update tests

tests/testthat/test-vcf-comp.R

@@ -4,14 +4,13 @@ rawvcf <- system.file("extdata", "raw.gt.vcf.gz", package="vcfppR")
 imputedvcf <- system.file("extdata", "imputed.gt.vcf.gz", package="vcfppR")
 
 test_that("can work for F1 score", {
-  samples <- "HG00133,HG00143,HG00262"
-  res <- vcfcomp(imputedvcf, imputedvcf, stats = "f1", format=c("GT", 'GT'), samples = samples)
+  samples <- "HG00133,HG00262"
+  res <- vcfcomp(rawvcf, imputedvcf, stats = "f1", format=c("GT", 'GT'), samples = samples)
   expect_identical(paste0(res$samples, collapse = ","), samples)  
-  expect_identical(res$f1, rep(1,3))
+  expect_identical(res$f1, rep(1,2))
 })
 
 test_that("can work for correlation r2 between DS and GT", {
   res <- vcfcomp(imputedvcf, imputedvcf)
-  r2 <- res$r2
   expect_identical(as.numeric(res$r2[5,]), c(16, 16, 1, 1))
 })

tests/testthat/test-vcf-writer.R

@@ -1,7 +1,6 @@
 library(testthat)
 
 test_that("vcfwriter: writing variant works", {
-  ## skip_on_os(c("windows"), arch = NULL)
   outvcf <- file.path(paste0(tempfile(), ".vcf.gz"))
   bw <- vcfwriter$new(outvcf, "VCF4.3")
   bw$addLine('##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">')
@@ -12,12 +11,11 @@ test_that("vcfwriter: writing variant works", {
   bw$writeline(s1)
   bw$close()
   ## tests
+  skip_on_os(c("windows"), arch = NULL)
   br <- vcfreader$new(outvcf)
   print(br$header())
   br$variant()
-  s2 <- gsub("\n", "", br$string())
   expect_identical(br$chr(), "chr20")
-  expect_identical(s1, s2)
   s2 <- br$line()
   expect_identical(s1, s2)
 })