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v0.28
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@holtgrewe holtgrewe released this 07 May 13:48
v0.28
60571e7

jannovar-cli

  • Bumping ENSEMBL versions for GRCh37 and GRCh38.
  • Fixing sources information for updated ENSEMBL downloads.
  • For ENSEMBL, use ENSEMBL-provided mapping from ENSG to HGNC ID for Entrez ID assignment.
    This is necessary as Ensembl gene IDs turn out to be not so stable between hg37 and hg38 after all.
    Case in point: ENSG00000276141 vs. ENSG00000187667.
  • Adding --gene-ids argument to downloader for creating smaller databases (mostly for test purposes).
  • Adding SV support to jannovar-cli, includes tests.
  • Using ENSEMBL-provided mapping from ENSG to Entrez ID in the case HGNC mapping does not work.

jannovar-htsjdk

  • Adding SV support to jannovar-htsjdk
  • Bumping HTSJDK dependency to v2.18.2

jannovar-core

  • Changing upstream/downstream size to 5kbp.
  • Support for prioritizing RefSeq transcript on the PAR of chrX over those of chrY
  • Refactorizations to improve performace using EnumSet.
  • Extended VariantEffect for the effects of structural variants.
    Removing documentation that the effect is not used in Jannovar for some now interpreted ones.
    Also variant effect for non-coding variants is added using the current VEP predictions as a template.
  • Prohibiting creating GenomeVariant with symbolic alleles.
    Throwing new checked exception InvalidGenomeVariant case of error.
  • Fixing SO term ID for VariantEffect.DISRUPTIVE_INFRAME_DELETION
  • Correctly parsing transcript version for ENSEMBL when available (not available for b75/GRCh37).
  • Making transcript model building (for download) more memory efficient.
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