Commit e32832d3 authored by pjvan_thof's avatar pjvan_thof

Changing name blah ;)

parent 28db4a1e
...@@ -246,24 +246,24 @@ class VcfStatsTest extends TestNGSuite with Matchers { ...@@ -246,24 +246,24 @@ class VcfStatsTest extends TestNGSuite with Matchers {
def testCheckGeneral(): Unit = { def testCheckGeneral(): Unit = {
val record = new VCFFileReader(new File(resourcePath("/chrQ.vcf.gz"))).iterator().next() val record = new VCFFileReader(new File(resourcePath("/chrQ.vcf.gz"))).iterator().next()
val blah = checkGeneral(record, List()) val generalStats = checkGeneral(record, List())
blah.get("SampleDistribution-NonInformative") shouldEqual Some(Map(0 -> 1)) generalStats.get("SampleDistribution-NonInformative") shouldEqual Some(Map(0 -> 1))
blah.get("SampleDistribution-Called") shouldEqual Some(Map(3 -> 1)) generalStats.get("SampleDistribution-Called") shouldEqual Some(Map(3 -> 1))
blah.get("SampleDistribution-Mixed") shouldEqual Some(Map(0 -> 1)) generalStats.get("SampleDistribution-Mixed") shouldEqual Some(Map(0 -> 1))
blah.get("SampleDistribution-Hom") shouldEqual Some(Map(1 -> 1)) generalStats.get("SampleDistribution-Hom") shouldEqual Some(Map(1 -> 1))
blah.get("SampleDistribution-HomRef") shouldEqual Some(Map(1 -> 1)) generalStats.get("SampleDistribution-HomRef") shouldEqual Some(Map(1 -> 1))
blah.get("SampleDistribution-Available") shouldEqual Some(Map(3 -> 1)) generalStats.get("SampleDistribution-Available") shouldEqual Some(Map(3 -> 1))
blah.get("QUAL") shouldEqual Some(Map(1541 -> 1)) generalStats.get("QUAL") shouldEqual Some(Map(1541 -> 1))
blah.get("SampleDistribution-HetNonRef") shouldEqual Some(Map(0 -> 1)) generalStats.get("SampleDistribution-HetNonRef") shouldEqual Some(Map(0 -> 1))
blah.get("SampleDistribution-Het") shouldEqual Some(Map(2 -> 1)) generalStats.get("SampleDistribution-Het") shouldEqual Some(Map(2 -> 1))
blah.get("SampleDistribution-NoCall") shouldEqual Some(Map(0 -> 1)) generalStats.get("SampleDistribution-NoCall") shouldEqual Some(Map(0 -> 1))
blah.get("SampleDistribution-Filtered") shouldEqual Some(Map(0 -> 1)) generalStats.get("SampleDistribution-Filtered") shouldEqual Some(Map(0 -> 1))
blah.get("SampleDistribution-HomVar") shouldEqual Some(Map(0 -> 1)) generalStats.get("SampleDistribution-HomVar") shouldEqual Some(Map(0 -> 1))
blah.get("SampleDistribution-Variant") shouldEqual Some(Map(2 -> 1)) generalStats.get("SampleDistribution-Variant") shouldEqual Some(Map(2 -> 1))
blah.get("general") should not be empty generalStats.get("general") should not be empty
val general = blah("general") val general = generalStats("general")
general.get("PolymorphicInSamples") shouldEqual Some(1) general.get("PolymorphicInSamples") shouldEqual Some(1)
general.get("ComplexIndel") shouldEqual Some(0) general.get("ComplexIndel") shouldEqual Some(0)
...@@ -285,7 +285,7 @@ class VcfStatsTest extends TestNGSuite with Matchers { ...@@ -285,7 +285,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
general.get("Symbolic") shouldEqual Some(0) general.get("Symbolic") shouldEqual Some(0)
general.get("SimpleInsertion") shouldEqual Some(1) general.get("SimpleInsertion") shouldEqual Some(1)
val total = blah val total = generalStats
total.get("SampleDistribution-NonInformative") shouldEqual Some(Map(0 -> 1)) total.get("SampleDistribution-NonInformative") shouldEqual Some(Map(0 -> 1))
total.get("SampleDistribution-Called") shouldEqual Some(Map(3 -> 1)) total.get("SampleDistribution-Called") shouldEqual Some(Map(3 -> 1))
total.get("SampleDistribution-Mixed") shouldEqual Some(Map(0 -> 1)) total.get("SampleDistribution-Mixed") shouldEqual Some(Map(0 -> 1))
