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biopet.biopet
Commits
4aae09e9
Commit
4aae09e9
authored
Apr 14, 2017
by
Peter van 't Hof
Browse files
Style fixes
parent
2c17add4
Changes
2
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mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
View file @
4aae09e9
...
...
@@ -314,8 +314,7 @@ class MultisampleMapping(val parent: Configurable) extends QScript with Multisam
object
MultisampleMapping
extends
PipelineCommand
{
object
MergeStrategy
extends
Enumeration
{
val
None
,
MergeSam
,
MarkDuplicates
,
PreProcessMergeSam
,
PreProcessMarkDuplicates
,
PreProcessSambambaMarkdup
=
Value
val
None
,
MergeSam
,
MarkDuplicates
,
PreProcessMergeSam
,
PreProcessMarkDuplicates
,
PreProcessSambambaMarkdup
=
Value
}
/** When file is not absolute an error is raise att the end of the script of a pipeline */
...
...
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
View file @
4aae09e9
...
...
@@ -14,20 +14,20 @@
*/
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
import
nl.lumc.sasc.biopet.extensions.centrifuge.Centrifuge
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
MergeSamFiles
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
MergeSamFiles
}
import
nl.lumc.sasc.biopet.extensions.sambamba.SambambaMarkdup
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.config.Config
import
org.apache.commons.io.FileUtils
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
AfterClass
,
DataProvider
,
Test
}
import
org.testng.annotations.
{
AfterClass
,
DataProvider
,
Test
}
/**
* Created by pjvanthof on 15/05/16.
...
...
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