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@holtgrewe holtgrewe released this Jul 30, 2019 · 17 commits to master since this release

overall

  • Fixing ANN annotation field to have ./unbound cardinality.
  • Bumping several dependencies, including HTSJDK.

manual

  • Adding conda support in installation documentation
  • Fixing broken link in quickstart

jannovar-core

  • Fixing annotation of SVs that look like sequence variants (#456).
    Interpretation is to use the sequence variant annotation code now.
    This fixes a bug with annotating latest ClinVar for GRCh38.
  • Prevent Annotation.{getPutativeImpact,getPutativeImpact}() from returning null (#458).
  • Correctly parsing RefSeq mitochondrial transcripts.
    Bumping the required versin to 0.33-SNAPSHOT to higlight this (#463).
Assets 2

@holtgrewe holtgrewe released this Jun 13, 2019 · 26 commits to master since this release

overall

  • Changing log4j version to 2.11.2
  • Changing slf4j version to 1.7.25

jannovar-cli

  • Adding a simple REST server for annotating single variants.
    • Launch with jannovar-cli rest-server -d data/hg19_refseq.ser -d data/hg19_ensembl.ser
    • Then, query with /annotate-var/refseq/hg19/chr7/140453136/A/T or /annotate-var/ensembl/hg19/chr7/140453136/A/T
Assets 2

@holtgrewe holtgrewe released this May 23, 2019 · 30 commits to master since this release

This release fixes an important issue with RefSeq transcripts that align with gaps to the genome (issues #447 #450). Overall 500 genes are affected including MYH7! You probably want to upgrade to this release.

jannovar-core

  • Introducing classes for representation of gapped sequences, alignments, and position projection.
  • Fixing bug in ENSEMBL transcript database generation (tx version was appended twice)
  • Adding flags for "has substitutions" and "has indels" to TranscriptModel that get filled for RefSeq transcripts.
  • Correctly parsing of RefSeq transcripts with indels.

jannovar-cli

  • Using HTTP protocol instead of FTP everywhere as it's possible (#451).
  • Fixing HGVS conversion for indels (#452).
Assets 2

@holtgrewe holtgrewe released this May 21, 2019 · 42 commits to master since this release

Bugfix release.

jannovar-core

  • Fixing interpretation of INFO/SVTYPE, urldecode and only use the first component after splitting at ":".
  • Interpreting SV type annotation for SV2 more correctly.
Assets 2

@holtgrewe holtgrewe released this May 7, 2019 · 46 commits to master since this release

jannovar-core

  • Putative impact of splice_region_variant has changed from MODERATE to LOW (see issue #439)
  • Decreasing log verbosity in one location when building database.
  • Fixing CDS region import in RefSeqParser
  • Putative impact of splice_region_variant has changed from MODERATE to LOW (see issue #439)
  • Fixing SV annotation using hg38/ucsc for transcripts without gene ID (see #444).
  • Adding support for rn6 RefSeq transcripts.
    Adding allowNonCodingNm directive for data source INI file to disable check that RefSeq NM transcript has CDS.
  • Adding versions to ENST accessions for ENSEMBL.

jannovar-vardbs

  • Bugfix: TSVAnnotator did not use end given column.
Assets 2

@holtgrewe holtgrewe released this May 7, 2019 · 67 commits to master since this release

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.
Assets 2

@holtgrewe holtgrewe released this May 7, 2019 · 98 commits to master since this release

jannovar-cli

  • Integrating support for thousand genomes VCF
  • Integrating thousand genomes/ExAc count limits into inheritance filter

jannovar-vardbs

  • Adding support for thousand genomes VCF

jannovar-htsjdk

  • Adding support for limiting genomes/ExAc counts into inheritance filter
Assets 2

@holtgrewe holtgrewe released this May 7, 2019 · 102 commits to master since this release

jannovar-cli

  • Making OneParentGtFiltered filter optional. The default setting to false (specify --one-parent-gt-filtered-filters-affected to enable).

jannovar-core

  • Moving variants in non-coding transcripts after UTR variants.

jannovar-hgvs

  • Fixing parser issue for nucleotide indels (#408).

jannovar-htsjdk

  • Obey the options.escapeAnnField parameter for escaping the variant effect in the ANN field.
Assets 2