Vcf2fhir

Latest version: v0.1.1

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0.1.1

Added
* Updated code to handle records with multiple alts ([97](https://github.com/elimuinformatics/vcf2fhir/pull/97)).

Changed
* Genomic Source Class to a required parameter ([97](https://github.com/elimuinformatics/vcf2fhir/pull/97)).
* GitHub Action workflow to install dependencies from requirements.txt ([103](https://github.com/elimuinformatics/vcf2fhir/pull/103)).

Fixed
* Variant Inner-End calculation ([98](https://github.com/elimuinformatics/vcf2fhir/pull/98)).
* Installation error due to PyVCF by switching to PyVCF3 ([103](https://github.com/elimuinformatics/vcf2fhir/pull/103)).

0.1.0

This is our first minor version release with support for structural variant conversion and incorporation of clinical annotations. For more details follow [Readme](README.md). We would love to hear your feedback! If you find any issue please open an [Issue](https://github.com/elimuinformatics/vcf2fhir/issues/new/choose).

Added
* Support for Structural Variants ([86](https://github.com/elimuinformatics/vcf2fhir/pull/86)).
* Support for Clinical Annotations ([89](https://github.com/elimuinformatics/vcf2fhir/pull/89)).

0.0.17

Added
* Exposed a new parameter to configure ratio for determining Homoplasmic vs Heteroplasmic ([19](https://github.com/elimuinformatics/vcf2fhir/issues/19)).

Changed
* Build process to PEP 517 ([18](https://github.com/elimuinformatics/vcf2fhir/issues/18)).

Fixed
* Excluded records with incorrect CHROM values in vcf file ([19](https://github.com/elimuinformatics/vcf2fhir/issues/19)).
* Removed 'Human reference sequence assembly version' component from variant observation ([36](https://github.com/elimuinformatics/vcf2fhir/issues/36)).
* Case where conversion region is not studied ([66](https://github.com/elimuinformatics/vcf2fhir/issues/66)).
* FHIR validation errors and warnings ([77](https://github.com/elimuinformatics/vcf2fhir/pull/77)).

0.0.1

Converts VCF variants into a [FHIR Genomics Diagnostic Report](http://hl7.org/fhir/uv/genomics-reporting/index.html).

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.

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