Oakvar

Latest version: v2.12.7

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2.5.29

- `--run_name` is required for `ov run` when multiple input files are given.

2.5.28

- The interactive result viewer can now handle more than 100,000 variants in a job result file, by using pagination.
- The size of one page in the variant level table of the interactive result viewer can be defined in the user configuration file (oakvar.yml. To know where this file is, do `ov config user`) with the key `gui_result_pagesize`.
- VCF2VCF mode can perform liftover. For example, `ov run input.vcf --vcf2vcf -l hg19` will convert hg19 coordinates to hg38 ones.
- VCF2VCF mode can handle chromosome names without "chr".
- The interactive result viewer's query builder will show "no option available" message instead of an empty selection box.

2.5.23

- `ov store register` can accept `-f` for a file with code and data URLs. For example, `urls.txt` can have

code_url:
- https://dropbox.com/xxx/module1__1.0.0__code.zip000
data_url:
- https://dropbox.com/xxx/module1__1.0.0__data.zip000
- https://dropbox.com/xxx/module1__1.0.0__data.zip001
- https://dropbox.com/xxx/module1__1.0.0__data.zip002

and `ov store register module1 -f urls.txt` will register the module.

2.5.22

- `ov module install` will download zip file chunks if available. If downloading one of them fails, `ov module install` resumes with the failed chunk and onward.
- `ov module pack --split` produces zip file chunks to upload.
- Improved `ov gui` update modules.
- Improved `ov system setup`.

2.5.17

- Improved VCF2VCF with long form sequence ontology terms.
- Improved the UI of the web store.
- Improved the log and the err log output regarding invalid variants.
- `ov gui` will launch despite any error in loading webapps.
- Fixed package dependencies.
- Fixed the module detail dialog on the web store.

2.5.14

- `ov gui` launches in less than a second (from its second run).
- Improved the speed of `ov module ls -a`.
- Fixed installation message output in `ov gui`.
- Fixed system update message output in `ov gui`.
- Fixed an error due to distutils package.

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