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biopet.biopet
Commits
c7cca543
Commit
c7cca543
authored
Apr 29, 2016
by
Peter van 't Hof
Browse files
Style fixes
parent
fbc7a317
Changes
2
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shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
View file @
c7cca543
...
...
@@ -15,20 +15,20 @@
*/
package
nl.lumc.sasc.biopet.pipelines.shiva
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
java.nio.file.Paths
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.breakdancer.
{
BreakdancerCaller
,
BreakdancerConfig
,
BreakdancerVCF
}
import
nl.lumc.sasc.biopet.extensions.breakdancer.
{
BreakdancerCaller
,
BreakdancerConfig
,
BreakdancerVCF
}
import
nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import
nl.lumc.sasc.biopet.extensions.delly.DellyCaller
import
nl.lumc.sasc.biopet.extensions.pindel.
{
PindelCaller
,
PindelConfig
,
PindelVCF
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.extensions.pindel.
{
PindelCaller
,
PindelConfig
,
PindelVCF
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.config.Config
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
DataProvider
,
Test
}
import
org.testng.annotations.
{
DataProvider
,
Test
}
import
scala.collection.mutable.ListBuffer
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
c7cca543
...
...
@@ -39,16 +39,16 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
}
}
def
raw
:
Boolean
=
false
def
bcftools
:
Boolean
=
false
def
bcftools_singlesample
:
Boolean
=
false
def
haplotypeCallerGvcf
:
Boolean
=
false
def
haplotypeCallerAllele
:
Boolean
=
false
def
unifiedGenotyperAllele
:
Boolean
=
false
def
unifiedGenotyper
:
Boolean
=
false
def
haplotypeCaller
:
Boolean
=
false
def
freebayes
:
Boolean
=
false
def
varscanCnsSinglesample
:
Boolean
=
false
def
raw
:
Boolean
=
false
def
bcftools
:
Boolean
=
false
def
bcftools_singlesample
:
Boolean
=
false
def
haplotypeCallerGvcf
:
Boolean
=
false
def
haplotypeCallerAllele
:
Boolean
=
false
def
unifiedGenotyperAllele
:
Boolean
=
false
def
unifiedGenotyper
:
Boolean
=
false
def
haplotypeCaller
:
Boolean
=
false
def
freebayes
:
Boolean
=
false
def
varscanCnsSinglesample
:
Boolean
=
false
@DataProvider
(
name
=
"shivaVariantcallingOptions"
)
def
shivaVariantcallingOptions
=
{
...
...
@@ -114,46 +114,46 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
class
ShivaVariantcallingNoVariantcallersTest
extends
ShivaVariantcallingTestTrait
class
ShivaVariantcallingAllTest
extends
ShivaVariantcallingTestTrait
{
override
def
raw
:
Boolean
=
true
override
def
bcftools
:
Boolean
=
true
override
def
bcftools_singlesample
:
Boolean
=
true
override
def
haplotypeCallerGvcf
:
Boolean
=
true
override
def
haplotypeCallerAllele
:
Boolean
=
true
override
def
unifiedGenotyperAllele
:
Boolean
=
true
override
def
unifiedGenotyper
:
Boolean
=
true
override
def
haplotypeCaller
:
Boolean
=
true
override
def
freebayes
:
Boolean
=
true
override
def
varscanCnsSinglesample
:
Boolean
=
true
override
def
raw
:
Boolean
=
true
override
def
bcftools
:
Boolean
=
true
override
def
bcftools_singlesample
:
Boolean
=
true
override
def
haplotypeCallerGvcf
:
Boolean
=
true
override
def
haplotypeCallerAllele
:
Boolean
=
true
override
def
unifiedGenotyperAllele
:
Boolean
=
true
override
def
unifiedGenotyper
:
Boolean
=
true
override
def
haplotypeCaller
:
Boolean
=
true
override
def
freebayes
:
Boolean
=
true
override
def
varscanCnsSinglesample
:
Boolean
=
true
}
class
ShivaVariantcallingRawTest
extends
ShivaVariantcallingTestTrait
{
override
def
raw
:
Boolean
=
true
override
def
raw
:
Boolean
=
true
}
class
ShivaVariantcallingBcftoolsTest
extends
ShivaVariantcallingTestTrait
{
override
def
bcftools
:
Boolean
=
true
override
def
bcftools
:
Boolean
=
true
}
class
ShivaVariantcallingBcftoolsSinglesampleTest
extends
ShivaVariantcallingTestTrait
{
override
def
bcftools_singlesample
:
Boolean
=
true
override
def
bcftools_singlesample
:
Boolean
=
true
}
class
ShivaVariantcallingHaplotypeCallerGvcfTest
extends
ShivaVariantcallingTestTrait
{
override
def
haplotypeCallerGvcf
:
Boolean
=
true
override
def
haplotypeCallerGvcf
:
Boolean
=
true
}
class
ShivaVariantcallingHaplotypeCallerAlleleTest
extends
ShivaVariantcallingTestTrait
{
override
def
haplotypeCallerAllele
:
Boolean
=
true
override
def
haplotypeCallerAllele
:
Boolean
=
true
}
class
ShivaVariantcallingUnifiedGenotyperAlleleTest
extends
ShivaVariantcallingTestTrait
{
override
def
unifiedGenotyperAllele
:
Boolean
=
true
override
def
unifiedGenotyperAllele
:
Boolean
=
true
}
class
ShivaVariantcallingUnifiedGenotyperTest
extends
ShivaVariantcallingTestTrait
{
override
def
unifiedGenotyper
:
Boolean
=
true
override
def
unifiedGenotyper
:
Boolean
=
true
}
class
ShivaVariantcallingHaplotypeCallerTest
extends
ShivaVariantcallingTestTrait
{
override
def
haplotypeCaller
:
Boolean
=
true
override
def
haplotypeCaller
:
Boolean
=
true
}
class
ShivaVariantcallingFreebayesTest
extends
ShivaVariantcallingTestTrait
{
override
def
freebayes
:
Boolean
=
true
override
def
freebayes
:
Boolean
=
true
}
class
ShivaVariantcallingVarscanCnsSinglesampleTest
extends
ShivaVariantcallingTestTrait
{
override
def
varscanCnsSinglesample
:
Boolean
=
true
override
def
varscanCnsSinglesample
:
Boolean
=
true
}
object
ShivaVariantcallingTest
{
...
...
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