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Commit 7d0148d6 authored by Peter van 't Hof's avatar Peter van 't Hof
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Remove duplicate tests

parent 1efcf0c5
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biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
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......@@ -284,44 +284,6 @@ class VcfStatsTest extends TestNGSuite with Matchers {
general.get("NotFiltered") shouldEqual Some(1)
general.get("Symbolic") shouldEqual Some(0)
general.get("SimpleInsertion") shouldEqual Some(1)
val total = generalStats
total.get("SampleDistribution-NonInformative") shouldEqual Some(Map(0 -> 1))
total.get("SampleDistribution-Called") shouldEqual Some(Map(3 -> 1))
total.get("SampleDistribution-Mixed") shouldEqual Some(Map(0 -> 1))
total.get("SampleDistribution-Hom") shouldEqual Some(Map(1 -> 1))
total.get("SampleDistribution-HomRef") shouldEqual Some(Map(1 -> 1))
total.get("SampleDistribution-Available") shouldEqual Some(Map(3 -> 1))
total.get("QUAL") shouldEqual Some(Map(1541 -> 1))
total.get("SampleDistribution-HetNonRef") shouldEqual Some(Map(0 -> 1))
total.get("SampleDistribution-Het") shouldEqual Some(Map(2 -> 1))
total.get("SampleDistribution-NoCall") shouldEqual Some(Map(0 -> 1))
total.get("SampleDistribution-Filtered") shouldEqual Some(Map(0 -> 1))
total.get("SampleDistribution-HomVar") shouldEqual Some(Map(0 -> 1))
total.get("SampleDistribution-Variant") shouldEqual Some(Map(2 -> 1))
generalStats.get("general") should not be empty
val totGeneral = generalStats("general")
totGeneral.get("PolymorphicInSamples") shouldEqual Some(1)
totGeneral.get("ComplexIndel") shouldEqual Some(0)
totGeneral.get("FullyDecoded") shouldEqual Some(0)
totGeneral.get("PointEvent") shouldEqual Some(0)
totGeneral.get("MNP") shouldEqual Some(0)
totGeneral.get("Indel") shouldEqual Some(1)
totGeneral.get("Biallelic") shouldEqual Some(1)
totGeneral.get("SimpleDeletion") shouldEqual Some(0)
totGeneral.get("Variant") shouldEqual Some(1)
totGeneral.get("SymbolicOrSV") shouldEqual Some(0)
totGeneral.get("MonomorphicInSamples") shouldEqual Some(0)
totGeneral.get("SNP") shouldEqual Some(0)
totGeneral.get("Filtered") shouldEqual Some(0)
totGeneral.get("StructuralIndel") shouldEqual Some(0)
totGeneral.get("Total") shouldEqual Some(1)
totGeneral.get("Mixed") shouldEqual Some(0)
totGeneral.get("NotFiltered") shouldEqual Some(1)
totGeneral.get("Symbolic") shouldEqual Some(0)
totGeneral.get("SimpleInsertion") shouldEqual Some(1)
}
@Test
......@@ -354,29 +316,5 @@ class VcfStatsTest extends TestNGSuite with Matchers {
general.get("Available") shouldEqual Some(1)
general.get("Het") shouldEqual Some(1)
general.get("HetNonRef") shouldEqual Some(0)
val total = genotypeStats
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 = genotypeStats("general")
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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