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biopet.biopet
Commits
ad09bed2
Commit
ad09bed2
authored
Dec 12, 2016
by
Peter van 't Hof
Browse files
Format fixes
parent
2a90eac3
Changes
4
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateVcf.scala
View file @
ad09bed2
...
...
@@ -16,7 +16,7 @@ package nl.lumc.sasc.biopet.extensions.tools
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommandFunction
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommandFunction
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.Input
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateVcf.scala
View file @
ad09bed2
...
...
@@ -4,13 +4,13 @@ import java.io.File
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.intervals.
{
BedRecord
,
BedRecordList
}
import
nl.lumc.sasc.biopet.utils.intervals.BedRecordList
import
scala.collection.JavaConversions._
/**
* Created by pjvanthof on 10/12/2016.
*/
* Created by pjvanthof on 10/12/2016.
*/
object
ValidateVcf
extends
ToolCommand
{
case
class
Args
(
inputVcf
:
File
=
null
,
reference
:
File
=
null
,
...
...
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/ValidateVcfTest.scala
View file @
ad09bed2
...
...
@@ -7,8 +7,8 @@ import org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
/**
* Created by pjvan_thof on 12-12-16.
*/
* Created by pjvan_thof on 12-12-16.
*/
class
ValidateVcfTest
extends
TestNGSuite
with
Matchers
{
private
def
resourcePath
(
p
:
String
)
:
String
=
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @
ad09bed2
...
...
@@ -16,7 +16,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
}
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
}
import
nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import
nl.lumc.sasc.biopet.extensions.gatk._
import
nl.lumc.sasc.biopet.extensions.tools.ValidateVcf
...
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