SapFhir-CLI

Join genomic variation graphs with public data or internal medical data e.g. FHIR. by having a FAIR data access, using W3C sparql as a standard protocol.

This is a command line tool to quickly test the concept.

Building

You need local checkouts of

handlegraph4j handlegraph4jGFA handlegraph4jRDF handlegraph4j-simple sapfhir

Build them with maven on java 11+

for i in handlegraph4j handlegraph4jGFA handlegraph4jRDF handlegraph4j-simple sapfhir
cd $i
    mvn install
cd ..

mvn package

Run

java -jar target/sapfhir-cli-0.2-SNAPSHOT-jar-with-dependencies.jar \
    --gfa ~/git/odgi/test/t.gfa \
    -Xmx12g \
    "PREFIX vg:<http://biohackathon.org/resource/vg#> SELECT ?path WHERE {?path a vg:Path}"

Status

This is a RDF4j SAIL implementation that can take any handlegraph4j implementation and represent it as a W3C sparql 1.1 endpoint.

It is believed to be functionally complete.