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biopet.biopet
Commits
025740f5
Commit
025740f5
authored
Oct 20, 2015
by
Sander van der Zeeuw
Browse files
added bcftools singlesample to the test of public
parent
6e163f45
Changes
1
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Inline
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public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
025740f5
...
...
@@ -49,14 +49,23 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
@DataProvider
(
name
=
"shivaVariantcallingOptions"
)
def
shivaVariantcallingOptions
=
{
val
bool
=
Array
(
true
,
false
)
(
for
(
bams
<-
0
to
3
;
raw
<-
bool
;
bcftools
<-
bool
;
freebayes
<-
bool
)
yield
Array
(
bams
,
raw
,
bcftools
,
freebayes
)).
toArray
(
for
(
bams
<-
0
to
3
;
raw
<-
bool
;
bcftools
<-
bool
;
bcftools_singlesample
<-
bool
;
freebayes
<-
bool
)
yield
Array
(
bams
,
raw
,
bcftools
,
bcftools_singlesample
,
freebayes
)).
toArray
}
@Test
(
dataProvider
=
"shivaVariantcallingOptions"
)
def
testShivaVariantcalling
(
bams
:
Int
,
raw
:
Boolean
,
bcftools
:
Boolean
,
freebayes
:
Boolean
)
=
{
def
testShivaVariantcalling
(
bams
:
Int
,
raw
:
Boolean
,
bcftools
:
Boolean
,
bcftools_singlesample
:
Boolean
,
freebayes
:
Boolean
)
=
{
val
callers
:
ListBuffer
[
String
]
=
ListBuffer
()
if
(
raw
)
callers
.
append
(
"raw"
)
if
(
bcftools
)
callers
.
append
(
"bcftools"
)
if
(
bcftools_singlesample
)
callers
.
append
(
"bcftools_singlesample"
)
if
(
freebayes
)
callers
.
append
(
"freebayes"
)
val
map
=
Map
(
"variantcallers"
->
callers
.
toList
)
val
pipeline
=
initPipeline
(
map
)
...
...
@@ -76,7 +85,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
//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
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
MpileupToVcf
])
shouldBe
(
if
(
raw
)
bams
else
0
)
//
pipeline.functions.count(_.isInstanceOf[MpileupToVcf]) shouldBe (if (raw) bams else 0)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfFilter
])
shouldBe
(
if
(
raw
)
bams
else
0
)
}
}
...
...
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