diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index c95299b0d4c47ef189a22fce2fcd1dfaff9183f8..56c4796002986026ca6bd6f84a43766085f297de 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -23,9 +23,7 @@ import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import nl.lumc.sasc.biopet.utils.Logging
import org.broadinstitute.gatk.queue.{ QScript, QSettings }
import org.broadinstitute.gatk.queue.function.QFunction
-import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
-import org.broadinstitute.gatk.utils.commandline.Argument
/** Base for biopet pipeline */
trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
index 03b229a9c24899c0f55bad0b72897ad5abd93c36..05a3025efb2372ec057a1d07456064b8c9aef6f7 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BaseCounter.scala
@@ -15,14 +15,14 @@
*/
package nl.lumc.sasc.biopet.extensions.tools
-import java.io.{PrintWriter, File}
+import java.io.{ PrintWriter, File }
import nl.lumc.sasc.biopet.core.ToolCommandFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
- *
+ *
*/
class BaseCounter(val root: Configurable) extends ToolCommandFunction {
def toolObject = nl.lumc.sasc.biopet.tools.BaseCounter
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
index 7cf07938a1b2882cf229249c961ddbbcb67c82c3..69f8b652c272dd386bbb5a7ca30d5bc98d1843af 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
@@ -1,17 +1,17 @@
package nl.lumc.sasc.biopet.tools
-import java.io.{PrintWriter, File}
+import java.io.{ PrintWriter, File }
-import htsjdk.samtools.{SAMRecord, SamReaderFactory}
+import htsjdk.samtools.{ SAMRecord, SamReaderFactory }
import nl.lumc.sasc.biopet.utils.ToolCommand
-import nl.lumc.sasc.biopet.utils.intervals.{BedRecordList, BedRecord}
-import picard.annotation.{Gene, GeneAnnotationReader}
+import nl.lumc.sasc.biopet.utils.intervals.{ BedRecordList, BedRecord }
+import picard.annotation.{ Gene, GeneAnnotationReader }
import scala.collection.JavaConversions._
/**
- * Created by pjvanthof on 22/01/16.
- */
+ * Created by pjvanthof on 22/01/16.
+ */
object BaseCounter extends ToolCommand {
case class Args(refFlat: File = null,
@@ -20,13 +20,13 @@ object BaseCounter extends ToolCommand {
prefix: String = "output") extends AbstractArgs
class OptParser extends AbstractOptParser {
- opt[File]('r', "refFlat") required() valueName "<file>" action { (x, c) =>
+ opt[File]('r', "refFlat") required () valueName "<file>" action { (x, c) =>
c.copy(refFlat = x)
}
- opt[File]('o', "outputDir") required() valueName "<directory>" action { (x, c) =>
+ opt[File]('o', "outputDir") required () valueName "<directory>" action { (x, c) =>
c.copy(outputDir = x)
}
- opt[File]('b', "bam") required() valueName "<file>" action { (x, c) =>
+ opt[File]('b', "bam") required () valueName "<file>" action { (x, c) =>
c.copy(bamFile = x)
}
opt[String]('p', "prefix") valueName "<prefix>" action { (x, c) =>
@@ -38,7 +38,7 @@ object BaseCounter extends ToolCommand {
val argsParser = new OptParser
val cmdArgs: Args = argsParser.parse(args, Args()) match {
case Some(x) => x
- case _ => throw new IllegalArgumentException
+ case _ => throw new IllegalArgumentException
}
//Sets picard logging level
@@ -63,11 +63,11 @@ object BaseCounter extends ToolCommand {
}
/**
- * This function will write all counts that are concatenated on transcript level. Each line is 1 transcript.
- * Exonic: then it's seen as an exon on 1 of the transcripts
- * Intronic: then it's not seen as an exon on 1 of the transcripts
- * Exonic + Intronic = Total
- */
+ * This function will write all counts that are concatenated on transcript level. Each line is 1 transcript.
+ * Exonic: then it's seen as an exon on 1 of the transcripts
+ * Intronic: then it's not seen as an exon on 1 of the transcripts
+ * Exonic + Intronic = Total
+ */
def writeTranscriptCounts(genes: List[GeneCount], outputDir: File, prefix: String): Unit = {
val transcriptTotalWriter = new PrintWriter(new File(outputDir, s"$prefix.base.transcript.counts"))
val transcriptTotalSenseWriter = new PrintWriter(new File(outputDir, s"$prefix.base.transcript.sense.counts"))
@@ -141,11 +141,11 @@ object BaseCounter extends ToolCommand {
}
/**
- * This function will write all counts that are concatenated on gene level. Each line is 1 gene.
- * Exonic: then it's seen as an exon on 1 of the transcripts
- * Intronic: then it's not seen as an exon on 1 of the transcripts
- * Exonic + Intronic = Total
- */
+ * This function will write all counts that are concatenated on gene level. Each line is 1 gene.
