Commit e8b087a1 authored by Sander Bollen's avatar Sander Bollen
Browse files

finishing up VcfStatsTEst

parent 74a7b056
......@@ -264,7 +264,6 @@ class VcfStatsTest extends TestNGSuite with Matchers {
val record = new VCFFileReader(new File(resourcePath("/chrQ.vcf.gz"))).iterator().next()
val blah = checkGeneral(record, List())
println(blah.toString())
blah.get("chrQ") should not be empty
blah.get("total") should not be empty
......@@ -324,7 +323,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
total.get("SampleDistribution-Variant") shouldEqual Some(Map(2 -> 1))
chrq.get("general") should not be empty
val totGeneral = chrq.get("general").get
val totGeneral = total.get("general").get
totGeneral.get("PolymorphicInSamples") shouldEqual Some(1)
totGeneral.get("ComplexIndel") shouldEqual Some(0)
......@@ -349,6 +348,61 @@ class VcfStatsTest extends TestNGSuite with Matchers {
@Test
def testCheckGenotype = {
//stub
val record = new VCFFileReader(new File(resourcePath("/chrQ.vcf.gz"))).iterator().next()
val genotype = record.getGenotype(0)
val blah = checkGenotype(record, genotype, List())
blah.get("chrQ") should not be empty
blah.get("total") should not be empty
val chrq = blah.get("chrQ").get
chrq.get("GQ") shouldEqual Some(Map(99 -> 1))
chrq.get("AD") shouldEqual Some(Map(24 -> 1, 21 -> 1))
chrq.get("AD-used") shouldEqual Some(Map(24 -> 1, 21 -> 1))
chrq.get("DP") shouldEqual Some(Map(45 -> 1))
chrq.get("AD-alt") shouldEqual Some(Map(21 -> 1))
chrq.get("AD-ref") shouldEqual Some(Map(24 -> 1))
chrq.get("general") should not be empty
val general = chrq.get("general").get
general.get("Hom") shouldEqual Some(0)
general.get("NoCall") shouldEqual Some(0)
general.get("Variant") shouldEqual Some(1)
general.get("Filtered") shouldEqual Some(0)
general.get("NonInformative") shouldEqual Some(0)
general.get("Called") shouldEqual Some(1)
general.get("Total") shouldEqual Some(1)
general.get("HomVar") shouldEqual Some(0)
general.get("HomRef") shouldEqual Some(0)
general.get("Mixed") shouldEqual Some(0)
general.get("Available") shouldEqual Some(1)
general.get("Het") shouldEqual Some(1)
general.get("HetNonRef") shouldEqual Some(0)
val total = blah.get("total").get
total.get("GQ") shouldEqual Some(Map(99 -> 1))
total.get("AD") shouldEqual Some(Map(24 -> 1, 21 -> 1))
total.get("AD-used") shouldEqual Some(Map(24 -> 1, 21 -> 1))
total.get("DP") shouldEqual Some(Map(45 -> 1))
total.get("AD-alt") shouldEqual Some(Map(21 -> 1))
total.get("AD-ref") shouldEqual Some(Map(24 -> 1))
total.get("general") should not be empty
val totGeneral = total.get("general").get
totGeneral.get("Hom") shouldEqual Some(0)
totGeneral.get("NoCall") shouldEqual Some(0)
totGeneral.get("Variant") shouldEqual Some(1)
totGeneral.get("Filtered") shouldEqual Some(0)
totGeneral.get("NonInformative") shouldEqual Some(0)
totGeneral.get("Called") shouldEqual Some(1)
totGeneral.get("Total") shouldEqual Some(1)
totGeneral.get("HomVar") shouldEqual Some(0)
totGeneral.get("HomRef") shouldEqual Some(0)
totGeneral.get("Mixed") shouldEqual Some(0)
totGeneral.get("Available") shouldEqual Some(1)
totGeneral.get("Het") shouldEqual Some(1)
totGeneral.get("HetNonRef") shouldEqual Some(0)
}
}
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