Skip to content

CHANGELOG.md

Latest commit

 

History

History
52 lines (50 loc) · 2.52 KB

CHANGELOG.md

File metadata and controls

52 lines (50 loc) · 2.52 KB
Raw

Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

About changelog here

[unreleased]

Added

  • Use the rust-htslib for reading VCF files (#1)
  • First Variant model and parsing modules (#2)
  • Parse alleles and missing docstrings (#3)
  • Variant type enum (clinical or research) key/values passed to main function (#5)
  • Custom issues and pull requests templates (#9)
  • Pass case _id from CLI (#10)
  • Parse variant.FILTER field (#11)
  • Parse variant.QUAL field (#12)
  • Parse compounds field (#14)
  • Parse the 4 variant IDs: simple_id, variant_id, display_name, document_id (#15)
  • Parse rank_score and norm_rank_scorefrom VCF (#16)
  • Infer complete coordinate data (#17)
  • Parse cytobands and collect cytoband start and end for each variant (#18)
  • Parse genmod genetic models (#19)
  • Parsing specific variant fields: str_swegen_mean and str_swegen_std (STRs) and somatic_score (cancer and cancer_sv variants) (#20)
  • Parse a number of STR-related fields (#21)
  • Parse SCOUT_CUSTOM INFO field (#22)
  • Parse strs source fields (SourceDisplay, Source, SourceId) (#23)
  • Parse mei info: name and polarity (#24)
  • Parse genotype info (#25)
  • Parse eventual dbSNP IDs (#27)
  • Parse INFO.MATEID as mate_id, when available (#28)
  • Parse AZLENGTH and AZQUAL values, when available (#31)
  • Parse fusion variants INFO field (#32)
  • Set fusion genes from fusion variant INFO (#33)
  • Parse MitoMap-associated diseases (#34)
  • Parse HmtVar annotations (#35)
  • Parsing Genes and transcript annotations from VEP annotations - basic parsing (#36)
  • Create list of genes from parsed VEP transcripts (#40)
  • Create list of variant HGNC ids from variant genes (#41)
  • Parse clnsig from VEP transcripts (#42)
  • Parse oncogenicity clnsig from ONC, ONCREVSTAT, ONCDN, CLNVID INFO fields (#43)
  • Parse external databases' frequencies from INFO field and parsed VEP transcripts (#44)
  • Parse LoqusDB frequencies and metadata (#45)
  • Added GitHub Action for linting, tests and changelog enforcement (#47)

Changed

  • Structure of parsed entities, to reflect documents saved in the database (#20)
  • Improved and simplified code (#22)
  • Refactored VEP annotations parsing module (#38)

Fixed

  • Normalize chromosome names by stripping the chr prefix (#4)
  • Parsing of end chromosome (#29)
  • Parsing of variant sub-category (non SNVs) and end chromosome (#29)
  • Parsing of multi-transcript genes from VEP CSQ field (#37)