+ * Exonic: then it's seen as an exon on 1 of the transcripts
+ * Intronic: then it's not seen as an exon on 1 of the transcripts
+ * Exonic + Intronic = Total
+ */
def writeGeneCounts(genes: List[GeneCount], outputDir: File, prefix: String): Unit = {
val geneTotalWriter = new PrintWriter(new File(outputDir, s"$prefix.base.gene.counts"))
val geneTotalSenseWriter = new PrintWriter(new File(outputDir, s"$prefix.base.gene.sense.counts"))
@@ -181,9 +181,9 @@ object BaseCounter extends ToolCommand {
}
/**
- * This function will print all counts that exist on exonic regions,
- * each base withing the gene is only represented once but all regions are separated
- */
+ * This function will print all counts that exist on exonic regions,
+ * each base withing the gene is only represented once but all regions are separated
+ */
def writeMergeExonCount(genes: List[GeneCount], outputDir: File, prefix: String): Unit = {
val exonWriter = new PrintWriter(new File(outputDir, s"$prefix.base.exon.merge.counts"))
val exonSenseWriter = new PrintWriter(new File(outputDir, s"$prefix.base.exon.merge.sense.counts"))
@@ -203,9 +203,9 @@ object BaseCounter extends ToolCommand {
}
/**
- * This function will print all counts that does *not* exist on exonic regions,
- * each base withing the gene is only represented once but all regions are separated
- */
+ * This function will print all counts that does *not* exist on exonic regions,
+ * each base withing the gene is only represented once but all regions are separated
+ */
def writeMergeIntronCount(genes: List[GeneCount], outputDir: File, prefix: String): Unit = {
val intronWriter = new PrintWriter(new File(outputDir, s"$prefix.base.intron.merge.counts"))
val intronSenseWriter = new PrintWriter(new File(outputDir, s"$prefix.base.intron.merge.sense.counts"))
@@ -285,7 +285,7 @@ object BaseCounter extends ToolCommand {
.map(e => BedRecord(gene.getContig, e.start - 1, e.end)))
.combineOverlap
def intronRegions = BedRecordList.fromList(BedRecord(gene.getContig, gene.getStart - 1, gene.getEnd) :: exonRegions.allRecords.toList)
- .squishBed(false, false)
+ .squishBed(false, false)
val exonCounts = exonRegions.allRecords.map(e => new RegionCount(e.start + 1, e.end))
val intronCounts = intronRegions.allRecords.map(e => new RegionCount(e.start + 1, e.end))
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index cf42e8dfe9e51105f3c4950819b3528d2097a13b..8bf19381ed25f995fe73bc507f5029830a3b1cb0 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -16,10 +16,10 @@
package nl.lumc.sasc.biopet.pipelines.gentrap
import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.annotations.{RibosomalRefFlat, AnnotationRefFlat}
+import nl.lumc.sasc.biopet.core.annotations.{ RibosomalRefFlat, AnnotationRefFlat }
import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import nl.lumc.sasc.biopet.extensions.tools.WipeReads
-import nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap.{StrandProtocol, ExpMeasures}
+import nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap.{ StrandProtocol, ExpMeasures }
import nl.lumc.sasc.biopet.pipelines.gentrap.measures._
import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
@@ -56,7 +56,7 @@ class Gentrap(val root: Configurable) extends QScript
lazy val expMeasures = config("expression_measures", default = Nil).asStringList.map(value =>
ExpMeasures.values.find(x => Gentrap.camelize(x.toString) == value) match {
case Some(v) => v
- case _ => throw new IllegalArgumentException(s"'$value' is not a valid Expression measurement")
+ case _ => throw new IllegalArgumentException(s"'$value' is not a valid Expression measurement")
}
).toSet
@@ -65,7 +65,7 @@ class Gentrap(val root: Configurable) extends QScript
val value: String = config("strand_protocol")
StrandProtocol.values.find(x => Gentrap.camelize(x.toString) == value) match {
case Some(v) => v
- case other =>
+ case other =>
Logging.addError(s"'$other' is no strand_protocol or strand_protocol is not given")
StrandProtocol.NonSpecific
}
@@ -79,12 +79,12 @@ class Gentrap(val root: Configurable) extends QScript
"htseqcount" -> Map("stranded" -> (strandProtocol match {
case StrandProtocol.NonSpecific => "no"
case StrandProtocol.Dutp => "reverse"
- case otherwise => throw new IllegalStateException(otherwise.toString)
+ case otherwise => throw new IllegalStateException(otherwise.toString)
})),
"cufflinks" -> Map("library_type" -> (strandProtocol match {
case StrandProtocol.NonSpecific => "fr-unstranded"
case StrandProtocol.Dutp => "fr-firststrand"
- case otherwise => throw new IllegalStateException(otherwise.toString)
+ case otherwise => throw new IllegalStateException(otherwise.toString)
})),
"merge_strategy" -> "preprocessmergesam",
"gsnap" -> Map(
@@ -99,7 +99,7 @@ class Gentrap(val root: Configurable) extends QScript
"strand_specificity" -> (strandProtocol match {
case StrandProtocol.NonSpecific => StrandSpecificity.NONE.toString
case StrandProtocol.Dutp => StrandSpecificity.SECOND_READ_TRANSCRIPTION_STRAND.toString
- case otherwise => throw new IllegalStateException(otherwise.toString)
+ case otherwise => throw new IllegalStateException(otherwise.toString)
})
)
else Map()) ++ (if (ribosomalRefFlat != null) ribosomalRefFlat.map("ribosomal_intervals" -> _.getAbsolutePath).toList else Nil))