v2.5.3

• ov module info shows the module's location.
• ov report with --cols option lets you extract the desired columns only for reports.
• stdoutreporter is provided as a default module.
• Documentation is available at https://docs.oakvar.com.

v2.5.2

• Works with Roakvar v2.5.2.

v2.5.1

• OakVar store has been launched.
• Added ov run —vcf2vcf option for VCF input-to-VCF output files workflow, which produces annotated VCF output files orders of magnitude faster than without it. For sample-heavy input such as 1000 Genomes files, this option is critical. With this release, only VCF output files are generated without SQLite result files. However, future development is planned for keeping this speed up and generating result database files.
• Added convenient setup command ov system setup. After installing OakVar, ov system setup will take care of all setup work.
• Added command-line interface commands for the OakVar store, including:
  • ov store account create: creates a store account
  • ov store account delete: deletes a store account
  • ov store account change: change a store account’s password
  • ov store account check: checks if you are logged in at the OakVar store
  • ov store account login: logs in to the OakVar store
  • ov store account logout: logs out from the OakVar store
  • ov store account reset: resets a store account’s password
  • ov store fetch: fetches the cache of the OakVar store
  • ov module pack: generates a zip file for the code and the data of a module, respectively
  • ov store register: registers a module at the OakVar store
  • ov store oc: commands to interface with OpenCRAVAT store
• Major refactoring of the entire codebase
• Other minor bug fixes and improvements

v2.4.8

• Sped up ov gui and CLI commands.
• Added ov config oakvar CLI command.
• Added ov manifest fetch CLI command to update the store data cache. Store data is locally cached.
• Added ov store pack CLI command (no use for now).
• Fixed debug traceback for ov gui.
• Fixed Python3.8-compatibility.
• Fixed --quiet option for CLI commands.

v2.4.7

• Fixed console output of ov module CLI commands.

v2.4.6

• Multi-core gene mapping is default.
• Fixed ov system setup, ov system config, and ov system md to show output.
• Fixed Ctrl-C while ov module installbase.
• Fixed processing default command-line argument.
• Fixed importing inout and admin_util by modules.

v2.4.5

• Line breaks in annotation results are correctly escaped with ov report. This fixes the issue at KarchinLab/open-cravat#106.
• CLI commands alignment among CLI, Python, and R. For example:

CLI:

>ov module ls

Python:

>import oakvar
>oakvar.ov_module_ls()

R:

>devtools::install_github("rkimoakbioinformatics/roakvar")
>library(roakvar)
>ov.module.ls()

• Python subprocess calls to CLI functions such as oakvar.ov_module_ls() will return returncode 0 if no error was produced.
• ov gui will print error messages to stdout if —debug option is given.
• ov module install will automatically install PyPI dependencies defined in OakVar modules’ yml files with requires_pypi or pypi_dependency.- Improved the speed of handling configuration files.
• Improved exception handling.
• Fixed that the number of unique variants did not show on the job table of ov gui.
• Fixed a bug in using —package option with ov run and ov report.
• Refactored the mechanism for handling —package and --confpath options to ov run and ov report.
• Refactored the handling of CLI command functions for better alignment among CLI, Python, and R.
• Refactored the code so that no error nor warning is reported by pyright and pylance.

v2.4.2

• ov system setup is the new command to set up OakVar after pip install oakvar. A system conf yaml file can be given as ov system setup -f setup.yaml for consistent setup.
• ov system command has been added to handle OakVar system operations.
• System configuration can be defined with environmental variables. All the fields in cravat-system.yml can be defined with environmental variables using a consistent naming convention. For example, the root data directory of OakVar is defined in root_dir field in cravat-system.yml. An environmental variable OV_ROOT_DIR will override what is in cravat-system.yml. The OakVar modules directory is defined in modules_dir field, which can be overridden with OV_MODULES_DIR. The naming convention is OV_ + the upper case version of the system conf field.
• Exception handling has been improved.

v2.4.1

• Significantly faster launch of ov CLI commands
• Python 3.8 is the minimum Python version requirement.
• Refactored codes.
• ov run and other CLI commands can have --md option to fix KarchinLab/open-cravat#112.
• The PyPI packages required for a module can be defined with requires_pypi field in the module's yml file and they will be automatically installed with ov module install.
• All secondary input fields, including those with None value, will be provided to annotator modules' annotate function for consistency in handling them.

v2.4.0

• Works with Roakvar, an R wrapper of oakvar. See https://github.com/rkimoakbioinformatics/roakvar.
• Cleaned CLI commands.
• Works with existing OpenCRAVAT modules.
• Overall code refactoring