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biopet.biopet
Commits
e9a7187e
Commit
e9a7187e
authored
Apr 24, 2017
by
Peter van 't Hof
Browse files
fixing unit tests
parent
1d22fa44
Changes
2
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basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
View file @
e9a7187e
...
...
@@ -102,7 +102,7 @@ class BastyTest extends TestNGSuite with Matchers {
// Gatk preprocess
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
IndelRealigner
])
shouldBe
(
if
(
realign
)
numberSamples
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
RealignerTargetCreator
])
shouldBe
(
numberLibs
*
(
if
(
realign
)
1
else
0
)
+
(
if
(
sample2
&&
realign
)
1
else
0
)
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
RealignerTargetCreator
])
shouldBe
(
if
(
realign
)
numberSamples
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
BaseRecalibrator
])
shouldBe
(
if
(
dbsnp
&&
baseRecalibration
)
(
numberLibs
*
2
)
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
PrintReads
])
shouldBe
(
if
(
dbsnp
&&
baseRecalibration
)
numberLibs
else
0
)
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
e9a7187e
...
...
@@ -105,7 +105,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
// Gatk preprocess
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
IndelRealigner
])
shouldBe
(
if
(
realign
)
numberSamples
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
RealignerTargetCreator
])
shouldBe
(
numberLibs
*
(
if
(
realign
)
1
else
0
)
+
(
if
(
sample2
&&
realign
)
1
else
0
)
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
RealignerTargetCreator
])
shouldBe
(
if
(
realign
)
numberSamples
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
BaseRecalibrator
])
shouldBe
(
if
(
dbsnp
&&
baseRecalibration
)
(
numberLibs
*
2
)
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
PrintReads
])
shouldBe
(
if
(
dbsnp
&&
baseRecalibration
&&
usePrintReads
)
numberLibs
else
0
)
...
...
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