Commit d37ebc75 authored by Peter van 't Hof's avatar Peter van 't Hof

Style fixes

parent 91dfe546
...@@ -14,20 +14,20 @@ ...@@ -14,20 +14,20 @@
*/ */
package nl.lumc.sasc.biopet.pipelines.basty package nl.lumc.sasc.biopet.pipelines.basty
import java.io.{File, FileOutputStream} import java.io.{ File, FileOutputStream }
import com.google.common.io.Files import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions.{Raxml, RunGubbins} 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.gatk.{ BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator }
import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import nl.lumc.sasc.biopet.extensions.tools.{BastyGenerateFasta, VcfStats} import nl.lumc.sasc.biopet.extensions.tools.{ BastyGenerateFasta, 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 nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite 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. * Created by pjvanthof on 27/09/16.
......
...@@ -61,7 +61,6 @@ class MultisampleReportBuilderTest extends TestNGSuite with Matchers { ...@@ -61,7 +61,6 @@ class MultisampleReportBuilderTest extends TestNGSuite with Matchers {
} }
val tempDir = Files.createTempDir() val tempDir = Files.createTempDir()
tempDir.deleteOnExit() tempDir.deleteOnExit()
val args = Array("-s", dbFile.getAbsolutePath, "-o", tempDir.getAbsolutePath) val args = Array("-s", dbFile.getAbsolutePath, "-o", tempDir.getAbsolutePath)
......
...@@ -21,7 +21,7 @@ import com.google.common.io.Files ...@@ -21,7 +21,7 @@ import com.google.common.io.Files
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import org.scalatest.Matchers import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{DataProvider, Test} import org.testng.annotations.{ DataProvider, Test }
import scala.concurrent.Await import scala.concurrent.Await
import scala.concurrent.duration.Duration import scala.concurrent.duration.Duration
......
...@@ -14,20 +14,20 @@ ...@@ -14,20 +14,20 @@
*/ */
package nl.lumc.sasc.biopet.core.summary package nl.lumc.sasc.biopet.core.summary
import java.io.{File, PrintWriter} import java.io.{ File, PrintWriter }
import com.google.common.io.Files import com.google.common.io.Files
import nl.lumc.sasc.biopet.core._ 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 nl.lumc.sasc.biopet.utils.summary.Summary
import org.broadinstitute.gatk.queue.function.CommandLineFunction 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.Matchers
import org.scalatest.testng.TestNGSuite import org.scalatest.testng.TestNGSuite
import WriteSummaryTest._ import WriteSummaryTest._
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import org.apache.commons.io.FileUtils 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.Await
import scala.concurrent.duration.Duration import scala.concurrent.duration.Duration
...@@ -98,7 +98,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers { ...@@ -98,7 +98,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile) val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
basicSummaryTest(summary, qscript.summaryRunId, dir) 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") 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 { ...@@ -119,7 +119,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile) val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
basicSummaryTest(summary, qscript.summaryRunId, dir) 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") 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 { ...@@ -140,7 +140,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile) val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
basicSummaryTest(summary, qscript.summaryRunId, dir) 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") 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 { ...@@ -161,7 +161,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile) val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
basicSummaryTest(summary, qscript.summaryRunId, dir) 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") 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 { ...@@ -202,7 +202,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile) val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
basicSummaryTest(summary, qscript.summaryRunId, dir) 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") Await.result(summary.getFile(qscript.summaryRunId, Right("test"), Some(Right("tool_1")), None, None, key = "file_1"), Duration.Inf).map(_.md5) shouldBe Some("checksum")
} }
......
