:36.672Z (almost 2 years ago)
• Language: OCaml
• Size: 258 KB
• Stars: 9
• Watchers: 4
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
Plawireg: Play With The Reference Graph

=======================================

This project is an experiment on representing the reference genome as a graph.

Nothing really interesting to see for now …

Build

-----

This project uses the `omake` build-system, just run:

    omake

Run Tests

---------

One can generate some very small test data files:

    ./plawireg generate test fasta mini-reference.fasta

    ./plawireg generate test dbsnp mini-dbsnp.vcf

and run some stuff:

    ./plawireg test-load all 6 mini-reference.fasta mini-dbsnp.vcf

    

You can make things more verbose:

    VERBOSE=true ./plawireg test-load all 6 mini-reference.fasta mini-dbsnp.vcf

Or ask for “linux-only” memory-usage stats along the way:

    ./plawireg test-load all 6 mini-reference.fasta mini-dbsnp.vcf memory-stats

The test dumps a `out.dot` file that one can observe:

    dot -Tpng out.dot -O

It should give something like this:

![Output as of 2015-03-06][plawireg-dot-output]

[plawireg-dot-output]: https://cloud.githubusercontent.com/assets/617111/6535827/f161ffd8-c415-11e4-8b21-b2f97655c407.png