biocommons/anyvar

Issues

• Add back missing response models to openapi.json

  #91 opened 2 months ago by ehclark
  2

• Parameterize creating different translator

  #56 opened 2 months ago by korikuzma
  7

• Catch timeout error when establishing variation normalizer connection

  #49 opened 2 months ago by jsstevenson
  1

• Demo notebook should include input vcf file

  #62 opened a year ago by korikuzma
  4

• Set up CI

  #23 opened 3 months ago by jsstevenson
  5

• Support copy number variations

  #45 opened 2 years ago by jsstevenson
  3

• Investigate different NoSQL storage backends

  #25 opened 2 years ago by jsstevenson
  5

• Decouple VRS python class dependencies

  #53 opened a year ago by larrybabb
  3

• Deploy demo version

  #35 opened 5 months ago by jsstevenson
  3

• Import/export between AnyVar instances

  #39 opened 5 months ago by jsstevenson
  3

• Add database connection lifecycle management

  #87 opened 6 months ago by ehclark
  0

• Update unit tests to match latest serialization model for VRS 2.0.0a5

  #85 opened 6 months ago by ehclark
  11

• Support private key authentication for Snowflake storage connector

  #88 opened 7 months ago by ehclark
  0

• Snowflake storage connector explicitly sets collation for vrs_id column

  #89 opened 7 months ago by ehclark
  0

• Update VcfRegistrar._get_vrs_object() for compatibility with vrs-python changes

  #84 opened 8 months ago by ehclark
  0

• postgres setup command typo

  #78 opened 8 months ago by larrybabb
  1

• Fix postgres connection issue

  #81 opened 8 months ago by theferrit32
  0

• Apply formatting to codebase

  #80 opened 8 months ago by theferrit32
  0

• Summary statistics miss deletions where state isn't empty

  #44 opened 2 years ago by jsstevenson
  1

• Handle API changes in VRS-Python VCF translator

  #55 opened a year ago by jsstevenson
  0

• Update the VcfRegistrar to support reference assemblies other than GRCh38

  #67 opened 9 months ago by ehclark
  0

• Add a parameter to the /vcf endpoint that ensures all async VRS object writes are completed before returning

  #65 opened 9 months ago by ehclark
  1

• Update put_object to take advantage of vrs-python API changes and avoid unnecessary VRS computation

  #71 opened 9 months ago by ehclark
  0

• Add a shutdown API to enable graceful termination of AnyVar

  #66 opened 9 months ago by ehclark
  1

• Add parameter to /vcf REST endpoint to control whether or not VRS IDs are computed for reference alleles

  #72 opened 9 months ago by ehclark
  3

• Support Snowflake database as a storage backend

  #64 opened 9 months ago by ehclark
  1

• Development setup fails with build error

  #68 opened 10 months ago by ehclark
  0

• Demonstrate loading ClinVar into AnyVar

  #7 opened 10 months ago by reece
  2

• Clean up storage directory

  #22 opened 10 months ago by jsstevenson
  2

• Correct installation instructions in read.me

  #21 opened 10 months ago by jsstevenson
  2

• Modularize translator/data proxy layer

  #24 opened 10 months ago by jsstevenson
  2

• Ensure basic exposure of SeqRepo functions

  #36 opened 10 months ago by jsstevenson
  2

• Store more complex kinds of variations

  #38 opened 10 months ago by jsstevenson
  2

• Endpoints for all variations/locations/etc

  #42 opened 10 months ago by jsstevenson
  2

• Speed up Postgres writes

  #47 opened 10 months ago by jsstevenson
  2

• Migrate class dependencies to VRS 2-alpha1

  #52 opened a year ago by larrybabb
  1

• Create a vrs-python translator

  #51 opened a year ago by larrybabb
  1

• Load the gnomAD small variants VCF as demo/benchmark

  #37 opened a year ago by jsstevenson
  0

• VCF input/annotation

  #40 opened 2 years ago by jsstevenson
  0

• PostgreSQL PUT operations are making redundant records

  #26 opened 2 years ago by jsstevenson
  0

• self._db references raise AttributeError in Postgres module

  #28 opened 2 years ago by jsstevenson
  0

• Register VRS objects

  #41 opened 2 years ago by jsstevenson
  0

• Investigate different API libraries

  #27 opened 2 years ago by jsstevenson
  0

• Catch exceptions for unrecognized sequences in /sequence/

  #30 opened 2 years ago by jsstevenson
  1

• Allele PUT response should include location ID

  #29 opened 2 years ago by jsstevenson
  0

• AttributeError when AnyVar.__name__ == '__main__'

  #17 opened 2 years ago by jsstevenson
  0

• Query alleles in genomic region

  #12 opened 2 years ago by andreasprlic
  0

• Get endpoint that provides statistics about the content of anyvar

  #13 opened 2 years ago by andreasprlic
  0

• Create a postgres based storage plugin

  #10 opened 2 years ago by andreasprlic
  0

• Upgrade Anyvar to point to publicly hosted seqrepo

  #8 opened 2 years ago by andreasprlic
  2