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CHANGELOG.rst

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Changelog

v1.0.4

  • SvAnna - update dependency versions.
  • svanna-io - Fix issue with VCF files compressed by newer compressor versions

v1.0.3

  • SvAnna - update dependency versions.
  • svanna-cli - Add support for v1 and v2 phenopacket in JSON, YAML, or protobuf binary formats. - Rework the logging functionality to log all output to standard error output and to allow setting the logging granularity via -v CLI option.

v1.0.2

  • SvAnna - update dependency versions.
  • svanna-core - Fix bug that assigned wrong score to multi-gene inversions based on promoter overlap.

v1.0.1

  • svanna-core - Fix bug leading to wrong query coordinates for getting the population variants.
  • svanna-cli - Fix logback configuration.

v1.0.0

  • SvAnna - SvannaVariant has a GenomicVariant and it is not a GenomicVariant anymore. - Updated dependencies: phenol v2.0.0-RC2, phenopackets v2.0.0, protobuf v3.14.0, spring-boot-starter-parent v2.6.7. - Simplify the documentation. - Change the namespace.
  • svanna-cli - Remove the config YAML file and expose the CLI parameters instead.
  • svanna-ingest - Ingest the resources into a ZIP file, calculate sha256 checksums.

v1.0.0-RC5

  • changes required for benchmarking the other SV prioritization tools
  • drop Jannovar

v1.0.0-RC4

  • Treat deletion and duplications that affect CDS but do not change the reading frame in a milder way
  • Drop the TAD idea and only evaluate the variant with respect to the overlapping genomic elements
  • Externalize gene model and gene definition sources
  • Report a track with dosage sensitive regions in the HTML report
  • Store gene/disease/phenotype mapping in the database instead of the files in the data directory
  • Improve logging - create a log file in the current working directory and store DEBUG info in the file

v1.0.0-RC3

  • Bug fixes - fix null pointer that was thrown when processing translocation that involved non-primary contig (alt, unplaced, etc.) - fix incorrect generation of SVGs for translocation

v1.0.0-RC2

  • Implement VCF output format
  • Clean up the repo from the obsolete code
  • Improve documentation & test coverage
  • Bug fixes - remove null pointer in GeneService - do not run coverage filter if the coverage data is missing for a variant

v1.0.0-RC1

  • Rename annotate CLI command to prioritize
  • Multiple minor adjustments

v0.3.1

  • Major progress in algorithm development

v0.3.0

  • Adding phenopacket support