vcfstats -

• Now vcf (the instance of cyvcf2.VCF is allowed to be passed as 2nd argument to continuous and categorical macros (#45).

```python from vcfstats.macros import cont

@cont def GLOBALPOS(variant, vcf): chrom = variant.CHROM.replace("chr", "") chridx = 23 if chrom == "X" else 24 if chrom == "Y" else int(chrom) prevchromlens = sum(vcf.seqlens[:(chridx-1)] return prevchrom_lens + variant.POS ``` Check the API documentation of cyvcf2 to see what information we can get from vcf.

- Python
Published by pwwang over 2 years ago

vcfstats -

• ➕ Use argx instead of pyparam

- Python
Published by pwwang about 3 years ago

vcfstats -

• 🚑 Fix numpy error raised from plotnine (#35)
• 📝 Update usage with docker in README.md (#33)
• 👷 Add python3.10 to CI

- Python
Published by pwwang about 3 years ago

vcfstats - 0.4.2

• 🐛 Fix config file not used correctly (#27)

What's Changed

• 0.4.2 by @pwwang in https://github.com/pwwang/vcfstats/pull/28

Full Changelog: https://github.com/pwwang/vcfstats/compare/0.4.1...0.4.2

- Python
Published by pwwang over 3 years ago

vcfstats - 0.4.1

• 📝 Add more examples regarding #20
• 🐛 Fix devpars by default a Namespace rather than a dict (#21, #22)

What's Changed

• 0.4.1 by @pwwang in https://github.com/pwwang/vcfstats/pull/23

Full Changelog: https://github.com/pwwang/vcfstats/compare/0.4.0...0.4.1

- Python
Published by pwwang over 3 years ago

vcfstats -

• ⬆️ Drop support for python 3.8 (brentp/cyvcf2#181)
• 🚨 Use python3.9 in Dockerfile
• ⬆️️ Upgrade pyparam to 0.5
• ⬆️ Upgrade and pin deps
• 📝 Add more examples (#15, #17)
• 👷 Add docker build in CI

- Python
Published by pwwang almost 4 years ago

vcfstats -

• Introduce enhancements (pwwang/vcfstats#15)

- Python
Published by pwwang about 4 years ago

vcfstats -

• Use plotnine instead of ggplot2 so no R is needed
• Add figfmt to generate different format of figures other than png

- Python
Published by pwwang over 4 years ago

vcfstats -

• Use lark-parser to parse formulas
• Add ggrepel in Dockerfile
• Use rich.table to print macros
• Allow python -m, avoid root logger configuration.

- Python
Published by pwwang over 4 years ago

vcfstats -

• Adopt lastest pyparam.

- Python
Published by pwwang over 5 years ago