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biopet.biopet
Commits
af816bfa
Commit
af816bfa
authored
Apr 24, 2017
by
Peter van 't Hof
Browse files
Fixing unit tests
parent
8b2b1732
Changes
2
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Inline
Side-by-side
basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
View file @
af816bfa
...
...
@@ -101,7 +101,7 @@ class BastyTest extends TestNGSuite with Matchers {
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
MarkDuplicates
])
shouldBe
(
numberLibs
+
numberSamples
)
// Gatk preprocess
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
IndelRealigner
])
shouldBe
(
numberLibs
*
(
if
(
realign
)
1
else
0
)
+
(
if
(
sample2
&&
realign
)
1
else
0
)
)
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
[
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 @
af816bfa
...
...
@@ -104,7 +104,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
MarkDuplicates
])
shouldBe
(
numberLibs
+
numberSamples
)
// Gatk preprocess
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
IndelRealigner
])
shouldBe
(
numberLibs
*
(
if
(
realign
)
1
else
0
)
+
(
if
(
sample2
&&
realign
)
1
else
0
)
)
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
[
BaseRecalibrator
])
shouldBe
(
if
(
dbsnp
&&
baseRecalibration
)
(
numberLibs
*
2
)
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
PrintReads
])
shouldBe
(
if
(
dbsnp
&&
baseRecalibration
&&
usePrintReads
)
numberLibs
else
0
)
...
...
@@ -120,7 +120,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
sample
.
libraries
.
foreach
{
case
(
libId
,
lib
)
=>
lib
.
summarySettings
.
get
(
"library_variantcalling"
)
shouldBe
Some
(
libraryCalling
)
lib
.
summarySettings
.
get
(
"use_indel_realigner"
)
shouldBe
Some
(
realign
)
lib
.
summarySettings
.
get
(
"use_indel_realigner"
)
shouldBe
None
// Should not exist anymore
lib
.
summarySettings
.
get
(
"use_base_recalibration"
)
shouldBe
Some
(
baseRecalibration
&&
dbsnp
)
}
}
...
...
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