...@@ -72,7 +72,6 @@ class SummaryDbTest extends TestNGSuite with Matchers { ...@@ -72,7 +72,6 @@ class SummaryDbTest extends TestNGSuite with Matchers {
Await.result(db.getLibraries(), Duration.Inf) shouldBe empty Await.result(db.getLibraries(), Duration.Inf) shouldBe empty
val libraryId = Await.result(db.createLibrary("test_lib", runId, sampleId), Duration.Inf) 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.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.getLibraryName(libraryId), Duration.Inf) shouldBe Some("test_lib")
Await.result(db.getLibraryId(runId, sampleId, "test_lib"), Duration.Inf) shouldBe Some(libraryId) Await.result(db.getLibraryId(runId, sampleId, "test_lib"), Duration.Inf) shouldBe Some(libraryId)
...@@ -328,21 +327,20 @@ class SummaryDbTest extends TestNGSuite with Matchers { ...@@ -328,21 +327,20 @@ class SummaryDbTest extends TestNGSuite with Matchers {
val libraryId = Await.result(db.createLibrary("test_library", runId, sampleId), Duration.Inf) 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.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.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.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.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.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.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0, 0, None, None, None, "key", "path2", "md5", link = false, 1))
// Test join queries // 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.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.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.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() db.close()
} }
@Test @Test
def testExecutable(): Unit = { def testExecutable(): Unit = {
val dbFile = File.createTempFile("summary.", ".db") val dbFile = File.createTempFile("summary.", ".db")
......
...@@ -18,12 +18,12 @@ import java.io.File ...@@ -18,12 +18,12 @@ import java.io.File
import com.google.common.io.Files import com.google.common.io.Files
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.extensions.centrifuge.{Centrifuge, CentrifugeKreport} import nl.lumc.sasc.biopet.extensions.centrifuge.{ Centrifuge, CentrifugeKreport }
import nl.lumc.sasc.biopet.extensions.kraken.{Kraken, KrakenReport} import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
import nl.lumc.sasc.biopet.extensions.picard.SamToFastq import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import nl.lumc.sasc.biopet.extensions.tools.KrakenReportToJson 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 nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings import org.broadinstitute.gatk.queue.QSettings
......
...@@ -17,13 +17,13 @@ package nl.lumc.sasc.biopet.pipelines.gears ...@@ -17,13 +17,13 @@ package nl.lumc.sasc.biopet.pipelines.gears
import java.io.File import java.io.File
import com.google.common.io.Files 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 nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite 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. * Created by pjvanthof on 04/02/16.
......
...@@ -23,7 +23,7 @@ import org.apache.commons.io.FileUtils ...@@ -23,7 +23,7 @@ import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite 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. * Created by pjvan_thof on 13-5-16.
......
...@@ -14,22 +14,22 @@ ...@@ -14,22 +14,22 @@
*/ */
package nl.lumc.sasc.biopet.pipelines.gentrap package nl.lumc.sasc.biopet.pipelines.gentrap
import java.io.{File, FileOutputStream} import java.io.{ File, FileOutputStream }
import com.google.common.io.Files 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._
import nl.lumc.sasc.biopet.extensions.gmap.Gsnap import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import nl.lumc.sasc.biopet.extensions.hisat.Hisat2 import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
import nl.lumc.sasc.biopet.extensions.tools.{BaseCounter, WipeReads} import nl.lumc.sasc.biopet.extensions.tools.{ BaseCounter, WipeReads }
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 nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.utils.camelize import nl.lumc.sasc.biopet.utils.camelize
import org.apache.commons.io.FileUtils import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite 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 { abstract class GentrapTestAbstract(val expressionMeasures: List[String]) extends TestNGSuite with Matchers {
......
...@@ -24,7 +24,7 @@ import org.apache.commons.io.FileUtils ...@@ -24,7 +24,7 @@ import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite 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. * Created by pjvan_thof on 4/11/16.
......
...@@ -23,7 +23,7 @@ import org.apache.commons.io.FileUtils ...@@ -23,7 +23,7 @@ import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite 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. * Created by pjvan_thof on 31-5-16.
......
...@@ -14,17 +14,17 @@ ...@@ -14,17 +14,17 @@
*/ */
package nl.lumc.sasc.biopet.pipelines.kopisu package nl.lumc.sasc.biopet.pipelines.kopisu
import java.io.{File, FileOutputStream} import java.io.{ File, FileOutputStream }
import com.google.common.io.Files 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.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Config import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, DataProvider, Test} import org.testng.annotations.{ AfterClass, DataProvider, Test }
import scala.collection.mutable.ListBuffer import scala.collection.mutable.ListBuffer
......
