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Mirrors
biopet.biopet
Commits
d37ebc75
Commit
d37ebc75
authored
Mar 02, 2017
by
Peter van 't Hof
Browse files
Style fixes
parent
91dfe546
Changes
18
Hide whitespace changes
Inline
Side-by-side
basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
View file @
d37ebc75
...
...
@@ -14,20 +14,20 @@
*/
package
nl.lumc.sasc.biopet.pipelines.basty
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.
{
Raxml
,
RunGubbins
}
import
nl.lumc.sasc.biopet.extensions.gatk.
{
BaseRecalibrator
,
IndelRealigner
,
PrintReads
,
RealignerTargetCreator
}
import
nl.lumc.sasc.biopet.extensions.
{
Raxml
,
RunGubbins
}
import
nl.lumc.sasc.biopet.extensions.gatk.
{
BaseRecalibrator
,
IndelRealigner
,
PrintReads
,
RealignerTargetCreator
}
import
nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import
nl.lumc.sasc.biopet.extensions.tools.
{
BastyGenerateFasta
,
VcfStats
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
BastyGenerateFasta
,
VcfStats
}
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 27/09/16.
...
...
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala
View file @
d37ebc75
...
...
@@ -61,7 +61,6 @@ class MultisampleReportBuilderTest extends TestNGSuite with Matchers {
}
val
tempDir
=
Files
.
createTempDir
()
tempDir
.
deleteOnExit
()
val
args
=
Array
(
"-s"
,
dbFile
.
getAbsolutePath
,
"-o"
,
tempDir
.
getAbsolutePath
)
...
...
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala
View file @
d37ebc75
...
...
@@ -21,7 +21,7 @@ import com.google.common.io.Files
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
DataProvider
,
Test
}
import
org.testng.annotations.
{
DataProvider
,
Test
}
import
scala.concurrent.Await
import
scala.concurrent.duration.Duration
...
...
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
View file @
d37ebc75
...
...
@@ -14,20 +14,20 @@
*/
package
nl.lumc.sasc.biopet.core.summary
import
java.io.
{
File
,
PrintWriter
}
import
java.io.
{
File
,
PrintWriter
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.utils.config.
{
Config
,
Configurable
}
import
nl.lumc.sasc.biopet.utils.config.
{
Config
,
Configurable
}
import
nl.lumc.sasc.biopet.utils.summary.Summary
import
org.broadinstitute.gatk.queue.function.CommandLineFunction
import
org.broadinstitute.gatk.queue.
{
QScript
,
QSettings
}
import
org.broadinstitute.gatk.queue.
{
QScript
,
QSettings
}
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
WriteSummaryTest._
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import
org.apache.commons.io.FileUtils
import
org.testng.annotations.
{
AfterClass
,
Test
}
import
org.testng.annotations.
{
AfterClass
,
Test
}
import
scala.concurrent.Await
import
scala.concurrent.duration.Duration
...
...
@@ -98,7 +98,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val
summary
=
SummaryDb
.
openSqliteSummary
(
qscript
.
summaryDbFile
)
basicSummaryTest
(
summary
,
qscript
.
summaryRunId
,
dir
)
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
Await
.
result
(
summary
.
getFile
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
None
,
None
,
key
=
"file_1"
),
Duration
.
Inf
).
map
(
_
.
md5
)
shouldBe
Some
(
"checksum"
)
}
...
...
@@ -119,7 +119,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val
summary
=
SummaryDb
.
openSqliteSummary
(
qscript
.
summaryDbFile
)
basicSummaryTest
(
summary
,
qscript
.
summaryRunId
,
dir
)
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
Await
.
result
(
summary
.
getFile
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
None
,
None
,
key
=
"file_1"
),
Duration
.
Inf
).
map
(
_
.
md5
)
shouldBe
Some
(
"checksum"
)
}
...
...
@@ -140,7 +140,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val
summary
=
SummaryDb
.
openSqliteSummary
(
qscript
.
summaryDbFile
)
basicSummaryTest
(
summary
,
qscript
.
summaryRunId
,
dir
)
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
Await
.
result
(
summary
.
getFile
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
None
,
None
,
key
=
"file_1"
),
Duration
.
