Play with The Reference Graph
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README.md

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