-
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