v1.0.4

A minor release with several improvements:

• Fix bug leading to premature termination of some compressed VCF files.
• Update dependencies

What's Changed

• Update dependencies by @ielis in #236

Full Changelog: v1.0.3...v1.0.4

v1.0.3

Release with updated dependencies to improve performance and mitigate security vulnerabilities. The release works with the new SvAnna data release 2304 that is available for download as described in the documentation.

• 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

What's Changed

• Fix bug in scoring of multi-gene inversions. by @ielis in #219
• Update dependencies by @ielis in #220

Full Changelog: v1.0.1...v1.0.2

v1.0.1

What's Changed

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

Full Changelog: v1.0.0...v1.0.1

1.0.0

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.

1.0.0-RC5

What's Changed

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

Version upgrades

• Svart v2.0.0-RC1
• SilentGenes v0.2.0

Full Changelog: v1.0.0-RC4...v1.0.0-RC5

1.0.0-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

1.0.0-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

1.0.0-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

1.0.0-RC1

The first release candidate to test.