piggyback::pb_download(repo = "soroushmdg/gwid",
                       tag = "v0.0.1",
                       dest = tempdir())
ibd_data_file <- paste0(tempdir(),"//chr3.ibd")
genome_data_file <- paste0(tempdir(),"//chr3.gds")
phase_data_file <- paste0(tempdir(),"//chr3.vcf")
case_control_data_file <- paste0(tempdir(),"//case-cont-RA.withmap.Rda")

case_control <- gwid::case_control(case_control_rda = case_control_data_file)
snp_data_gds <- gwid::build_gwas(gds_data = genome_data_file,caco = case_control,gwas_generator = TRUE)
haplotype_data <- gwid::build_phase(phased_vcf = phase_data_file,caco = case_control)
ibd_data <- gwid::build_gwid(ibd_data = ibd_data_file,gwas = snp_data_gds)


test_that("build section works", {
  expect_length(snp_data_gds,n = 7)
  expect_s3_class(snp_data_gds,"gwas")
  expect_length(haplotype_data,n = 2)
  expect_s3_class(haplotype_data,"phase")
  expect_equal(dim(haplotype_data[[1]]),dim(haplotype_data[[2]]))
  expect_length(ibd_data,n = 5)
  expect_s3_class(ibd_data,"gwid")
  expect_s3_class(ibd_data$res,"result_snps")

})