update

.Rbuildignore

@@ -10,3 +10,5 @@ src/vcf/txtReader.o
 src/vcf/variantIndex.o
 src/vcf/vcfReaderDebug.o
 DEploid.utils/libs/DEploid.utils.so
+*png
+*pdf

tests/testthat.R

@@ -0,0 +1,5 @@
+if (require("testthat")) {
+  test_check("DEploid.utils")
+} else {
+  warning("testthat not available. Skipping unittests!")
+}

tests/testthat/test-vcfreader.R

@@ -0,0 +1,74 @@
+vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
+                           package = "DEploid.utils")
+plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
+                            package = "DEploid.utils")
+panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
+                             package = "DEploid.utils")
+refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid.utils")
+altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid.utils")
+
+PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
+plaf <- extractPLAF(plafFileName)
+
+
+test_that("Extracted coverage", {
+  PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
+  expect_that(PG0390CoverageTxt, is_a("data.frame"))
+  expect_that(PG0390CoverageVcf, is_a("data.frame"))
+  expect_equal(PG0390CoverageTxt, PG0390CoverageVcf)
+})
+
+
+test_that("Extracted plaf", {
+  expect_that(plaf, is_a("numeric"))
+})
+
+
+test_that("computeObsWSAF", {
+  expect_equal(computeObsWSAF(0, 0), 0)
+  expect_equal(computeObsWSAF(0, 100), 0)
+  expect_equal(computeObsWSAF(1, 99), 0.01)
+  expect_equal(computeObsWSAF(99, 1), 0.99)
+  expect_equal(computeObsWSAF(50, 50), 0.5)
+  expect_equal(computeObsWSAF(50, 100), 0.3333333333333)
+})
+
+
+test_that("WSAF Related", {
+  obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
+                            PG0390CoverageVcf$refCount)
+  potentialOutliers <- c(5, 12, 25, 30, 35, 50)
+
+  expect_that(histWSAF(obsWSAF), is_a("histogram"))
+  png("histWSAF.png")
+  histWSAF(obsWSAF)
+  dev.off()
+
+  ####
+  expect_null(plotWSAFvsPLAF(plaf, obsWSAF))
+  png("WSAFvsPLAF.png")
+  plotWSAFvsPLAF(plaf, obsWSAF)
+  dev.off()
+})
+
+
+test_that("plotAltVsRef", {
+  expect_null(plotAltVsRef(PG0390CoverageVcf$refCount,
+                           PG0390CoverageVcf$altCount))
+  png("AltVsRef.png")
+  plotAltVsRef(PG0390CoverageVcf$refCount, PG0390CoverageVcf$altCount)
+  dev.off()
+})
+
+
+test_that("plotAltVsRefWithOutliers", {
+  potentialOutliers <- c(1, 10, 20, 30, 40)
+  expect_null(plotAltVsRef(PG0390CoverageVcf$refCount,
+                           PG0390CoverageVcf$altCount,
+                           potentialOutliers = potentialOutliers))
+  png("AltVsRefOutlier.png")
+  plotAltVsRef(PG0390CoverageVcf$refCount, PG0390CoverageVcf$altCount,
+               potentialOutliers = potentialOutliers)
+  dev.off()
+})
+