...@@ -14,19 +14,19 @@ ...@@ -14,19 +14,19 @@
*/ */
package nl.lumc.sasc.biopet.pipelines.mapping package nl.lumc.sasc.biopet.pipelines.mapping
import java.io.{File, FileOutputStream} import java.io.{ File, FileOutputStream }
import com.google.common.io.Files import com.google.common.io.Files
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.extensions.centrifuge.Centrifuge 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.utils.{ConfigUtils, Logging} import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Config import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite 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. * Created by pjvanthof on 15/05/16.
......
...@@ -14,16 +14,16 @@ ...@@ -14,16 +14,16 @@
*/ */
package nl.lumc.sasc.biopet.pipelines.sage package nl.lumc.sasc.biopet.pipelines.sage
import java.io.{File, FileOutputStream} import java.io.{ File, FileOutputStream }
import com.google.common.io.Files 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 nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite 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. * Created by pjvanthof on 28/09/16.
......
...@@ -14,21 +14,21 @@ ...@@ -14,21 +14,21 @@
*/ */
package nl.lumc.sasc.biopet.pipelines.shiva package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.{File, FileOutputStream} import java.io.{ File, FileOutputStream }
import java.nio.file.Paths import java.nio.file.Paths
import com.google.common.io.Files 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.clever.CleverCaller
import nl.lumc.sasc.biopet.extensions.delly.DellyCaller import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
import nl.lumc.sasc.biopet.extensions.pindel.{PindelCaller, PindelConfig, PindelVCF} import nl.lumc.sasc.biopet.extensions.pindel.{ PindelCaller, PindelConfig, PindelVCF }
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 nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, DataProvider, Test} import org.testng.annotations.{ AfterClass, DataProvider, Test }
import scala.collection.mutable.ListBuffer import scala.collection.mutable.ListBuffer
......
...@@ -14,19 +14,19 @@ ...@@ -14,19 +14,19 @@
*/ */
package nl.lumc.sasc.biopet.pipelines.shiva package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.{File, FileOutputStream} import java.io.{ File, FileOutputStream }
import com.google.common.io.Files 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.picard.MarkDuplicates
import nl.lumc.sasc.biopet.extensions.tools.VcfStats 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 nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, DataProvider, Test} import org.testng.annotations.{ AfterClass, DataProvider, Test }
/** /**
* Class for testing shiva * Class for testing shiva
......
...@@ -19,22 +19,22 @@ ...@@ -19,22 +19,22 @@
*/ */
package nl.lumc.sasc.biopet.pipelines.shiva package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.{File, FileOutputStream} import java.io.{ File, FileOutputStream }
import com.google.common.io.Files import com.google.common.io.Files
import nl.lumc.sasc.biopet.core.BiopetPipe import nl.lumc.sasc.biopet.core.BiopetPipe
import nl.lumc.sasc.biopet.extensions.Freebayes import nl.lumc.sasc.biopet.extensions.Freebayes
import nl.lumc.sasc.biopet.extensions.bcftools.{BcftoolsCall, BcftoolsMerge} 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.gatk.{ CombineVariants, GenotypeConcordance, HaplotypeCaller, UnifiedGenotyper }
import nl.lumc.sasc.biopet.utils.config.Config import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.tools.{MpileupToVcf, VcfFilter, VcfStats} 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.vt.{ VtDecompose, VtNormalize }
import nl.lumc.sasc.biopet.utils.ConfigUtils import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.apache.commons.io.FileUtils import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, DataProvider, Test} import org.testng.annotations.{ AfterClass, DataProvider, Test }
import scala.collection.mutable.ListBuffer import scala.collection.mutable.ListBuffer
......
...@@ -25,7 +25,7 @@ import org.apache.commons.io.FileUtils ...@@ -25,7 +25,7 @@ import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite 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. * Created by pjvan_thof on 4/11/16.
......
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