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v0.18
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@holtgrewe holtgrewe released this 08 Dec 16:03
· 604 commits to main since this release
v0.18
79f30ac

As with all recent releases, Jannovar is best installed through Maven Central.
Alternatively you can directly download the compiled jannovar-cli-0.18.jar.

all

  • replace charite email of p. robinson with the new one of jax

jannovar-cli

  • Renaming tx-to-chrom to hgvs-to-vcf, also in Java module names.
  • CLI changes such that one VCF input and one VCF output path can be used only
  • Replacing apache commons-cli with argparse4j for a more modern and usable CLI
  • Consistently writing out HUGO symbols for gene names, using the hgnc_complete_set.txt information downloaded when building the annotation DB
  • Upgrading from ENSEMBL-74 to ENSEMBL-75 for annotation database files
  • Removing support for old Jannovar-style annotations (#241)
  • Adding new command for annotating csv files (annotate-csv)

jannovar-htsjdk

  • Properly annotating Mendelian inheritance for intergenic variants

jannovar-core

  • downloading hgnc_complete_set.txt together with data sets, TranscriptModel objects now consistently contain additional IDs
  • making ENSEMBL parsing more robust (falling back to transcript name if no transcript ID)
  • fixing bug #248 for ENSEMBL that used gene_id for gene_name
  • bugfix of NullPointerException in RefSeqParser while parsing refSeq curated
  • bugfix space in SeqOID of SYNONYMOUS_VARIANT
  • Update link to HGVS Nomenclature
  • Now BestAnnotationListTextGenerator shows really the best and not all annotations!

Manual

  • Documenting cli changes
  • Adding additional sites contributing, FAQ and how to filter
  • Better description of installations and quickstart
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