Nalini Ganapati

Use Protobuf in the query api

1

@kgururaj mentioned in https://github.com/GenomicsDB/GenomicsDB/pull/41#pullrequestreview-256039972 that some of the structures used have a lot in common with the Protobuf structs and that they can be unified.

It would be useful for `query_variants()` to optionally return top-level variant information without the genotypes field. This should make it easy to associate calls from `query_variant_calls()` back to variant metadata...

Since the query json allows for filter expressions, we should extend query_variants and query_variant_calls api to accept filter expressions. _Originally posted by @mlathara in https://github.com/GenomicsDB/GenomicsDB/pull/41_

@mlathara, do you want to go over the changes and see if we need to merge in these changes? Thanks.

Refine gt_mpi_gather and other tools

1

GenomicsDB tools should not be throwing exceptions and core dump for expected issues, rather should exit gracefully with meaningful messages.

Query based on attribute filters

1

This seems to be an oft-requested feature on the lines of "Is there any option we can filter with attribute, example BaseQRankSum > 1.23?" See https://github.com/Intel-HLS/GenomicsDB/issues/213.

Referencing Issue "CSV Data Import in GenomicsDB" in new repository.

9

Referencing [Issue 227](https://github.com/Intel-HLS/GenomicsDB/issues/227) as development has moved [here](https://github.com/GenomicsDB/GenomicsDB.git).

Azure URIs and GenomicsDB

1

@lbergelson, just want to discuss some issues here- 1. We currently have to use `--avoid-nio` with `--sample-name-map` and `--bypass-feature-reader` to get `GenomicsDBImport` to work with azure URIs. Why don't we...

See https://github.com/GenomicsDB/GenomicsDB/pull/327