Beta v0.6.0

New Features:

• Optionally output posterior allele frequencies #135
• Optionally specify a prior allele frequencies in mchap call and mchap call-exact #120
• Optionally filter input haplotypes by input frequencies in mchap call and mchap call-exact #113
• Improve PMF performance for mchap call and mchap call-exact #125
• Allow pooling of all samples into single sample #140
• Allow arbitrary ploidy in PMFs #124

CLI Changes:

• Default to constant base error rate without using phred scores #127
• Replaced --ignore-base-phred-scores with --use-base-phred-scores #127
• Increased default MCMC steps and burnin to 2000 and 1000 respectively #137
• Removed --sample-list argument #128
• Merged --genotype-likelihoods and --genotype-posteriors into --report #128
• Added option to report AFP via --report #135
• Added --sample-pool argument #140
• Added --haplotype-frequencies parameter to mchap call and mchap call-exact
• Added --haplotype-frequencies-prior flag to mchap call and mchap call-exact
• Added --skip-rare-haplotypes parameter to mchap call and mchap call-exact
• Removed pedigraph tool #138

VCF Changes:

• Replaced KMERCOV with MECP (MEC / RCALLS) #134
• Optional AFP field to report posterior allele frequencies #135

Beta v0.5.1

Bug Fixes:

• Fix addition of null allele counts to final allele #115
• Fix integer overflow with many haplotypes #117

Beta v0.5.0

New features:

• Added Gibbs sampler re-calling tool: mchap call #110, #104
• Added exact re-calling tool:mchap call-exact #110

Changes to CLI:

• Removed exact re-calling option from mchap assemble #110
• Reordering of some CLI arguments to facilitate reusing arguments between sub-tools

Internal changes:

• Move CLI parser arguments into reusable components
• Reuse CLI tool methods via inheritance
• Prior and likelihood functions for known sets of haplotypes
• Generate Locus objects from pysam variant records
• Reorganize internal sub-modules

Beta v0.4.2

Features:

• Per-sample specification of temperatures for parallel-tempering #99

Beta v0.4.1

Minor changes to de-clutter the output VCF.

VCF changes:

• Removed FORMAT/FT from header #101
• Removed INFO/AD and FORMAT/AD #98
• Dynamically omit FORMAT/GL and FORMAT/GP fields from VCF when they are not used #102

Beta v0.4.0

New features:

• Haplotype inclusion based on haplotype posterior threshold rather than genotype/phenotype #93
• Recalling genotypes based on observed haplotypes #93
• Removed per-sample filters and replaced with metadata for downstream filtering #96
• Options to call full genotype posterior or likelihoods over all genotypes #93
• Improve specification of per-locus assembly for better integration with asub #90
  • --region and --region-id arguments
  • --sample-bams argument
• Mechanism to cache log-likelihoods for reuse #21
• Enable caching of JIT compiled functions #94

Bug fixes:

• Fix bug in which read counts are ignored when excluding SNPs based on --mcmc-fix-homozygous threshold

VCF changes:

• Added fields:
  • INFO/DP
  • INFO/RCOUNT
  • INFO/NVAR
  • FORMAT/KMERCOV
  • FORMAT/MCI
  • FORMAT/GL
  • FORMAT/GP
• Removed fields:
  • FORMAT/DOSEXP

Beta v0.3.0

Initial Beta release.

New features:

• Parallel-tempering #65
• Option to use inbreeding coefficient to inform prior #75
• Separate recombination and dosage swap sub-steps
• Control of recombination and dosage swap sub-steps via probabilities
• Arguments to exclude/include duplicate, qcfail and supplementary reads #74
• Added AD format field #63
• Added filters for chain in-congruence #69 #70
• Specification on constant error rate via --base-error-rate and --ignore-base-phred-scores #83

VCF Changes:

• Added AD format field #63
• Added filters for chain in-congruence #69 #70
• Rename format fields MPED to DOSEXP and PPM to PHPM
• Remove MPGP and RASSIGN format fields #63
• Fix off-by-1 error of variant positions in VCF output

Bug Fixes:

• Added missing dependencies #61
• Correction for null prior probability
• Correct Metropolis-Hastings transition probabilities #66
• Improve single core method for running assemble program
• Use simple plain-text pedigree format for pedigraph tool #49
• Correct use or region string argument in pedigraph tool #42
• Fix off-by-1 error of variant positions in VCF output
• Replace ndarray tostring calls with tobytes #62

Internal Changes:

• Add minimal set of functions to top level API #77
• Simplify main loop of assemble program #76
• Simplify MCMC file hierarchy
• Enforce formatting with Black and Flake8 #78
• Optimization by de-duplication of identical reads #83
• Removal of old unused "brute force" assembler
• Improved exception handling during assembly #88

Alpha v0.2.3

Fixes bug in filter introduced in v0.2.2

Alpha v0.2.2

• Add filter for chain incongruence #64
• Add filter to identify CNV across chains #69
• Fix potential bug with masked allele llk from np.empty

Alpha v0.2.1

• Add missing sub-module for statistics on integer encoded sequences