Changelog

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