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biopet.biopet
Commits
3f119436
Commit
3f119436
authored
Jan 18, 2017
by
Peter van 't Hof
Browse files
Format fixes
parent
e279c724
Changes
3
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biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala
View file @
3f119436
...
...
@@ -18,9 +18,9 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender
import
nl.lumc.sasc.biopet.core.extensions.Md5sum
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.broadinstitute.gatk.queue.
{
QScript
,
QSettings
}
import
org.broadinstitute.gatk.queue.
{
QScript
,
QSettings
}
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
...
...
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineStatusTest.scala
View file @
3f119436
package
nl.lumc.sasc.biopet.core
import
java.io.
{
File
,
PrintWriter
}
import
java.io.
{
File
,
PrintWriter
}
import
com.google.common.io.Files
import
org.scalatest.Matchers
...
...
@@ -11,8 +11,8 @@ import nl.lumc.sasc.biopet.utils.IoUtils._
import
org.apache.commons.io.FileUtils
/**
* Created by pjvan_thof on 10-1-17.
*/
* Created by pjvan_thof on 10-1-17.
*/
class
PipelineStatusTest
extends
TestNGSuite
with
Matchers
{
@Test
def
testDefault
()
:
Unit
=
{
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala
View file @
3f119436
...
...
@@ -14,22 +14,22 @@
*/
package
nl.lumc.sasc.biopet.tools.vcfstats
import
java.io.
{
File
,
FileOutputStream
,
IOException
,
PrintWriter
}
import
java.io.
{
File
,
FileOutputStream
,
IOException
,
PrintWriter
}
import
htsjdk.samtools.util.Interval
import
htsjdk.variant.variantcontext.
{
Genotype
,
VariantContext
}
import
htsjdk.variant.variantcontext.
{
Genotype
,
VariantContext
}
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.utils.intervals.BedRecordList
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
FastaUtils
,
ToolCommand
,
VcfUtils
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
FastaUtils
,
ToolCommand
,
VcfUtils
}
import
scala.collection.JavaConversions._
import
scala.collection.mutable
import
scala.io.Source
import
scala.sys.process.
{
Process
,
ProcessLogger
}
import
scala.sys.process.
{
Process
,
ProcessLogger
}
import
scala.util.Random
import
scala.concurrent.ExecutionContext.Implicits.global
import
scala.concurrent.duration._
import
scala.concurrent.
{
Await
,
Future
}
import
scala.concurrent.
{
Await
,
Future
}
/**
* This tool will generate statistics from a vcf file
...
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