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biopet.biopet
Commits
b03d3473
Commit
b03d3473
authored
Nov 17, 2016
by
Sander Bollen
Browse files
fix tests
parent
8036de74
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala
View file @
b03d3473
...
...
@@ -15,10 +15,11 @@
package
nl.lumc.sasc.biopet.core
import
java.io.File
import
java.lang.IllegalStateException
import
nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender
import
nl.lumc.sasc.biopet.core.extensions.Md5sum
import
nl.lumc.sasc.biopet.utils.
{
Logging
,
ConfigUtils
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.config.Config
import
org.broadinstitute.gatk.queue.QScript
import
org.scalatest.Matchers
...
...
@@ -119,6 +120,11 @@ class MultiSampleQScriptTest extends TestNGSuite with Matchers {
"Dash (-) and underscore (_) are permitted."
}
@Test
def
testNoLibSample
()
:
Unit
=
{
an
[
IllegalStateException
]
shouldBe
thrownBy
(
MultiSampleQScriptTest
(
noLibSample
::
Nil
))
}
}
object
MultiSampleQScriptTest
{
...
...
@@ -153,10 +159,48 @@ object MultiSampleQScriptTest {
"lib1"
->
Map
(
"test"
->
"4-1"
)
))))
val
child
=
Map
(
"samples"
->
Map
(
"child"
->
Map
(
"tags"
->
Map
(
"gender"
->
"male"
,
"father"
->
"father"
,
"mother"
->
"mother"
))))
val
father
=
Map
(
"samples"
->
Map
(
"father"
->
Map
(
"tags"
->
Map
(
"gender"
->
"male"
))))
val
mother
=
Map
(
"samples"
->
Map
(
"mother"
->
Map
(
"tags"
->
Map
(
"gender"
->
"female"
))))
val
child
=
Map
(
"samples"
->
Map
(
"child"
->
Map
(
"tags"
->
Map
(
"gender"
->
"male"
,
"father"
->
"father"
,
"mother"
->
"mother"
),
"libraries"
->
Map
(
"lib1"
->
Map
(
"test"
->
"child-1"
)
)
)
)
)
val
father
=
Map
(
"samples"
->
Map
(
"father"
->
Map
(
"tags"
->
Map
(
"gender"
->
"male"
),
"libraries"
->
Map
(
"lib1"
->
Map
(
"test"
->
"father-1"
)
)
)
)
)
val
mother
=
Map
(
"samples"
->
Map
(
"mother"
->
Map
(
"tags"
->
Map
(
"gender"
->
"female"
),
"libraries"
->
Map
(
"lib1"
->
Map
(
"test"
->
"mother-1"
)
)
)
)
)
val
noLibSample
=
Map
(
"samples"
->
Map
(
"sample1"
->
Map
(
"tags"
->
Map
(
"gender"
->
"female"
)
)
)
)
def
apply
(
configs
:
List
[
Map
[
String
,
Any
]],
only
:
List
[
String
]
=
Nil
)
=
{
new
QScript
with
MultiSampleQScript
{
qscript
=>
...
...
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