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biopet.biopet
Commits
7d0148d6
Commit
7d0148d6
authored
Jul 27, 2017
by
Peter van 't Hof
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Remove duplicate tests
parent
1efcf0c5
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-62
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
...c/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
+0
-62
No files found.
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
View file @
7d0148d6
...
...
@@ -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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