Added SamToFastq

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

+package nl.lumc.sasc.biopet.extensions.picard
+
+import java.io.File
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+
+class SamToFastq(val root: Configurable) extends Picard {
+  javaMainClass = "picard.sam.SortSam"
+
+  @Input(doc = "The input SAM or BAM files to analyze.", required = true)
+  var input: File = _
+
+  @Output(doc = "R1", required = true)
+  var fastqR1: File = _
+  
+  @Output(doc = "R1", required = false)
+  var fastqR2: File = _
+  
+  @Output(doc = "Unpaired", required = false)
+  var fastqUnpaired: File = _
+  
+  @Argument(doc = "Output per readgroup", required = false)
+  var outputPerRg: Boolean = config("outputPerRg", default = false)
+  
+  @Argument(doc = "Output dir", required = false)
+  var outputDir: String = config("outputDir")
+  
+  @Argument(doc = "re reverse", required = false)
+  var reReverse: Boolean = config("reReverse", default = false)
+  
+  @Argument(doc = "The output file to bam file to", required = false)
+  var interleave: Boolean = config("interleave", default = false)
+  
+  @Argument(doc = "includeNonPjReads", required = false)
+  var includeNonPjReads: Boolean = config("includeNonPjReads", default = false)
+  
+  @Argument(doc = "clippingAtribute", required = false)
+  var clippingAtribute: String = config("clippingAtribute")
+  
+  @Argument(doc = "clippingAction", required = false)
+  var clippingAction: String = config("clippingAction")
+  
+  @Argument(doc = "read1Trim", required = false)
+  var read1Trim: Option[Int] = config("read1Trim")
+  
+  @Argument(doc = "read1MaxBasesToWrite", required = false)
+  var read1MaxBasesToWrite: Option[Int] = config("read1MaxBasesToWrite")
+  
+  @Argument(doc = "read2Trim", required = false)
+  var read2Trim: Option[Int] = config("read2Trim")
+  
+  @Argument(doc = "read2MaxBasesToWrite", required = false)
+  var read2MaxBasesToWrite: Option[Int] = config("read2MaxBasesToWrite")
+  
+  @Argument(doc = "includeNonPrimaryAlignments", required = false)
+  var includeNonPrimaryAlignments: Boolean = config("includeNonPrimaryAlignments", default = false)
+
+  override def commandLine = super.commandLine +
+    required("INPUT=", input, spaceSeparated = false) +
+    required("FASTQ=", fastqR1, spaceSeparated = false) +
+    optional("SECOND_END_FASTQ=", fastqR2, spaceSeparated = false) +
+    optional("UNPAIRED_FASTQ=", fastqUnpaired, spaceSeparated = false) +
+    conditional(outputPerRg, "OUTPUT_PER_RG=TRUE") +
+    optional("OUTPUT_DIR=", outputDir, spaceSeparated = false) +
+    conditional(reReverse, "RE_REVERSE=TRUE") +
+    conditional(interleave, "INTERLEAVE=TRUE") +
+    conditional(includeNonPjReads, "INCLUDE_NON_PF_READS=TRUE") +
+    optional("CLIPPING_ATTRIBUTE=", clippingAtribute, spaceSeparated = false) +
+    optional("CLIPPING_ACTION=", clippingAction, spaceSeparated = false) +
+    optional("READ1_TRIM=", read1Trim, spaceSeparated = false) +
+    optional("READ1_MAX_BASES_TO_WRITE=", read1MaxBasesToWrite, spaceSeparated = false) +
+    optional("READ2_TRIM=", read2Trim, spaceSeparated = false) +
+    optional("READ2_MAX_BASES_TO_WRITE=", read2MaxBasesToWrite, spaceSeparated = false) +
+    conditional(includeNonPrimaryAlignments, "INCLUDE_NON_PRIMARY_ALIGNMENTS=TRUE")
+}
+
+object SamToFastq {
+  def apply(root: Configurable, input: File, fastqR1: File, fastqR2: File = null): SamToFastq = {
+    val samToFastq = new SamToFastq(root)
+    samToFastq.input = input
+    samToFastq.fastqR1 = fastqR1
+    samToFastq.fastqR2 = fastqR2
+    return samToFastq
+  }
+}
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