Changes in version 0.99.8 (2026-04-12)                 

  - Restored core parental transmission inference behavior in
    haplotype_infer():
    
      - reinstated deterministic Mendelian inference for
        non-triple-heterozygote patterns
      - reinstated local haplotype-based inference for
        triple-heterozygote sites
      - restored explicit handling of ambiguous and low-similarity
        haplotype matches

  - Clarified output structure:
    
      - retained parati_run() as an R-object-returning interface
      - formalized separation of outputs into transmitted alleles,
        non-transmitted alleles, and haplotype-matching summary
        diagnostics
      - documented the relationship between the updated transmitted
        output and the original single-file VCF result

  - Improved internal helper behavior:
    
      - cleaned duplicated internal helper definitions in io_helpers.R
      - added minimal compatibility handling for genotype fields
        containing additional FORMAT subfields
      - improved chromosome alias handling for inputs such as 1 and chr1

  - Improved VCF export support:
    
      - fixed conversion of internal data.table outputs to vcfR objects
      - improved examples and vignette guidance for exporting standard
        VCF outputs

  - Improved package build compatibility:
    
      - added package-level data.table awareness handling
      - added explicit namespace import for data.table:::=
      - adjusted code patterns that previously triggered avoidable
        BiocCheck notes

  - Improved validation:
    
      - verified toy-data transmitted output against the original
        implementation
      - added and updated tests to better reflect expected trio
        inference behavior

  - Improved vignette documentation:
    
      - added explicit guidance for exporting transmitted,
        non-transmitted, and summary outputs
      - documented the meaning of sim_perc_summary columns for
        downstream users

                 Changes in version 0.99.6 (2026-03-16)                 

  - Revised the package interface to better align with Bioconductor
    standards.
  - Updated parati_run():
      - now accepts either a VCF file path or a VariantAnnotation::VCF
        object
      - now returns R objects by default instead of writing files to
        disk
      - reduced repeated merging inside loops by collecting intermediate
        results first
  - Added internal helpers for:
      - reading family tables from file paths, data.frame, or data.table
      - converting VariantAnnotation::VCF objects into internal
        data.table representation
  - Improved Bioconductor integration:
      - added support for VariantAnnotation, SummarizedExperiment,
        BiocGenerics, and GenomeInfoDb
      - updated vignette to demonstrate integration with Bioconductor
        VCF workflows
  - Removed incomplete placeholder functionality:
      - removed vcf_to_plink()
  - Improved documentation:
      - updated function documentation and return value sections
      - cleaned up roxygen2-generated man pages
  - Improved tests:
      - replaced minimal structural tests with unit tests covering
        expected transmission inference behavior on toy data
      - ensured core tests are suitable for Bioconductor build checking
  - Updated vignette:
      - added abstract and motivation for inclusion in Bioconductor
      - replaced static code blocks with executable R code chunks
      - provided runnable examples using the included toy data
  - Minor code cleanup:
      - removed redundant requireNamespace() calls for imported packages
      - updated package metadata and biocViews