v2.0.1

What's Changed

• Add --out-dir option, rework prefix by @ielis in #44
• Fix hard-coded versions by @ielis in #47
• Fix bug in allele generator by @ielis in #51

Full Changelog: v2.0.0...v2.0.1

v2.0.0

What's Changed

• Simplify CLI - the configuration file is no longer necessary
• Update download links by @ielis in #33
• Add bootstrap module to enable configuration without Spring by @ielis in #32
• Use Svart v2.0.0 and SilentGenes v0.2.3 by @ielis in #39
• Fix unclear instruction about output file by @ielis in #40
• Support HGVS g. token in annotate-pos input by @ielis in #41
• Externalize the project files required for building Squirls database. by @ielis in #42

Full Changelog: v1.0.0...v2.0.0

v1.0.0

The manuscript version

• squirls-cli
  • allow to block-compress (bgzip) the annotated VCF on the fly by using -f vcfgz option
  • do not fail due to an exception being thrown by Jannovar when annotating a VCF file
  • do not sort variants in the VCF output if the required header lines are missing
  • allow precalculating scores for regions of interest with precalculate command
  • use vmvt v0.9.4
• squirls-ingest
  • prevent ingesting transcripts with duplicate ENST id

v1.0.0-RC4

Squirls

• make the code repository public, enable Read the Docs integration
  squirls-cli
• finalize the HTML report and SVG graphics layout
• allow writing results in multiple result formats, including VCF, TSV/CSV
• report positions of candidate cryptic variants
• add distribution zip
  squirls-core
• use apiguardian-api to label the API elements
• use svart v1.0.0 to represent variants, genomic regions, and the other genomic coordinates
• remove external dependencies such as JBlas,
  squirls-ingest
• download genomic assembly report
• calculate SHA256 checksums
• replace argparse4j by picocli
squirls-io
• create the module for handling creation of Squirls structures
  squirls-spring-boot-autoconfigure
• fix bug involving database initialization in HPC environments

v1.0.0-RC3

Pre-release with the following improvements:

• Squirls
  • improve documentation
  • use Jannovar v0.35, SLF4J v1.7.30
• squirls-cli
  • use Picocli for CLI definition, prettify CLI
  • support HTML and VCF output formats
  • numerous bug fixes
  • allow to specify # threads
  • improve progress reporting
• squirls-core
  • mark API classes
• squirls-ingest
  • create a ZIP file after ingest
  • add sanity checks for transcripts

v1.0.0-RC2

Pre-release with the following improvements:

• squirls-cli
  • implement commands annotate-csv, annotate-vcf, and annotate-pos
  • prettify the HTML report produced by analyze-vcf command
• squirls-core
  • performance improvements, increase test coverage
  • improve handling of positions with missing conservation scores

v1.0.0-RC1

The v1.0.0 release candidate