Merge branch 'feature-igvtools' into 'develop'

Feature igvtools

Using IGVtools `count` to create TDF or WIG files...

Need some more work - in next commits..

See merge request !73

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala

+/**
+ * Created by wyleung on 5-1-15.
+ */
+
+package nl.lumc.sasc.biopet.extensions.igvtools
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+
+abstract class IGVTools extends BiopetCommandLineFunction {
+  executable = config("exe", default = "igvtools", submodule = "igvtools", freeVar = false)
+  override def versionCommand = executable + " version"
+  override val versionRegex = """IGV Version: ([\d\.]) .*""".r
+  override val versionExitcode = List(0)
+}
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala

+
+package nl.lumc.sasc.biopet.extensions.igvtools
+
+import java.nio.file.InvalidPathException
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+import java.io.{ FileNotFoundException, File }
+
+/**
+ * IGVTools `count` wrapper
+ *
+ * @constructor create a new IGVTools instance from a `.bam` file
+ *
+ */
+
+class IGVToolsCount(val root: Configurable) extends IGVTools {
+  @Input(doc = "Bam File")
+  var input: File = _
+
+  @Input(doc = "<genome>.chrom.sizes File")
+  var genomeChromSizes: File = _
+
+  @Output
+  var tdf: Option[File] = _
+
+  @Output
+  var wig: Option[File] = _
+
+  var maxZoom: Option[Int] = config("maxZoom")
+  var windowSize: Option[Int] = config("windowSize")
+  var extFactor: Option[Int] = config("extFactor")
+
+  var preExtFactor: Option[Int] = config("preExtFactor")
+  var postExtFactor: Option[Int] = config("postExtFactor")
+
+  var windowFunctions: Option[String] = config("windowFunctions")
+  var strands: Option[String] = config("strands")
+  var bases: Boolean = config("bases", default = false)
+
+  var query: Option[String] = config("query")
+  var minMapQuality: Option[Int] = config("minMapQuality")
+  var includeDuplicates: Boolean = config("includeDuplicates", default = false)
+
+  var pairs: Boolean = config("pairs", default = false)
+
+  override def afterGraph {
+    super.afterGraph
+    if (!input.exists()) throw new FileNotFoundException("Input bam is required for IGVToolsCount")
+
+    if (!wig.isEmpty && !wig.get.getAbsolutePath.endsWith(".wig")) throw new IllegalArgumentException("Wiggle file should have a .wig file-extension")
+    if (!tdf.isEmpty && !tdf.get.getAbsolutePath.endsWith(".tdf")) throw new IllegalArgumentException("TDF file should have a .tdf file-extension")
+  }
+
+  def cmdLine = {
+    required(executable) +
+      required("count") +
+      optional("--maxZoom", maxZoom) +
+      optional("--windowSize", windowSize) +
+      optional("--extFactor", extFactor) +
+      optional("--preExtFactor", preExtFactor) +
+      optional("--postExtFactor", postExtFactor) +
+      optional("--windowFunctions", windowFunctions) +
+      optional("--strands", strands) +
+      conditional(bases, "--bases") +
+      optional("--query", query) +
+      optional("--minMapQuality", minMapQuality) +
+      conditional(includeDuplicates, "--includeDuplicates") +
+      conditional(pairs, "--pairs") +
+      required(input) +
+      required(outputArg) +
+      required(genomeChromSizes)
+  }
+
+  /**
+   * This part should never fail, these values are set within this wrapper
+   *
+   */
+  private def outputArg: String = {
+    (tdf, wig) match {
+      case (None, None)       => throw new IllegalArgumentException("Either TDF or WIG should be supplied");
+      case (Some(a), None)    => a.getAbsolutePath;
+      case (None, Some(b))    => b.getAbsolutePath;
+      case (Some(a), Some(b)) => a.getAbsolutePath + "," + b.getAbsolutePath;
+    }
+  }
+}
+
+object IGVToolsCount {
+  /**
+   * Create an object by specifying the `input` (.bam),
+   * and the `genomename` (hg18,hg19,mm10)
+   *
+   * @param input Bamfile to count reads from
+   * @return a new IGVToolsCount instance
+   * @throws FileNotFoundException bam File is not found
+   * @throws IllegalArgumentException tdf or wig not supplied
+   */
+  def apply(root: Configurable, input: File, genomeChromSizes: File): IGVToolsCount = {
+    val counting = new IGVToolsCount(root)
+    counting.input = input
+    counting.genomeChromSizes = genomeChromSizes
+    return counting
+  }
+}
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