David Steinberg

In order to perform ETL of the gencode gff3, we provide a script that parses that file. To close this issue, move that software to a different module and test...

Repo manager should not accept a blank name

4

Although checks are in place to keep the inferred names from being empty, it appears one can manually set the name to be empty. `python repo_dev.py add-readgroupset l a ga4gh-example-data/HG00096.bam...

Support remote FASTAs using local index

5

It appears the index files are optional in the current references implementation. We ought to explicitly pass the index path using `filepath_index` so that repositories can be read only directories,...

Add a variantset from BEDPE

1

For interchanging structural variants.

The list reference bases request will throw an exception is the end is out of range. This is an undue pressure placed on clients and doesn't seem to be a...

Load testing

5

Hi everyone! In order to prepare for our demonstration server with the 1kg VCFs I've started to perform some rudimentary single node load testing. Both server and client are in...

Variant annotation search by reference ID

3

Variant annotation supports searching by referenceName and referenceId. Currently, only search by referenceName is supported.

VCF Indexfiles option ignored

10

I'm working with the add-variantset to see whether remote VCF will work yet, or not. Here is the repo manager call `python repo_dev.py add-variantset ga4gh-example-data/repo.db test "http://s3.amazonaws.com/1000genomes/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" -I"/Users/david/1000genomes/1kvcf/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi" --referenceSetName NCBI37`...

To go with https://github.com/ga4gh/schemas/pull/706

There are annotated variants available in the thousand genomes FTP. By updating the script to access annotated variants we can demonstrate a larger part of the server.