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CHANGELOG.md

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v0.1.1 (2022-05-26)

Added

  • Updated code to handle records with multiple alts (#97).

Changed

  • Genomic Source Class to a required parameter (#97).
  • GitHub Action workflow to install dependencies from requirements.txt (#103).

Fixed

  • Variant Inner-End calculation (#98).
  • Installation error due to PyVCF by switching to PyVCF3 (#103).

v0.1.0 (2021-09-22)

This is our first minor version release with support for structural variant conversion and incorporation of clinical annotations. For more details follow Readme. We would love to hear your feedback! If you find any issue please open an Issue.

Added

  • Support for Structural Variants (#86).
  • Support for Clinical Annotations (#89).

v0.0.17 (2021-06-30)

Added

  • Exposed a new parameter to configure ratio for determining Homoplasmic vs Heteroplasmic (#19).

Changed

  • Build process to PEP 517 (#18).

Fixed

  • Excluded records with incorrect CHROM values in vcf file (#19).
  • Removed 'Human reference sequence assembly version' component from variant observation (#36).
  • Case where conversion region is not studied (#66).
  • FHIR validation errors and warnings (#77).

v0.0.1 - v0.0.16

Converts VCF variants into a FHIR Genomics Diagnostic Report.

Added

  • In scope are simple variants (SNVs, Indels), along with zygosity and phase relationships, for autosomes, sex chromosomes, and mitochondrial DNA.
  • Supports VCF file (text-based or bgzipped) and optionally tabix files for query.
  • Supports genome build ('GRCh37' or 'GRCh38');
  • Optionally supports a query region in the form of .bed or dictionary that indicates the region(s) to convert.
  • Optionally supports inclusion of 'region-studied' observations that detail which portions of the conversion region were studied, and of those studied regions, which portions were deemed uncallable.