...@@ -300,8 +300,8 @@ class VcfStatsTest extends TestNGSuite with Matchers { ...@@ -300,8 +300,8 @@ class VcfStatsTest extends TestNGSuite with Matchers {
total.get("SampleDistribution-HomVar") shouldEqual Some(Map(0 -> 1)) total.get("SampleDistribution-HomVar") shouldEqual Some(Map(0 -> 1))
total.get("SampleDistribution-Variant") shouldEqual Some(Map(2 -> 1)) total.get("SampleDistribution-Variant") shouldEqual Some(Map(2 -> 1))
blah.get("general") should not be empty generalStats.get("general") should not be empty
val totGeneral = blah("general") val totGeneral = generalStats("general")
totGeneral.get("PolymorphicInSamples") shouldEqual Some(1) totGeneral.get("PolymorphicInSamples") shouldEqual Some(1)
totGeneral.get("ComplexIndel") shouldEqual Some(0) totGeneral.get("ComplexIndel") shouldEqual Some(0)
...@@ -330,17 +330,17 @@ class VcfStatsTest extends TestNGSuite with Matchers { ...@@ -330,17 +330,17 @@ class VcfStatsTest extends TestNGSuite with Matchers {
val genotype = record.getGenotype(0) val genotype = record.getGenotype(0)
val blah = checkGenotype(record, genotype, List()) val genotypeStats = checkGenotype(record, genotype, List())
blah.get("GQ") shouldEqual Some(Map(99 -> 1)) genotypeStats.get("GQ") shouldEqual Some(Map(99 -> 1))
blah.get("AD") shouldEqual Some(Map(24 -> 1, 21 -> 1)) genotypeStats.get("AD") shouldEqual Some(Map(24 -> 1, 21 -> 1))
blah.get("AD-used") shouldEqual Some(Map(24 -> 1, 21 -> 1)) genotypeStats.get("AD-used") shouldEqual Some(Map(24 -> 1, 21 -> 1))
blah.get("DP") shouldEqual Some(Map(45 -> 1)) genotypeStats.get("DP") shouldEqual Some(Map(45 -> 1))
blah.get("AD-alt") shouldEqual Some(Map(21 -> 1)) genotypeStats.get("AD-alt") shouldEqual Some(Map(21 -> 1))
blah.get("AD-ref") shouldEqual Some(Map(24 -> 1)) genotypeStats.get("AD-ref") shouldEqual Some(Map(24 -> 1))
blah.get("general") should not be empty genotypeStats.get("general") should not be empty
val general = blah("general") val general = genotypeStats("general")
general.get("Hom") shouldEqual Some(0) general.get("Hom") shouldEqual Some(0)
general.get("NoCall") shouldEqual Some(0) general.get("NoCall") shouldEqual Some(0)
general.get("Variant") shouldEqual Some(1) general.get("Variant") shouldEqual Some(1)
...@@ -355,7 +355,7 @@ class VcfStatsTest extends TestNGSuite with Matchers { ...@@ -355,7 +355,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
general.get("Het") shouldEqual Some(1) general.get("Het") shouldEqual Some(1)
general.get("HetNonRef") shouldEqual Some(0) general.get("HetNonRef") shouldEqual Some(0)
val total = blah val total = genotypeStats
total.get("GQ") shouldEqual Some(Map(99 -> 1)) total.get("GQ") shouldEqual Some(Map(99 -> 1))
total.get("AD") shouldEqual Some(Map(24 -> 1, 21 -> 1)) total.get("AD") shouldEqual Some(Map(24 -> 1, 21 -> 1))
total.get("AD-used") shouldEqual Some(Map(24 -> 1, 21 -> 1)) total.get("AD-used") shouldEqual Some(Map(24 -> 1, 21 -> 1))
...@@ -364,7 +364,7 @@ class VcfStatsTest extends TestNGSuite with Matchers { ...@@ -364,7 +364,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
total.get("AD-ref") shouldEqual Some(Map(24 -> 1)) total.get("AD-ref") shouldEqual Some(Map(24 -> 1))
total.get("general") should not be empty total.get("general") should not be empty
val totGeneral = blah("general") val totGeneral = genotypeStats("general")
totGeneral.get("Hom") shouldEqual Some(0) totGeneral.get("Hom") shouldEqual Some(0)
totGeneral.get("NoCall") shouldEqual Some(0) totGeneral.get("NoCall") shouldEqual Some(0)
totGeneral.get("Variant") shouldEqual Some(1) totGeneral.get("Variant") shouldEqual Some(1)
......
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