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biopet.biopet
Commits
74a7b056
Commit
74a7b056
authored
Sep 09, 2015
by
Sander Bollen
Browse files
add testCheckGeneral
parent
e119b397
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
View file @
74a7b056
...
...
@@ -19,6 +19,7 @@ import java.io.File
import
java.nio.file.
{
Files
,
Paths
}
import
htsjdk.variant.variantcontext.Allele
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.tools.VcfStats._
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
...
...
@@ -260,7 +261,90 @@ class VcfStatsTest extends TestNGSuite with Matchers {
@Test
def
testCheckGeneral
=
{
//stub
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
val
chrq
=
blah
.
get
(
"chrQ"
).
get
chrq
.
get
(
"SampleDistribution-NonInformative"
)
shouldEqual
Some
(
Map
(
0
->
1
))
chrq
.
get
(
"SampleDistribution-Called"
)
shouldEqual
Some
(
Map
(
3
->
1
))
chrq
.
get
(
"SampleDistribution-Mixed"
)
shouldEqual
Some
(
Map
(
0
->
1
))
chrq
.
get
(
"SampleDistribution-Hom"
)
shouldEqual
Some
(
Map
(
1
->
1
))
chrq
.
get
(
"SampleDistribution-HomRef"
)
shouldEqual
Some
(
Map
(
1
->
1
))
chrq
.
get
(
"SampleDistribution-Available"
)
shouldEqual
Some
(
Map
(
3
->
1
))
chrq
.
get
(
"QUAL"
)
shouldEqual
Some
(
Map
(
1541
->
1
))
chrq
.
get
(
"SampleDistribution-HetNonRef"
)
shouldEqual
Some
(
Map
(
0
->
1
))
chrq
.
get
(
"SampleDistribution-Het"
)
shouldEqual
Some
(
Map
(
2
->
1
))
chrq
.
get
(
"SampleDistribution-NoCall"
)
shouldEqual
Some
(
Map
(
0
->
1
))
chrq
.
get
(
"SampleDistribution-Filtered"
)
shouldEqual
Some
(
Map
(
0
->
1
))
chrq
.
get
(
"SampleDistribution-HomVar"
)
shouldEqual
Some
(
Map
(
0
->
1
))
chrq
.
get
(
"SampleDistribution-Variant"
)
shouldEqual
Some
(
Map
(
2
->
1
))
chrq
.
get
(
"general"
)
should
not
be
empty
val
general
=
chrq
.
get
(
"general"
).
get
general
.
get
(
"PolymorphicInSamples"
)
shouldEqual
Some
(
1
)
general
.
get
(
"ComplexIndel"
)
shouldEqual
Some
(
0
)
general
.
get
(
"FullyDecoded"
)
shouldEqual
Some
(
0
)
general
.
get
(
"PointEvent"
)
shouldEqual
Some
(
0
)
general
.
get
(
"MNP"
)
shouldEqual
Some
(
0
)
general
.
get
(
"Indel"
)
shouldEqual
Some
(
1
)
general
.
get
(
"Biallelic"
)
shouldEqual
Some
(
1
)
general
.
get
(
"SimpleDeletion"
)
shouldEqual
Some
(
0
)
general
.
get
(
"Variant"
)
shouldEqual
Some
(
1
)
general
.
get
(
"SymbolicOrSV"
)
shouldEqual
Some
(
0
)
general
.
get
(
"MonomorphicInSamples"
)
shouldEqual
Some
(
0
)
general
.
get
(
"SNP"
)
shouldEqual
Some
(
0
)
general
.
get
(
"Filtered"
)
shouldEqual
Some
(
0
)
general
.
get
(
"StructuralIndel"
)
shouldEqual
Some
(
0
)
general
.
get
(
"Total"
)
shouldEqual
Some
(
1
)
general
.
get
(
"Mixed"
)
shouldEqual
Some
(
0
)
general
.
get
(
"NotFiltered"
)
shouldEqual
Some
(
1
)
general
.
get
(
"Symbolic"
)
shouldEqual
Some
(
0
)
general
.
get
(
"SimpleInsertion"
)
shouldEqual
Some
(
1
)
val
total
=
blah
.
get
(
"total"
).
get
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
))
chrq
.
get
(
"general"
)
should
not
be
empty
val
totGeneral
=
chrq
.
get
(
"general"
).
get
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
...
...
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