Beta v0.11.1

Maintenance:

• Switch to pyproject.toml #188
• Set versions manually without SCM #188
• Update to Numpy 2 and Pandas 2
• Add Python 3.13 to build matrix

Beta v0.11.0

Breaking Changes:

• Changed the default prior used in assemble to a flat prior across genotypes.
  This is a more sensible prior in almost all situations because the previous
  Dirichlet-multinomial prior had to assume that all possible haplotypes (i.e.,
  combinations of SNVS) where equally likely to be present in the sample population.
  In general, this inflated the prior probability of heterozygous genotypes.
  Note that this is not a significant issue when using the call program with
  known haplotypes (and a reasonable estimate of their frequencies).
  The previous Dirichlet-multinomial prior can still be used via the
  --use-dirmul-prior argument. #139
• Changed the default prior used in call and call-exact to a flat prior across
  genotypes. This is a better default option than the previous Dirichlet-multinomial
  prior when sample inbreeding and prior allele frequencies are not specified.
  The previous Dirichlet-multinomial prior can still be used via the --use-dirmul-prior
  argument which is now used to set both the sample inbreeding and prior on allele
  frequencies. This new argument replaces the --inbreeding and --prior-frequencies
  arguments. #139

Beta v0.10.0

New Features:

• New experimental atomize tool for splitting haplotypes into basis SNVs #72.
• New experimental call-pedigree tool fo pedigree informed genotype calling.
• Optionally specify just the INFO or FORMAT variant of an optional VCF field #174.
• Use setuptools_scm for versioning #179.
• Added example notebook from 2024 Tools for Polyploids workshop.

VCF Changes:

• Renamed PHQ and PHPM to SQ and SPM for clarity.
• Added INFO/UAN field for number of unique alleles called #174.
• Added INFO/MCI field for proportion of sample with Markov Chain incongruence.
• Added optional fields #174:
  • INFO/AOPSUM (sum of FORMAT/AOP).
  • INFO/ACP and FORMAT/ACP.
  • INFO/SNVDP and FORMAT/SNVDP.

call-pedigree alpha 3

Alpha release of the call-pedigree tool (on top of version 0.9.3)

Bug Fixes:

• Add pedigree submodule to setup.py #180
• Add call-pedigree development branch to CI #181

Beta v0.9.3

Bug Fixes:

• Correct usage of the AN field #176
• Improved error messages for io #163 and #177

call-pedigree alpha 2

Alpha release of the call-pedigree tool (on top of version 0.9.3)

Beta v0.9.2

Bug Fixes:

• Avoid holding alignment file handles open #173
  • Substantial reduction in memory usage and concurrent file handles

Beta v0.9.1

Beta 0.9.1

New Features:

• Allow complex sample pooling via the use of a tabular file

Beta v0.9.0

New Features:

• Added tool mchap find-snvs to generate a template VCF for assembly #166
• Option to report posterior probability of allele occurrence #162
• Added generic option to filter input haplotypes #168

Bug Fixes:

• Allow samples with multiple read groups #164
• Correct number of cores used when specifying multiple cores #150
• Simplify specification of prior allele frequencies #154
• Improve performance when working with CRAM files #167

CLI Changes:

• Added mchap find-snvs tool #166
• Added optional --reference argument to call and call-exact tools #167
• Replaced --skip-rare-haplotypes argument with --filter-input-haplotypes #168
• Replaced --haplotype-frequencies and --haplotype-frequencies-prior with --prior-frequencies #154

VCF Changes:

• Added AOP field to record posterior probability of an allele occurring at any copy number #162

Internal Changes:

• Changes to using multiple process to minimize file handel creation #167
• Added pandas as a dependency

Beta v0.8.1

Bug Fixes:

• Fixed integer overflow bug when calculating the total number of unique haplotypes in mchap assemble #157

Internal Changes:

• Minor performance improvement to SNP homozygosity testing in mchap assemble