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CHANGELOG.md

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  • v2.0.1
    • new option --output_read_label_prob
  • v2.0.0
    • Major version update
    • Includes msPBWT method of haplotype selection
    • Includes common and all SNP processing
    • Includes NIPT method for imputing mother and fetus from cfDNA NIPT sequence
  • v1.0.5
    • Be able to work with cram files
  • v1.0.4
    • Mostly small bugs and some future capabilities
  • v1.0.3
    • Simplify how QUILT HLA reference packages are built
  • v1.0.2
    • Fix minor but that prevented HLA reference panel from building on new reference data
  • v1.0.1
    • Fix minor but that prevented HLA reference panel from building
  • v1.0.0
    • Bump major version number as first version post paper release
    • Fix bugs related to rare haplotypes in full panel HMM
  • v0.1.9
    • Change default output of GT entry to phased value to facilitate ligating phase reslts together
    • Add code to try and re-run samples with different parameter values when underflow happens
  • v0.1.8
    • RAM decrease when running many samples
  • v0.1.7
    • Speedups and RAM decrease when using reference panels with fewer haplotypes
  • v0.1.6
    • Discovered bug where only 1 read caused an error. Fix (obviate) this by requiring 2 of more reads through parameter minimum_number_of_sample_reads with default currently 2, where samples with fewer than 2 reads have all missing output
  • v0.1.5
    • Export downsampleToCov and set to 30 to reduce underflow likelihood for high coverage regions
    • Add minGLValue as bound on haplotype genotype likelihoods also to reduce underflow likelihood
  • v0.1.4
    • Option to impute without specifying genetic map, just using expected genetic and physical distance
  • v0.1.3
    • Bugfixes
  • v0.1.2
    • More optimization, avoid normalization when possible, avoid unnecessary adds and mults
  • v0.1.1
    • Better acceptance tests
    • More validation
    • Use of genfile and/or phasefile
  • v0.1.0
    • First versionned beta release
  • v0.0.0
    • Generic development and pre-release version