Adding scala docs

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala

@@ -25,7 +25,7 @@ import scala.io.Source
 /**
  * General picard extension
  *
- * This is based on using class files directly from the jar
+ * This is based on using class files directly from the jar, if needed other picard jar can be used
  */
 abstract class Picard extends BiopetJavaCommandLineFunction {
   override def subPath = "picard" :: super.subPath

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.sambamba
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 
+/** General Sambamba extension */
 abstract class Sambamba extends BiopetCommandLineFunction {
   override val defaultVmem = "4G"
   override val defaultThreads = 2

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala

@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
+/** Extension for sambemba flagstat  */
 class SambambaFlagstat(val root: Configurable) extends Sambamba {
   override val defaultThreads = 2
 
@@ -28,6 +29,7 @@ class SambambaFlagstat(val root: Configurable) extends Sambamba {
   @Output(doc = "output File")
   var output: File = _
 
+  /** Returns command to execute */
   def cmdLine = required(executable) +
     required("flagstat") +
     optional("-t", nCoresRequest) +
@@ -35,24 +37,3 @@ class SambambaFlagstat(val root: Configurable) extends Sambamba {
     " > " +
     required(output)
 }
-
-object SambambaFlagstat {
-  def apply(root: Configurable, input: File, output: File): SambambaFlagstat = {
-    val flagstat = new SambambaFlagstat(root)
-    flagstat.input = input
-    flagstat.output = output
-    return flagstat
-  }
-
-  def apply(root: Configurable, input: File, outputDir: String): SambambaFlagstat = {
-    val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
-    val outputFile = new File(dir + swapExtension(input.getName))
-    return apply(root, input, outputFile)
-  }
-
-  def apply(root: Configurable, input: File): SambambaFlagstat = {
-    return apply(root, input, new File(swapExtension(input.getAbsolutePath)))
-  }
-
-  private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".flagstat"
-}
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala

@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
+/** Extension for sambemba index  */
 class SambambaIndex(val root: Configurable) extends Sambamba {
   override val defaultThreads = 2
 
@@ -28,30 +29,10 @@ class SambambaIndex(val root: Configurable) extends Sambamba {
   @Output(doc = "Output .bai file to")
   var output: File = _
 
+  /** Returns command to execute */
   def cmdLine = required(executable) +
     required("index") +
     optional("-t", nCoresRequest) +
     required(input) +
     required(output)
 }
-
-object SambambaIndex {
-  def apply(root: Configurable, input: File, output: File): SambambaIndex = {
-    val flagstat = new SambambaIndex(root)
-    flagstat.input = input
-    flagstat.output = output
-    return flagstat
-  }
-
-  def apply(root: Configurable, input: File, outputDir: String): SambambaIndex = {
-    val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
-    val outputFile = new File(dir + swapExtension(input.getName))
-    return apply(root, input, outputFile)
-  }
-
-  def apply(root: Configurable, input: File): SambambaIndex = {
-    return apply(root, input, new File(swapExtension(input.getAbsolutePath)))
-  }
-
-  private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".bam.bai"
-}
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala

@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
+/** Extension for sambemba markdup  */
 class SambambaMarkdup(val root: Configurable) extends Sambamba {
   override val defaultThreads = 4
 
@@ -36,6 +37,7 @@ class SambambaMarkdup(val root: Configurable) extends Sambamba {
   val overflow_list_size: Option[Int] = config("overflow-list-size", default = 200000)
   val io_buffer_size: Option[Int] = config("io-buffer-size", default = 128)
 
+  /** Returns command to execute */
   def cmdLine = required(executable) +
     required("markdup") +
     conditional(remove_duplicates, "--remove-duplicates") +
@@ -47,24 +49,3 @@ class SambambaMarkdup(val root: Configurable) extends Sambamba {
     required(input) +
     required(output)
 }
-
-object SambambaMarkdup {
-  def apply(root: Configurable, input: File, output: File): SambambaMarkdup = {
-    val flagstat = new SambambaMarkdup(root)
-    flagstat.input = input
-    flagstat.output = output
-    return flagstat
-  }
-
-  def apply(root: Configurable, input: File, outputDir: String): SambambaMarkdup = {
-    val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
-    val outputFile = new File(dir + swapExtension(input.getName))
-    return apply(root, input, outputFile)
-  }
-
-  def apply(root: Configurable, input: File): SambambaMarkdup = {
-    return apply(root, input, new File(swapExtension(input.getAbsolutePath)))
-  }
-
-  private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".bam.bai"
-}
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala

