Version 0.7.0

Changes:

• [BREAK] Add proper support for structural variants
• Improve logging for debugging issues
• Add support for querying VCFs with chr# contig names without needing to prefix the search term with chr
• Improve performance

Version 0.6.1

• Accommodates for floating-point QUAL values

Version 0.6.0

• Allow GET requests to search endpoints
• Update Flask to 2.0
• Update bento_lib to 3.0.1
• Update misc. dependencies

Version 0.5.4

Changes:

• Fix: don't include version in service ID by default

Version 0.5.3

Changes

• Fix: Minor VCF workflow error

Version 0.5.2

Changes

• Fix: VCF workflow errors due to weird WDL (or toil WDL) scatter behaviour
• Chore: update requirements
• Docs: Specify HTSlib and BCFtools versions

Version 0.5.1

Changes

• Fix: Allow Bento Docker deploys to communicate with DRS (Pass the X-CHORD-Internal header manually to get file access)

Version 0.5.0

Changes

• [BREAK] Use DRS_URL for overriding DRS base URL instead of the old config variable
  • Can use it to refer to Docker containers for example
• Allow external DRS access when the above is not set
• Add phasing info, PHRED quality, and read depth to variant model/schema
• Add more tests (for DRS now too)
• Update bento_lib to 2.2.1, requests to 2.15.x
• Update development dependencies
• Use GitHub actions for CI testing

Version 0.4.0

Changes

• chord_variant_service -> bento_variant_service
• Add file URI as an internally-queryable property on variants
• Add some missing schema IDs
• Update dependencies

Version 0.3.0

Changes

• Change table API to match new consensus with other data services
• Update helper.py script to use new ingest/table creation formats
  • Also improve JSON output to make it more readable
• Update dependencies