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CHANGELOG.md

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Changelog

Unreleased

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 a optional VCF field.
  • Use setuptools_scm for versioning #179.

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.

Beta v0.9.3

Bug Fixes:

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

Beta v0.9.2

Bug Fixes:

  • Avoid holding alignment file handles open #173

Beta v0.9.1

New Features:

  • Allow complex sample pooling via 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

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

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

CLI Changes:

  • 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

New Features:

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

Beta v0.4.1

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

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

Alpha v0.2.0

  • Use non-normalized probability encodings for reads #56
  • Remove probabilistic encoding sub-module
  • Rename allelic and symbolic encoding sub-modules to integer and character
  • Add MEC score to VCF output #58
  • Rename RC format field to RCOUNT
  • Add RCALLS format field to record the number of variant encoding bases among reads
  • Add RASSIGN format field to record approximate read assignment to haplotypes based on MEC
  • Improve string formatting of floats in VCF output to remove .0 from values without decimals

Alpha v0.1.0

  • Initial release