Format fixes

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -16,13 +16,13 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.annotations.{AnnotationRefFlat, RibosomalRefFlat}
+import nl.lumc.sasc.biopet.core.annotations.{ AnnotationRefFlat, RibosomalRefFlat }
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{BiopetFifoPipe, PipelineCommand, Reference, SampleLibraryTag}
-import nl.lumc.sasc.biopet.extensions.bedtools.{BedtoolsCoverage, BedtoolsIntersect, BedtoolsSort}
+import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, Reference, SampleLibraryTag }
+import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect, BedtoolsSort }
 import nl.lumc.sasc.biopet.extensions.picard._
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
-import nl.lumc.sasc.biopet.extensions.tools.{BamStats, BiopetFlagstat}
+import nl.lumc.sasc.biopet.extensions.tools.{ BamStats, BiopetFlagstat }
 import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.intervals.BedCheck

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -183,8 +183,9 @@ object BammetricsReport extends ReportBuilder {
     )
 
     val tables = getSampleLibraries(summary, sampleId, libId, libraryLevel)
-      .map { case (sample, lib) =>
-        getTableFromSummary(summary, paths(lib.map(l => s"$sample-$l").getOrElse(sample)), Some(sample), lib)
+      .map {
+        case (sample, lib) =>
+          getTableFromSummary(summary, paths(lib.map(l => s"$sample-$l").getOrElse(sample)), Some(sample), lib)
       }
     writeTableToTsv(tsvFile, mergeTables(tables.toArray, "insert_size"), "insert_size")
 
@@ -219,8 +220,9 @@ object BammetricsReport extends ReportBuilder {
     )
 
     val tables = getSampleLibraries(summary, sampleId, libId, libraryLevel)
-      .map { case (sample, lib) =>
-        getTableFromSummary(summary, paths(lib.map(l => s"$sample-$l").getOrElse(sample)), Some(sample), lib)
+      .map {
+        case (sample, lib) =>
+          getTableFromSummary(summary, paths(lib.map(l => s"$sample-$l").getOrElse(sample)), Some(sample), lib)
       }
     writeTableToTsv(tsvFile, mergeTables(tables.toArray, "coverage"), "coverage")
 
@@ -255,8 +257,9 @@ object BammetricsReport extends ReportBuilder {
     )
 
     val tables = getSampleLibraries(summary, sampleId, libId, libraryLevel)
-      .map { case (sample, lib) =>
-        getTableFromSummary(summary, paths(lib.map(l => s"$sample-$l").getOrElse(sample)), Some(sample), lib)
+      .map {
+        case (sample, lib) =>
+          getTableFromSummary(summary, paths(lib.map(l => s"$sample-$l").getOrElse(sample)), Some(sample), lib)
       }
     writeTableToTsv(tsvFile, mergeTables(tables.toArray, "normalized_position"), "normalized_position")
 
@@ -281,10 +284,11 @@ object BammetricsReport extends ReportBuilder {
                           paths: Map[String, List[String]],
                           sampleId: Option[String] = None,
                           libId: Option[String] = None): Map[String, Array[Any]] = {
-    val pathValues: Map[String, Array[Any]] = paths.map { case (key, path) =>
-      val value = summary.getValueAsArray(sampleId, libId, path:_*)
-      require(value.isDefined, s"Sample: $sampleId, library: $libId on path: '${path.mkString(",")}' does not exist in summary")
-      key -> value.get
+    val pathValues: Map[String, Array[Any]] = paths.map {
+      case (key, path) =>
+        val value = summary.getValueAsArray(sampleId, libId, path: _*)
+        require(value.isDefined, s"Sample: $sampleId, library: $libId on path: '${path.mkString(",")}' does not exist in summary")
+        key -> value.get
     }
     require(pathValues.map(_._2.size).toList.distinct == 1, s"Arrays in summary does not have the same number of values, $paths")
     pathValues
@@ -303,8 +307,9 @@ object BammetricsReport extends ReportBuilder {
     val keys = table.keys.filterNot(_ == firstColumn).toList.sorted
     val writer = new PrintWriter(tsvFile)
     writer.println((firstColumn :: keys).mkString("\t"))
-    table(firstColumn).zipWithIndex.foreach { case (c, i) =>
-      writer.println((c :: keys.map(x => table(x)(i))).mkString("\t"))
+    table(firstColumn).zipWithIndex.foreach {
+      case (c, i) =>
+        writer.println((c :: keys.map(x => table(x)(i))).mkString("\t"))
     }
     writer.close()
   }

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BamStats.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.tools
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.summary.Summarizable
-import nl.lumc.sasc.biopet.core.{Reference, ToolCommandFunction}
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFunction }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.Input
@@ -12,8 +12,8 @@ import scala.collection.JavaConversions._
 import scala.io.Source
 
 /**
-  * Created by pjvanthof on 18/11/2016.
-  */
+ * Created by pjvanthof on 18/11/2016.
+ */
 class BamStats(val root: Configurable) extends ToolCommandFunction with Reference with Summarizable {
   def toolObject = nl.lumc.sasc.biopet.tools.bamstats.BamStats
 
@@ -35,7 +35,7 @@ class BamStats(val root: Configurable) extends ToolCommandFunction with Referenc
   def getOutputFile(name: String, contig: Option[String] = None): File = {
     contig match {
       case Some(contig) => new File(outputDir, "contigs" + File.separator + contig + File.separator + name)
-      case _ => new File(outputDir, name)
+      case _            => new File(outputDir, name)
     }
   }
 
@@ -57,7 +57,6 @@ class BamStats(val root: Configurable) extends ToolCommandFunction with Referenc
     optional("--binSize", binSize) +
     optional("--threadBinSize", threadBinSize)
 
-
   def summaryFiles: Map[String, File] = Map()
 
   def summaryStats: Map[String, Any] = Map(

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala

@@ -80,7 +80,7 @@ class Summary(file: File) {
 
   /** Get value on nested path with prefix depending is sampleId and/or libId is None or not */
   def getValueAsArray(sampleId: Option[String], libId: Option[String], path: String*): Option[Array[Any]] = {
-    this.getValue(sampleId, libId, path:_*).map(ConfigUtils.any2list(_).toArray)
+    this.getValue(sampleId, libId, path: _*).map(ConfigUtils.any2list(_).toArray)
   }
 
   /**