open Bistro
open File_formats

class type relatedness_matrix =
  object
    inherit text

    method format : [ `gemma_relatedness_matrix ]
  end

val genotype_of_fasta : aminoacid_fasta file -> bimbam file

val phenotype_of_tree : nhx file -> bimbam file

val calculate_relatedness_matrix :
  mode:[ `Centered | `Standardized ] ->
  genotype:bimbam file ->
  phenotype:bimbam file ->
  relatedness_matrix file

class type univariate_lmm_output =
  object
    inherit tsv

    method format : [ `gemma_test_output ]
  end

val univariate_lmm :
  lmm:[ `Wald | `LRT | `Score | `All ] ->
  genotype:bimbam file ->
  phenotype:bimbam file ->
  relatedness_matrix:relatedness_matrix file ->
  univariate_lmm_output file

val result_table_of_output :
  aminoacid_fasta file -> univariate_lmm_output file -> cpt file