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I just set up a new RTD site for the server: https://readthedocs.org/projects/ga4gh-server
The old one is here: https://readthedocs.org/dashboard/ga4gh-reference-implementation
When we are sure …
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VCF has been extended to include a bunch of other annotations for the effects of a given variation. The resulting GA4GH messages are `VariantAnnotation` `VariantAnnotationSet` `TranscriptEffect` `Anal…
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This appears not to be the case:
https://github.com/ga4gh/server/issues/758
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The layer of code that uses pysam to answer GA4GH methods could be made more portable.
We might package up the datamodel classes that require `pysam` as it is probably our heaviest dependency and …
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(via pysam) A VCF that has repeated sample names causes htslib to crash. An offending VCF can be found here: https://github.com/ga4gh/server/tree/master/tests/faultydata/variants/duplicated_sampleid .…
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Per the connect discussions I believe it would be a good idea to set up a `stats` endpoint for DRS servers.
This will allow us to build something like a dashboard for existing DRS servers and show th…
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The [search_phenotype_association_sets](https://github.com/ga4gh/ga4gh-client/blob/master/ga4gh/client/client.py#L749-L758) method (and presumably other methods that use the `ga4gh.client.protocol` m…
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We could do more to automate the deploy, but I set up Apache to run a "beta" area so that we can host more protocol versions from the same box.
I noticed that someone is developing a client that us…
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As we enter our last development cycle before a stable release at schemas, we should shore up some of the orphaned code including removing g2p, vcf_to_ga, any unused or not helpful scripts, convert_er…
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## Background
The GA4GH has defined an API in the schemas which provides interfaces to the common genomic data types. The data types are meant to be accessed over an HTTP API, and Ensembl, EBI, and U…