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biopet.biopet
Commits
f7166e18
Commit
f7166e18
authored
Mar 02, 2017
by
Peter van 't Hof
Browse files
Fixed unit tests for shiva
parent
b3adee75
Changes
4
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kopisu/src/test/scala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala
View file @
f7166e18
...
...
@@ -38,7 +38,6 @@ class KopisuTest extends TestNGSuite with Matchers {
new
Kopisu
()
{
override
def
configNamespace
=
"kopisu"
override
def
globalConfig
=
new
Config
(
ConfigUtils
.
mergeMaps
(
map
,
KopisuTest
.
config
(
dir
)))
outputDir
=
dir
qSettings
=
new
QSettings
qSettings
.
runName
=
"test"
}
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
View file @
f7166e18
...
...
@@ -38,10 +38,10 @@ import scala.collection.mutable.ListBuffer
* Created by pjvan_thof on 3/2/15.
*/
class
ShivaSvCallingTest
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
],
outputD
ir
:
File
)
:
ShivaSvCalling
=
{
def
initPipeline
(
map
:
Map
[
String
,
Any
],
d
ir
:
File
)
:
ShivaSvCalling
=
{
new
ShivaSvCalling
{
override
def
configNamespace
=
"shivasvcalling"
override
def
globalConfig
=
new
Config
(
ConfigUtils
.
mergeMaps
(
map
,
ShivaSvCallingTest
.
config
(
outputD
ir
)))
override
def
globalConfig
=
new
Config
(
ConfigUtils
.
mergeMaps
(
map
,
ShivaSvCallingTest
.
config
(
d
ir
)))
qSettings
=
new
QSettings
qSettings
.
runName
=
"test"
}
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
f7166e18
...
...
@@ -193,7 +193,7 @@ object ShivaTest {
private
def
copyFile
(
name
:
String
)
:
Unit
=
{
val
is
=
getClass
.
getResourceAsStream
(
"/"
+
name
)
val
os
=
new
FileOutputStream
(
new
File
(
out
putDir
,
name
))
val
os
=
new
FileOutputStream
(
new
File
(
in
putDir
,
name
))
org
.
apache
.
commons
.
io
.
IOUtils
.
copy
(
is
,
os
)
os
.
close
()
}
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
f7166e18
...
...
@@ -44,10 +44,10 @@ import scala.collection.mutable.ListBuffer
* Created by pjvan_thof on 3/2/15.
*/
trait
ShivaVariantcallingTestTrait
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
],
outputD
ir
:
File
)
:
ShivaVariantcalling
=
{
def
initPipeline
(
map
:
Map
[
String
,
Any
],
d
ir
:
File
)
:
ShivaVariantcalling
=
{
new
ShivaVariantcalling
()
{
override
def
configNamespace
=
"shivavariantcalling"
override
def
globalConfig
=
new
Config
(
ConfigUtils
.
mergeMaps
(
map
,
ShivaVariantcallingTest
.
config
(
outputD
ir
)))
override
def
globalConfig
=
new
Config
(
ConfigUtils
.
mergeMaps
(
map
,
ShivaVariantcallingTest
.
config
(
d
ir
)))
qSettings
=
new
QSettings
qSettings
.
runName
=
"test"
}
...
...
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