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

Beta v0.8.0

New Features:

• Combine --bam, --bam-list and --sample-bam arguments #128
• Combine --ploidy and --sample-ploidy arguments #128
• Combine --inbreeding and --sample-inbreeding arguments #128
• Combine --mcmc-temperatures and --sample-mcmc-temperatures arguments #128
• Improvements to documentation

Beta v0.7.0

New Features:

• Mask reference allele when it is only reported to satisfy VCF spec #146
• Optionally report prior allele frequencies in AFPRIOR field
• Filtering for some edge cases where genotypes should not be reported (AF0 and NOA)

Bug Fixes:

• Handle edge-case where all prior allele frequencies are zero #145

VCF Changes:

• Added REFMASKED info flag to indicate reference allele is amsked and should be ignored
• Added AFPRIOR infor filed to indicate prior allele frequencies
• Added NOA filter to indicate loci where no alleles were observed (e.g., masked reference only)
• Added AF0 filter to indicate invalid prior allele frequencies in which all frequencies were zero