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biopet.biopet
Commits
23e05373
Commit
23e05373
authored
Mar 08, 2016
by
Peter van 't Hof
Browse files
Fixed tests
parent
25f487cc
Changes
2
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Inline
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public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
View file @
23e05373
...
...
@@ -129,7 +129,7 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
)
val
pipeline
=
initPipeline
(
map
)
pipeline
.
inputBams
=
Map
(
"bam"
->
Shiva
Variantc
allingTest
.
inputTouch
(
"bam"
+
".bam"
))
pipeline
.
inputBams
=
Map
(
"bam"
->
Shiva
SvC
allingTest
.
inputTouch
(
"bam"
+
".bam"
))
if
(!
del
&&
!
dup
&&
!
inv
&&
!
tra
)
intercept
[
IllegalArgumentException
]
{
pipeline
.
init
()
...
...
@@ -149,7 +149,7 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
val
map
=
Map
(
"sv_callers"
->
List
(
"this is not a caller"
))
val
pipeline
=
initPipeline
(
map
)
pipeline
.
inputBams
=
Map
(
"bam"
->
Shiva
Variantc
allingTest
.
inputTouch
(
"bam"
+
".bam"
))
pipeline
.
inputBams
=
Map
(
"bam"
->
Shiva
SvC
allingTest
.
inputTouch
(
"bam"
+
".bam"
))
intercept
[
IllegalArgumentException
]
{
pipeline
.
init
()
...
...
@@ -181,7 +181,7 @@ object ShivaSvCallingTest {
val
outputDir
=
Files
.
createTempDir
()
outputDir
.
deleteOnExit
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
def
inputTouch
(
name
:
String
)
:
File
=
{
private
def
inputTouch
(
name
:
String
)
:
File
=
{
val
file
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
name
).
getAbsoluteFile
Files
.
touch
(
file
)
file
...
...
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
23e05373
...
...
@@ -96,16 +96,13 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfFilter
])
shouldBe
(
if
(
raw
)
bams
else
0
)
}
}
@AfterClass
def
removeTempOutputDir
()
=
{
FileUtils
.
deleteDirectory
(
ShivaVariantcallingTest
.
outputDir
)
}
}
object
ShivaVariantcallingTest
{
val
outputDir
=
Files
.
createTempDir
()
outputDir
.
deleteOnExit
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
def
inputTouch
(
name
:
String
)
:
File
=
{
private
def
inputTouch
(
name
:
String
)
:
File
=
{
val
file
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
name
).
getAbsoluteFile
Files
.
touch
(
file
)
file
...
...
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