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Improve variant loading performance, expand gnomAD annotations, and fix variant filtering and parsing

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@northwestwitch northwestwitch released this 23 Oct 09:10
v0.2
1e9a09d
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[0.2]

Added

  • Loading MT variants from a separate file (#180)
  • Parse additional gnomAD fields from the VCF INFO field (#200)

Changed

  • Keep the highest-scoring variant when duplicate IDs occur within loading batch (#188)
  • Do not parse conservation data for STRs (#191)
  • Store null for spliceai_prediction when no prediction data is available (#198)

Fixed

  • Fix incorrect rank_score conversion that caused all variants to be loaded (#177)
  • Introduce an early variant inclusion check to avoid unnecessary processing (#177)
  • Refactor update_compounds to improve variant lookup and reduce MongoDB queries (#177)
  • Fix pathogenic variant filtering by matching VEP ClinVar significance fields case-insensitively (#182)
  • Fix MEI variant filtering to load all mobile element insertions regardless of rank score (#184)
  • Parsing of STRs genotypes (#190)
  • Format of clnsig accession Int64 -> Int32 (#194)
  • Parsing of spliceai_score and spliceai_position in gene documents (#195)
  • Fix copy number parsing by reading the CN FORMAT field as an integer instead of a float (#199)
Assets 6
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