@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
+/** Extension for sambemba merge  */
 class SambambaMerge(val root: Configurable) extends Sambamba {
   override val defaultThreads = 4
 
@@ -31,6 +32,7 @@ class SambambaMerge(val root: Configurable) extends Sambamba {
   // @doc: compression_level 6 is average, 0 = no compression, 9 = best
   val compression_level: Option[Int] = config("compression_level", default = 6)
 
+  /** Returns command to execute */
   def cmdLine = required(executable) +
     required("merge") +
     optional("-t", nCoresRequest) +
@@ -38,36 +40,3 @@ class SambambaMerge(val root: Configurable) extends Sambamba {
     required(output) +
     repeat("", input)
 }
-
-object SambambaMerge {
-  def apply(root: Configurable, input: List[File], output: File): SambambaMerge = {
-    val flagstat = new SambambaMerge(root)
-    flagstat.input = input
-    flagstat.output = output
-    return flagstat
-  }
-
-  def apply(root: Configurable, input: List[File], outputDir: String): SambambaMerge = {
-    val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
-    val outputFile = new File(dir + swapExtension(input.head.getName))
-    return apply(root, input, outputFile)
-  }
-
-  def apply(root: Configurable, input: List[File]): SambambaMerge = {
-    return apply(root, input, new File(swapExtension(input.head.getAbsolutePath)))
-  }
-
-  private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".merge.bam"
-}
-
-//
-//object MergeSamFiles {
-//  def apply(root: Configurable, input: List[File], outputDir: String, sortOrder: String = null): MergeSamFiles = {
-//    val mergeSamFiles = new MergeSamFiles(root)
-//    mergeSamFiles.input = input
-//    mergeSamFiles.output = new File(outputDir, input.head.getName.stripSuffix(".bam").stripSuffix(".sam") + ".merge.bam")
-//    if (sortOrder == null) mergeSamFiles.sortOrder = "coordinate"
-//    else mergeSamFiles.sortOrder = sortOrder
-//    return mergeSamFiles
-//  }
-//}
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.samtools
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 
+/** General class for samtools extensions */
 abstract class Samtools extends BiopetCommandLineFunction {
   override def subPath = "samtools" :: super.subPath
   executable = config("exe", default = "samtools")

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala

@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
+/** Extension for samtools flagstat */
 class SamtoolsFlagstat(val root: Configurable) extends Samtools {
   @Input(doc = "Bam File")
   var input: File = _
@@ -26,6 +27,7 @@ class SamtoolsFlagstat(val root: Configurable) extends Samtools {
   @Output(doc = "output File")
   var output: File = _
 
+  /** Returns command to execute */
   def cmdLine = required(executable) + required("flagstat") + required(input) + " > " + required(output)
 }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala

@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
+/** Extension for samtools mpileup */
 class SamtoolsMpileup(val root: Configurable) extends Samtools {
   @Input(doc = "Bam File")
   var input: File = _
@@ -45,6 +46,8 @@ class SamtoolsMpileup(val root: Configurable) extends Samtools {
     conditional(disableBaq, "-B")
   def cmdPipeInput = cmdBase + "-"
   def cmdPipe = cmdBase + required(input)
+
+  /** Returns command to execute */
   def cmdLine = cmdPipe + " > " + required(output)
 }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala

@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
+/** Extension for samtools view */
 class SamtoolsView(val root: Configurable) extends Samtools {
   @Input(doc = "Bam File")
   var input: File = _
@@ -37,6 +38,8 @@ class SamtoolsView(val root: Configurable) extends Samtools {
     conditional(h, "-h")
   def cmdPipeInput = cmdBase + "-"
   def cmdPipe = cmdBase + required(input)
+
+  /** Returns command to execute */
   def cmdLine = cmdPipe + " > " + required(output)
 }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala

@@ -17,9 +17,7 @@ package nl.lumc.sasc.biopet.extensions.seqtk
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 
-/**
- * Abstract class for all seqtk wrappers.
- */
+/** Abstract class for all seqtk wrappers. */
 abstract class Seqtk extends BiopetCommandLineFunction {
   override def subPath = "seqtk" :: super.subPath
   executable = config("exe", default = "seqtk", freeVar = true)