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v0.34
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@holtgrewe holtgrewe released this 07 Jun 15:43
v0.34
af315c6

jannovar-cli

  • disabeling ensemble for mouse (does not work with an hgnc file)
  • updating broken links in download source file
  • Adding faMT genomes for all refseq annotations
  • bumping dependency on lombok

jannovar-core

  • Remove hard-coded chrMT renaming. Filenames for download that have a ? in their URL will be splitted and only the first part before the ? is used a file name in the download path.
  • Making faMT annotation for refSeq optional
  • Update RefSeq parser that does not run into null-pointer exceptions on mouse and rat genome (e.g. when no exon defines the gene name)
  • Fixing issue with block substitutions (#475).
  • Fixing RefSeq build to properly assign transcript model (use best match with alignment) in the case of duplicates.
  • Fixing issue in projection in the case of leading gaps (has no effect on CDS position prediction).
  • Adding TranscriptModel.getTrimmedSequence() that removes leading and trailing (unaligned in RefSeq) sequence.

jannovar-htsjdk

  • Bumping HTSJDK dependency to v2.20.3 because 2.20.0 has a bug in the VariantContextBuilder
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