Inf
).
map
(
_
.
md5
)
shouldBe
Some
(
"checksum"
)
}
...
...
@@ -161,7 +161,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val
summary
=
SummaryDb
.
openSqliteSummary
(
qscript
.
summaryDbFile
)
basicSummaryTest
(
summary
,
qscript
.
summaryRunId
,
dir
)
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
Some
(
Right
(
"sampleName"
)),
Some
(
Right
(
"libName"
)),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
Some
(
Right
(
"sampleName"
)),
Some
(
Right
(
"libName"
)),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
Await
.
result
(
summary
.
getFile
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
Some
(
Right
(
"sampleName"
)),
Some
(
Right
(
"libName"
)),
key
=
"file_1"
),
Duration
.
Inf
).
map
(
_
.
md5
)
shouldBe
Some
(
"checksum"
)
}
...
...
@@ -202,7 +202,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val
summary
=
SummaryDb
.
openSqliteSummary
(
qscript
.
summaryDbFile
)
basicSummaryTest
(
summary
,
qscript
.
summaryRunId
,
dir
)
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
summary
.
getStatKeys
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
keyValues
=
Map
(
"key"
->
List
(
"key"
)))
shouldBe
Map
(
"key"
->
Some
(
"value"
))
Await
.
result
(
summary
.
getFile
(
qscript
.
summaryRunId
,
Right
(
"test"
),
Some
(
Right
(
"tool_1"
)),
None
,
None
,
key
=
"file_1"
),
Duration
.
Inf
).
map
(
_
.
md5
)
shouldBe
Some
(
"checksum"
)
}
...
...
biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDbTest.scala
View file @
d37ebc75
...
...
@@ -72,7 +72,6 @@ class SummaryDbTest extends TestNGSuite with Matchers {
Await
.
result
(
db
.
getLibraries
(),
Duration
.
Inf
)
shouldBe
empty
val
libraryId
=
Await
.
result
(
db
.
createLibrary
(
"test_lib"
,
runId
,
sampleId
),
Duration
.
Inf
)
Await
.
result
(
db
.
getLibraries
(),
Duration
.
Inf
)
shouldBe
Seq
(
Schema
.
Library
(
libraryId
,
"test_lib"
,
runId
,
sampleId
,
None
))
Await
.
result
(
db
.
getLibraryName
(
libraryId
),
Duration
.
Inf
)
shouldBe
Some
(
"test_lib"
)
Await
.
result
(
db
.
getLibraryId
(
runId
,
sampleId
,
"test_lib"
),
Duration
.
Inf
)
shouldBe
Some
(
libraryId
)
...
...
@@ -328,21 +327,20 @@ class SummaryDbTest extends TestNGSuite with Matchers {
val
libraryId
=
Await
.
result
(
db
.
createLibrary
(
"test_library"
,
runId
,
sampleId
),
Duration
.
Inf
)
Await
.
result
(
db
.
createOrUpdateFile
(
runId
,
pipelineId
,
None
,
None
,
None
,
"key"
,
"path"
,
"md5"
,
link
=
false
,
1
),
Duration
.
Inf
)
Await
.
result
(
db
.
getFile
(
runId
,
Left
(
pipelineId
),
None
,
None
,
None
,
"key"
),
Duration
.
Inf
)
shouldBe
Some
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
getFiles
(),
Duration
.
Inf
)
shouldBe
Seq
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
getFile
(
runId
,
Left
(
pipelineId
),
None
,
None
,
None
,
"key"
),
Duration
.
Inf
)
shouldBe
Some
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
getFiles
(),
Duration
.
Inf
)
shouldBe
Seq
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
createOrUpdateFile
(
runId
,
pipelineId
,
None
,
None
,
None
,
"key"
,
"path2"
,
"md5"
,
link
=
false
,
1
),
Duration
.
Inf
)
Await
.
result
(
db
.
getFile
(
runId
,
Left
(
pipelineId
),
None
,
None
,
None
,
"key"
),
Duration
.
