v.4.7.0

• Variant annotator now fully supports phased annotation

v4.6.2

• Bugfix: sort query param restored

v4.6.1

• Bug fixed could potentially lead Command Line to raise Null Pointer Exception

v4.6.0

• Variant Annotator compatible with VEP e90
• Variant Annotator performance improved up to 3x
• Clinical variants are now normalised
• New clinical data source: Database Of Curated Mutations (DOCM)
• New status WS provides details about the status of the installation: tomcats, DB machines, etc.
• New ping WS
• Unit tests improved

v4.5.6

• Parser updated to deal with ClinVar May 2018 release
• Variant annotator now understands "MT", "chrMT", "M" and "chrM" as the mitochondrial chromosome

v4.5.5

• Decomposition of block substitutions/MNVs was causing some problems when combined with custom annotation. A new CLI flag --skip-decompose has been enabled to prevent the normalization process from decomposing while indexing custom annotation files into RocksDB and annotating with the CellBase annotator.

v4.5.4

• variant-annotation command no longer fails once the annotation process has finished
• Java REST Client
  • Bugfix. When multiple ids were used as an input each of them returning more than 1000 results, could potentially happen that these result lists were not appropriately processed.
  • Thread safe issue fixed at CellBaseClient.
• Gene model: transcripts.xrefs field will now always include geneName, geneId, transcriptName and transcriptId, even if the Ensembl API returns no xrefs at all
• Improved initialisation of heritableTraitList and genomicFeatureList during ClinVar parsing to avoid Avro serialization issues
• If no path at all was provided for the variant-annotation output, i.e. -o test.json.gz rather than -o ./test.json.gz, an error was raised. This is now checked and error avoided.

v4.5.3

• Bug fix: HGVS variant annotation fixed

v4.5.2

• Important bugfix: variant-annotation CLI now correctly passes the assembly argument when annotating through WS
• REST client is now able to handle variant id parsing problems, e.g. 1:645710:A:INS:ME:ALU
• New variant-annotation parameter added to the CLI: --max-open-files can limit the number of file kept open by RocksDB
• All writes/reads are now in UTF-8
• HGVS normalization errors do no longer interrupt the whole annotation process and raise a warning instead
• Perl scripts querying ENSEMBL APIs improved to properly change ENSEMBL version as appropriate
• Annotator execution is no longer interrupted if an error raises while trying to normalize a variant. Likewise, will not get interrupted if errors raise during HTSJDK parsing of VCF lines. Warnings will be shown and corresponding variants skipped

v4.5.1

• Adaptors no longer modify the QueryOptions object they receive: avoids a potential out of memory exception
• Variant annotation processes properly terminate in case an exception is run during the execution
• HGVS bugfix: a bug was found when variant was located within a coding exon, between coding start and coding end, if the coding start did not coincide with the exon start position
• Swagger works now with https
• Data types within swagger documentation fixed: used to generate massive useless error logs
• Deprecated clinical WS fixed
• Imprecise queries require now all Variant.sv.getCi* != null
• dgiDB URL was outdated and has been fixed