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biopet.biopet
Commits
30696cab
Commit
30696cab
authored
Jan 19, 2016
by
Peter van 't Hof
Browse files
Fixed unit tests
parent
dd9a7060
Changes
1
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public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
30696cab
...
...
@@ -77,7 +77,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
pipeline
.
inputBams
=
(
for
(
n
<-
1
to
bams
)
yield
n
.
toString
->
ShivaVariantcallingTest
.
inputTouch
(
"bam_"
+
n
+
".bam"
)).
toMap
val
illegalArgumentException
=
pipeline
.
inputBams
.
isEmpty
||
(!
raw
&&
!
bcftools
&&
!
bcftoolsSinglesample
&&
!
freebayes
)
val
illegalArgumentException
=
pipeline
.
inputBams
.
isEmpty
||
(!
raw
&&
!
bcftools
&&
!
bcftoolsSinglesample
&&
!
freebayes
&&
!
varscanCnsSinglesample
)
if
(
illegalArgumentException
)
intercept
[
IllegalArgumentException
]
{
pipeline
.
script
()
...
...
@@ -86,7 +86,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
if
(!
illegalArgumentException
)
{
pipeline
.
script
()
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
CombineVariants
])
shouldBe
1
+
(
if
(
raw
)
1
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
CombineVariants
])
shouldBe
(
1
+
(
if
(
raw
)
1
else
0
)
+
(
if
(
varscanCnsSinglesample
)
1
else
0
))
//pipeline.functions.count(_.isInstanceOf[Bcftools]) shouldBe (if (bcftools) 1 else 0)
//FIXME: Can not check for bcftools because of piping
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
Freebayes
])
shouldBe
(
if
(
freebayes
)
1
else
0
)
...
...
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