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biopet.biopet
Commits
ef10b38d
Commit
ef10b38d
authored
May 11, 2016
by
Peter van 't Hof
Browse files
Added test in shiva for cnvcalling
parent
6c15d952
Changes
1
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shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
ef10b38d
...
...
@@ -60,6 +60,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
def
libraryCalling
=
false
def
dbsnp
=
true
def
svCalling
=
false
def
cnvCalling
=
false
def
annotation
=
false
@Test
(
dataProvider
=
"shivaOptions"
)
...
...
@@ -77,6 +78,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
"use_indel_realigner"
->
realign
,
"use_base_recalibration"
->
baseRecalibration
,
"sv_calling"
->
svCalling
,
"cnv_calling"
->
cnvCalling
,
"annotation"
->
annotation
),
m
)
}
...
...
@@ -151,6 +153,13 @@ class ShivaWithSvCallingTest extends ShivaTestTrait {
override
def
baseRecalibrationProvider
=
Array
(
false
)
override
def
svCalling
=
true
}
class
ShivaWithCnvCallingTest
extends
ShivaTestTrait
{
override
def
sample1
=
Array
(
true
)
override
def
sample2
=
Array
(
false
)
override
def
realignProvider
=
Array
(
false
)
override
def
baseRecalibrationProvider
=
Array
(
false
)
override
def
cnvCalling
=
true
}
class
ShivaWithAnnotationTest
extends
ShivaTestTrait
{
override
def
sample1
=
Array
(
true
)
override
def
sample2
=
Array
(
false
)
...
...
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