Inf
)
shouldBe
Some
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path2"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
getFiles
(),
Duration
.
Inf
)
shouldBe
Seq
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path2"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
getFile
(
runId
,
Left
(
pipelineId
),
None
,
None
,
None
,
"key"
),
Duration
.
Inf
)
shouldBe
Some
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path2"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
getFiles
(),
Duration
.
Inf
)
shouldBe
Seq
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path2"
,
"md5"
,
link
=
false
,
1
))
// Test join queries
Await
.
result
(
db
.
createOrUpdateFile
(
runId
,
pipelineId
,
Some
(
moduleId
),
Some
(
sampleId
),
Some
(
libraryId
),
"key"
,
"path3"
,
"md5"
,
link
=
false
,
1
),
Duration
.
Inf
)
Await
.
result
(
db
.
getFile
(
runId
,
Right
(
"test_pipeline"
),
Some
(
Right
(
"test_module"
)),
Some
(
Right
(
"test_sample"
)),
Some
(
Right
(
"test_library"
)),
"key"
),
Duration
.
Inf
)
shouldBe
Some
(
Schema
.
File
(
0
,
0
,
Some
(
moduleId
),
Some
(
sampleId
),
Some
(
libraryId
),
"key"
,
"path3"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
getFiles
(),
Duration
.
Inf
)
shouldBe
Seq
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path2"
,
"md5"
,
link
=
false
,
1
),
Schema
.
File
(
0
,
0
,
Some
(
moduleId
),
Some
(
sampleId
),
Some
(
libraryId
),
"key"
,
"path3"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
getFile
(
runId
,
Right
(
"test_pipeline"
),
Some
(
Right
(
"test_module"
)),
Some
(
Right
(
"test_sample"
)),
Some
(
Right
(
"test_library"
)),
"key"
),
Duration
.
Inf
)
shouldBe
Some
(
Schema
.
File
(
0
,
0
,
Some
(
moduleId
),
Some
(
sampleId
),
Some
(
libraryId
),
"key"
,
"path3"
,
"md5"
,
link
=
false
,
1
))
Await
.
result
(
db
.
getFiles
(),
Duration
.
Inf
)
shouldBe
Seq
(
Schema
.
File
(
0
,
0
,
None
,
None
,
None
,
"key"
,
"path2"
,
"md5"
,
link
=
false
,
1
),
Schema
.
File
(
0
,
0
,
Some
(
moduleId
),
Some
(
sampleId
),
Some
(
libraryId
),
"key"
,
"path3"
,
"md5"
,
link
=
false
,
1
))
db
.
close
()
}
@Test
def
testExecutable
()
:
Unit
=
{
val
dbFile
=
File
.
createTempFile
(
"summary."
,
".db"
)
...
...
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
View file @
d37ebc75
...
...
@@ -18,12 +18,12 @@ import java.io.File
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.extensions.centrifuge.
{
Centrifuge
,
CentrifugeKreport
}
import
nl.lumc.sasc.biopet.extensions.kraken.
{
Kraken
,
KrakenReport
}
import
nl.lumc.sasc.biopet.extensions.centrifuge.
{
Centrifuge
,
CentrifugeKreport
}
import
nl.lumc.sasc.biopet.extensions.kraken.
{
Kraken
,
KrakenReport
}
import
nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import
nl.lumc.sasc.biopet.extensions.tools.KrakenReportToJson
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
...
...
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
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d37ebc75
...
...
@@ -17,13 +17,13 @@ package nl.lumc.sasc.biopet.pipelines.gears
import
java.io.File
import
com.google.common.io.Files
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 04/02/16.
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...
generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomesTest.scala
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d37ebc75
...
...
@@ -23,7 +23,7 @@ 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
,
Test
}
import
org.testng.annotations.
{
AfterClass
,
Test
}
/**
* Created by pjvan_thof on 13-5-16.
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...
gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
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d37ebc75
...
...
@@ -14,22 +14,22 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gentrap
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.core.
