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biopet.biopet
Commits
74f11c8e
Commit
74f11c8e
authored
Feb 05, 2015
by
Peter van 't Hof
Browse files
Added basic testing
parent
0c2b2242
Changes
1
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Inline
Side-by-side
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
0 → 100644
View file @
74f11c8e
package
nl.lumc.sasc.biopet.tools
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
import
scala.collection.mutable
import
VcfStats._
/**
* Created by pjvan_thof on 2/5/15.
*/
class
VcfStatsTest
extends
TestNGSuite
with
Matchers
{
@Test
def
testSampleToSampleStats
:
Unit
=
{
val
s1
=
SampleToSampleStats
()
val
s2
=
SampleToSampleStats
()
s1
.
alleleOverlap
shouldBe
0
s1
.
genotypeOverlap
shouldBe
0
s2
.
alleleOverlap
shouldBe
0
s2
.
genotypeOverlap
shouldBe
0
s1
+=
s2
s1
.
alleleOverlap
shouldBe
0
s1
.
genotypeOverlap
shouldBe
0
s2
.
alleleOverlap
shouldBe
0
s2
.
genotypeOverlap
shouldBe
0
s2
.
alleleOverlap
=
2
s2
.
genotypeOverlap
=
3
s1
+=
s2
s1
.
alleleOverlap
shouldBe
2
s1
.
genotypeOverlap
shouldBe
3
s2
.
alleleOverlap
shouldBe
2
s2
.
genotypeOverlap
shouldBe
3
s1
+=
s2
s1
.
alleleOverlap
shouldBe
4
s1
.
genotypeOverlap
shouldBe
6
s2
.
alleleOverlap
shouldBe
2
s2
.
genotypeOverlap
shouldBe
3
}
@Test
def
testSampleStats
:
Unit
=
{
val
s1
=
SampleStats
()
val
s2
=
SampleStats
()
s1
.
sampleToSample
+=
"s1"
->
SampleToSampleStats
()
s1
.
sampleToSample
+=
"s2"
->
SampleToSampleStats
()
s2
.
sampleToSample
+=
"s1"
->
SampleToSampleStats
()
s2
.
sampleToSample
+=
"s2"
->
SampleToSampleStats
()
s1
.
sampleToSample
(
"s1"
).
alleleOverlap
=
1
s2
.
sampleToSample
(
"s2"
).
alleleOverlap
=
2
s1
.
genotypeStats
+=
"1"
->
mutable
.
Map
(
1
->
1
)
s2
.
genotypeStats
+=
"2"
->
mutable
.
Map
(
2
->
2
)
val
ss1
=
SampleToSampleStats
()
val
ss2
=
SampleToSampleStats
()
s1
+=
s2
s1
.
genotypeStats
shouldBe
mutable
.
Map
(
"1"
->
mutable
.
Map
(
1
->
1
),
"2"
->
mutable
.
Map
(
2
->
2
))
ss1
.
alleleOverlap
=
1
ss2
.
alleleOverlap
=
2
s1
.
sampleToSample
shouldBe
mutable
.
Map
(
"s1"
->
ss1
,
"s2"
->
ss2
)
s1
+=
s2
s1
.
genotypeStats
shouldBe
mutable
.
Map
(
"1"
->
mutable
.
Map
(
1
->
1
),
"2"
->
mutable
.
Map
(
2
->
4
))
s1
+=
s1
s1
.
genotypeStats
shouldBe
mutable
.
Map
(
"1"
->
mutable
.
Map
(
1
->
2
),
"2"
->
mutable
.
Map
(
2
->
8
))
}
}
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