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biopet.biopet
Commits
df5b8d8c
Commit
df5b8d8c
authored
May 15, 2016
by
Peter van 't Hof
Browse files
Fixed tests
parent
53c59c03
Changes
2
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
View file @
df5b8d8c
...
...
@@ -179,8 +179,8 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
/** Settings for the summary */
def
summarySettings
=
Map
(
"variantcallers"
->
configCallers
.
toList
,
"regions_of_interest"
->
roiBedFiles
.
map
(
_
.
getName
.
stripSuffix
(
".bed"
)
),
"amplicon_bed"
->
ampliconBedFile
.
map
(
_
.
get
Name
.
stripSuffix
(
".bed"
)
)
"regions_of_interest"
->
roiBedFiles
.
map
(
_
.
getName
),
"amplicon_bed"
->
ampliconBedFile
.
map
(
_
.
get
AbsolutePath
)
)
/** Files for the summary */
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
df5b8d8c
...
...
@@ -117,13 +117,13 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
(
if
(
haplotypeCallerAllele
)
1
else
0
)
+
(
if
(
haplotypeCallerGvcf
)
bams
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
UnifiedGenotyper
])
shouldBe
(
if
(
unifiedGenotyper
)
1
else
0
)
+
(
if
(
unifiedGenotyperAllele
)
1
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfStats
])
shouldBe
(
1
+
callers
.
size
+
(
roiBedFiles
++
ampliconBedFile
).
length
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfStats
])
shouldBe
(
1
+
callers
.
size
+
(
roiBedFiles
++
ampliconBedFile
).
length
*
(
1
+
callers
.
size
)
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VtNormalize
])
shouldBe
(
if
(
normalize
)
callers
.
size
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VtDecompose
])
shouldBe
(
if
(
decompose
)
callers
.
size
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
GenotypeConcordance
])
shouldBe
(
if
(
referenceVcf
.
isDefined
)
1
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
GenotypeConcordance
])
shouldBe
(
if
(
referenceVcf
.
isDefined
)
1
+
callers
.
size
else
0
)
pipeline
.
summarySettings
.
get
(
"variantcallers"
)
shouldBe
Some
(
callers
.
toList
)
pipeline
.
summarySettings
.
get
(
"amplicon_bed"
)
shouldBe
ampliconBedFile
.
map
(
_
.
getAbsolutePath
)
pipeline
.
summarySettings
.
get
(
"amplicon_bed"
)
shouldBe
Some
(
ampliconBedFile
.
map
(
_
.
getAbsolutePath
)
)
pipeline
.
summarySettings
.
get
(
"regions_of_interest"
)
shouldBe
Some
(
roiBedFiles
.
map
(
_
.
getAbsolutePath
))
}
}
...
...
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