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v0.36
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@holtgrewe holtgrewe released this 09 Jun 21:40
v0.36
c0e4ba9

Highlight: Pre-Built Databases

We now provide pre-built databases via Zenodo.
This addresses various issues that were caused by changing upstream data URLs.
See README.md for details.

overall

  • Switching to Github Workflows for continuous integration.
  • Bumping a couple of dependencies.
  • Switching to JUNIT 5.
  • Pre-built databases are now available via Zenodo (see README.md for instructions).
    We provide shell scripts instead of using Java programs for downloading the files.

jannovar-core

  • Apply fix for (#498, PR #499 by @roland-ewald of @limbus-medtec).
    This fixes a problem with right-shifting deletions on amino acid sequences.
    See the tickes and merge request for details.
  • Fixing problem with GRCh38 RefSeq annotation / projection (#524).

jannovar-cli

  • Adding command vardb-import for importing annotations from VCF files into H2 database files.
  • Adding command vardb-list for listing annotation meta data from vardb-import.
  • Adding command vardb-annotate for annotating VCF files from Jannovar H2 database files.

jannovar-vardbs

  • Deprecating previous content of the package.
    The deprecated classes are due to be removed in v0.36.
  • Adding modules for importing VCF files into H2 database files, listing the meta data conents, and annotating VCF files.

jannovar-hgvs

  • Fixing parsing of unchanged (=) for nucleic acide sequences (#493).
  • Fixing issue with HGVS delins with del bases but no ins bases (#491).
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