{
BiopetFifoPipe
,
BiopetPipe
}
import
nl.lumc.sasc.biopet.core.
{
BiopetFifoPipe
,
BiopetPipe
}
import
nl.lumc.sasc.biopet.extensions._
import
nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import
nl.lumc.sasc.biopet.extensions.hisat.Hisat2
import
nl.lumc.sasc.biopet.extensions.tools.
{
BaseCounter
,
WipeReads
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
BaseCounter
,
WipeReads
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.utils.camelize
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
}
abstract
class
GentrapTestAbstract
(
val
expressionMeasures
:
List
[
String
])
extends
TestNGSuite
with
Matchers
{
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gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala
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d37ebc75
...
...
@@ -24,7 +24,7 @@ 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
,
Test
}
import
org.testng.annotations.
{
AfterClass
,
Test
}
/**
* Created by pjvan_thof on 4/11/16.
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...
gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala
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d37ebc75
...
...
@@ -23,7 +23,7 @@ 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
,
Test
}
import
org.testng.annotations.
{
AfterClass
,
Test
}
/**
* Created by pjvan_thof on 31-5-16.
...
...
kopisu/src/test/scala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala
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d37ebc75
...
...
@@ -14,17 +14,17 @@
*/
package
nl.lumc.sasc.biopet.pipelines.kopisu
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.freec.
{
FreeC
,
FreeCAssessSignificancePlot
,
FreeCCNVPlot
}
import
nl.lumc.sasc.biopet.extensions.freec.
{
FreeC
,
FreeCAssessSignificancePlot
,
FreeCCNVPlot
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
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
}
import
scala.collection.mutable.ListBuffer
...
...
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
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d37ebc75
...
...
@@ -14,19 +14,19 @@
*/
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.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
MergeSamFiles
}
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.
...
...
sage/src/test/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala
View file @
d37ebc75
...
...
@@ -14,16 +14,16 @@
*/
package
nl.lumc.sasc.biopet.pipelines.sage
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
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 28/09/16.
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
View file @
d37ebc75
...
...
@@ -14,21 +14,21 @@
*/
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.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
}
import
scala.collection.mutable.ListBuffer
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
d37ebc75
...
...
@@ -14,19 +14,19 @@
*/
package
nl.lumc.sasc.biopet.pipelines.shiva
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.gatk.
{
BaseRecalibrator
,
IndelRealigner
,
PrintReads
,
RealignerTargetCreator
}
import
nl.lumc.sasc.biopet.extensions.gatk.
{
BaseRecalibrator
,
IndelRealigner
,
PrintReads
,
RealignerTargetCreator
}
import
nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import
nl.lumc.sasc.biopet.extensions.tools.VcfStats
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
}
/**
* Class for testing shiva
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
d37ebc75
...
...
@@ -19,22 +19,22 @@
*/
package
nl.lumc.sasc.biopet.pipelines.shiva
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.core.BiopetPipe
import
nl.lumc.sasc.biopet.extensions.Freebayes
import
nl.lumc.sasc.biopet.extensions.bcftools.
{
BcftoolsCall
,
BcftoolsMerge
}
import
nl.lumc.sasc.biopet.extensions.gatk.
{
CombineVariants
,
GenotypeConcordance
,
HaplotypeCaller
,
UnifiedGenotyper
}
import
nl.lumc.sasc.biopet.extensions.bcftools.
{
BcftoolsCall
,
BcftoolsMerge
}
import
nl.lumc.sasc.biopet.extensions.gatk.
{
CombineVariants
,
GenotypeConcordance
,
HaplotypeCaller
,
UnifiedGenotyper
}
import
nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.extensions.vt.
{
VtDecompose
,
VtNormalize
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.extensions.vt.
{
VtDecompose
,
VtNormalize
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
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
}
import
scala.collection.mutable.ListBuffer
...
...
toucan/src/test/scala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala
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d37ebc75
...
...
@@ -25,7 +25,7 @@ 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
,
Test
}
import
org.testng.annotations.
{
AfterClass
,
Test
}
/**
* Created by pjvan_thof on 4/11/16.
...
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