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ARCHITECTURE.md

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Architecture of imputef

src/
├── main.rs
│   ├── structs_and_traits.rs
│   ├── helpers.rs
│   ├── sync.rs
│   ├── vcf.rs
│   ├── geno.rs
│   ├── mvi.rs
│   ├── aldknni.rs
│   └── filter_missing.rs
└── phen.rs

Module description

  1. main.rs - the main script handling the user inputs via clap.
  2. structs_and_traits.rs - one-stop-shop for all the structs and traits used in the entire project
  3. helpers.rs - helper functions used throughout the project
  4. sync.rs - main genotype data parsing, filtering, and writing methods
  5. vcf.rs - vcf file parsing
  6. geno.rs - allele frequency table file parsing
  7. mvi.rs - mean value imputation including missing data simulation to estimate expected imputation accuracy for this imputation method
  8. aldknni.rs - allele frequency LD-kNN imputation methods including linkage and genetic distance estimation
  9. filter_missing.rs - genotype data filtering by depth, and sparsity per locus or sample
  10. phen.rs - non-critical in this project as we do not need phenotype data for imputation. This is reserved for quantitative and population genetics analyses in poolgen.