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biopet.biopet
Commits
b1f86146
Commit
b1f86146
authored
Nov 16, 2016
by
Sander Bollen
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slight improvement of message and autostyle fixes
parent
2546ec16
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2
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-2
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+1
-1
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
...a/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+1
-1
No files found.
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
b1f86146
...
...
@@ -143,7 +143,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
protected
def
libIds
:
Set
[
String
]
=
{
val
ids
=
ConfigUtils
.
getMapFromPath
(
globalConfig
.
map
,
List
(
"samples"
,
sampleId
,
"libraries"
)).
getOrElse
(
Map
()).
keySet
if
(
ids
.
isEmpty
)
{
throw
new
IllegalArgumentException
(
"No libraries found in config"
)
logger
.
error
(
s
"No libraries found in config for sample $sampleId"
,
IllegalArgumentException
)
}
ids
}
...
...
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
View file @
b1f86146
...
...
@@ -14,7 +14,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.mapping
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
...
...
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