Jules Jacobsen

Yes, but if you're using Java to do this there is a pre-built jar file on maven central already, so you don't need to build this yourself. If you're using...

Maven central: https://search.maven.org/artifact/org.phenopackets/phenopacket-schema/2.0.2/jar (also linked from top of readme and in https://phenopacket-schema.readthedocs.io/en/latest/java-build.html#rstjavabuild) GitHub releases page from the main repo page: https://github.com/phenopackets/phenopacket-schema/releases

@lindsmith can you add the other PRC members GitHub handles to the initial comment, please.

For context This is the HtsFile: ```proto // A file in one of the HTS formats (https://samtools.github.io/hts-specs) message HtsFile { enum HtsFormat { UNKNOWN = 0; SAM = 1; BAM...

A couple of possible options: 1. Replace it with a generic file: ```proto message File { string uri = 1; map stuff = 2; string description = 3; } ```...

@mbaudis @avsmith @jdylan @jgoecks We went with this: ```proto message File { // URI for the file e.g. file://data/genomes/file1.vcf.gz or https://opensnp.org/data/60.23andme-exome-vcf.231?1341012444 string uri = 1; // A map of identifiers...

@ianfore can you link to where this is defined and give an example of these?

There is no cumulative fractions in the ARGO spec https://docs.icgc-argo.org/dictionary, so I don't think we missed anything.

The Python code is generated on each build along with the Java code. I've not used the Python, but it will follow the style in the [protobuf Python docs](https://developers.google.com/protocol-buffers/docs/pythontutorial#parsing-and-serialization) i.e....

I've made some progress towards this, but there are still a few more steps to go through to fully-automate the whole thing.