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Recent Releases of mutyper

mutyper - v1.0.2

What's Changed

  • JOSS-requested affiliation edits by @WSDeWitt in https://github.com/harrispopgen/mutyper/pull/48

Full Changelog: https://github.com/harrispopgen/mutyper/compare/v1.0.0...v1.0.2

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt about 3 years ago

mutyper - v1.0.1

This is a patch with no changes. It triggers a consistent pypi release and zenodo archive.

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt about 3 years ago

mutyper - v1.0.0

Summary

  • Versioning for JOSS paper in response to Post-Review Checklist: https://github.com/openjournals/joss-reviews/issues/5227#issuecomment-1517014143
  • Triggers Zenodo archive with DOI
  • PR: JOSS review by @WSDeWitt in https://github.com/harrispopgen/mutyper/pull/47

Full Changelog: https://github.com/harrispopgen/mutyper/compare/v0.7.1...v1.0.0

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt about 3 years ago

mutyper - v0.7.1

What's Changed

  • JOSS prereview by @WSDeWitt in https://github.com/harrispopgen/mutyper/pull/40
  • Require python>=3.8

Full Changelog: https://github.com/harrispopgen/mutyper/compare/v0.7.0...v0.7.1

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt over 3 years ago

mutyper - v0.7.0

Adds a draft paper to be submitted to JOSS.

What's Changed

  • JOSS paper by @WSDeWitt in https://github.com/harrispopgen/mutyper/pull/39

Full Changelog: https://github.com/harrispopgen/mutyper/compare/v0.6.4...v0.7.0

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt over 3 years ago

mutyper - v0.6.4

What's Changed

  • issue 36: dealing with missing genotypes with mutyper variants by @Lukez-pi in https://github.com/harrispopgen/mutyper/pull/37
  • numpy implementation for spectra by @Lukez-pi in https://github.com/harrispopgen/mutyper/pull/38

Full Changelog: https://github.com/harrispopgen/mutyper/compare/v0.6.3...v0.6.4

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt over 3 years ago

mutyper - v0.6.3

What's Changed

  • Changed the 'number' type of 'mutation type' to A in the VCF header by @Lukez-pi in https://github.com/harrispopgen/mutyper/pull/35

New Contributors

  • @Lukez-pi made their first contribution in https://github.com/harrispopgen/mutyper/pull/35

Full Changelog: https://github.com/harrispopgen/mutyper/compare/v0.6.2...v0.6.3

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt almost 4 years ago

mutyper - v0.6.2

What's Changed

  • Don't count phased==True toward genotypes by @WSDeWitt in https://github.com/harrispopgen/mutyper/pull/34
  • resolves #30 (again)

Full Changelog: https://github.com/harrispopgen/mutyper/compare/v0.6.1...v0.6.2

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt almost 4 years ago

mutyper - v0.6.1

What's Changed

  • Added a fix for adding too many counts when the GT is unknown by @mrvollger in https://github.com/harrispopgen/mutyper/pull/31
  • Move docs build from the default branch to an orphan branch, and workflow to build on push to master by @WSDeWitt in https://github.com/harrispopgen/mutyper/pull/32
  • CLI tests, and more genotype fixes by @WSDeWitt in https://github.com/harrispopgen/mutyper/pull/33

Full Changelog: https://github.com/harrispopgen/mutyper/compare/v0.6.0...v0.6.1

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt over 4 years ago

mutyper -

New features

  • logging from CLI via the --verbose option
  • improved handling of compressed fastas
  • updated docs

Developer notes

  • python code should be formatted with Black. This will be checked in CI.
  • see new developer tools docs page: https://harrispopgen.github.io/mutyper/developer.html#developer-tools

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt almost 5 years ago

mutyper -

Patch to fix (and add tests for) the use of a BED file to define regions for which mutation types should be defined by the negative strand. This should be useful for polarizing mutations according to functional genomic annotations.

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt about 5 years ago

mutyper -

Patch to fix bug in mutyper ancestor when not using a bed file

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt about 5 years ago

mutyper -

Patch haploid double counting issue in mutyper spectra

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt about 5 years ago

mutyper -

Minor patch to mutyper variants to allow haploid VCF input.

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt over 5 years ago

mutyper -

Patch

Fixes incorrect genotypes from mutyper variants #17. This is an important fix for computing individual-wise variant spectra, and maintaining correct allele count AC info field after subsampling with bcftools.

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt over 5 years ago

mutyper -

New Feature

New argument --randomize for mutyper spectra assigns each variant to one random haplotype. This is intended to induce more independence between samples.

h/t @goldmich

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt over 5 years ago

mutyper -

Patch to squish a few more bugs in mutyper ancestor

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt almost 6 years ago

mutyper -

patch to address a bug in mutyper ancestor

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt almost 6 years ago

mutyper -

Breaking changes

  • The default value for the --chrom_pos argument to variants and targets subcommands is now 0, instead of 2, so ancestral FASTA files with headers that simply contain the chromosome name will work by default

New features

  • New CLI subcommand mutyper ancestor to estimate an ancestral genome using an aligned outgroup and a data set of variants with a callability mask

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt almost 6 years ago

mutyper - targets speedup

minor patch to improve performance of targets subcommand

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt almost 6 years ago

mutyper -

  • Adds an optional flag --population to the mutyper spectra command to compute population-wise spectra instead of individual
  • Fixes a bug in BED-filtering when running mutyper targets (introduced in v0.2.1)

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt almost 6 years ago

mutyper - strand-aware

patch implementing strand-aware mutation contexts via the strand_file option

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt almost 6 years ago

mutyper - package release

Pypi package and documentation

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt almost 6 years ago

mutyper - mutyper classic

for the brave

Scientific Software - Peer-reviewed - Python
Published by WSDeWitt almost 6 years ago