Added hisat2build extension

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala

+package nl.lumc.sasc.biopet.extensions.hisat
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.Input
+
+/**
+  * Created by pjvan_thof on 7-6-16.
+  */
+class Hisat2Build(val root: Configurable) extends BiopetCommandLineFunction with Version {
+
+  @Input(required = true)
+  var inputFasta: File = _
+
+  var hisat2IndexBase: String = _
+
+  @Input(required = false)
+  var snp: Option[File] = config("snp")
+
+  @Input(required = false)
+  var haplotype: Option[File] = config("haplotype")
+
+  @Input(required = false)
+  var ss: Option[File] = config("ss")
+
+  @Input(required = false)
+  var exon: Option[File] = config("exon")
+
+  executable = config("exe", default = "hisat2-build", freeVar = false)
+  def versionRegex = """.*hisat2-align-s version (.*)""".r
+  override def versionExitcode = List(0, 1)
+  def versionCommand = executable + " --version"
+
+  var bmax: Option[Int] = config("bmax")
+  var bmaxdivn: Option[Int] = config("bmaxdivn")
+  var dcv: Option[Int] = config("dcv")
+  var offrate: Option[Int] = config("offrate")
+  var ftabchars: Option[Int] = config("ftabchars")
+  var localoffrate: Option[Int] = config("localoffrate")
+  var localftabchars: Option[Int] = config("localftabchars")
+  var seed: Option[Int] = config("seed")
+
+  var large-index: Boolean = config("large-index", default = false)
+  var dcv: Boolean = config("dcv", default = false)
+  var memory-fitting: Boolean = config("memory-fitting", default = false)
+  var nodc: Boolean = config("nodc", default = false)
+  var noref: Boolean = config("noref", default = false)
+  var justref: Boolean = config("justref", default = false)
+  var quiet: Boolean = config("quiet", default = false)
+
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
+    val indexDir = new File(hisat2IndexBase).getParentFile
+    val indexName = new File(hisat2IndexBase).getName
+    jobOutputFile = new File(indexDir, s".$indexName.hisat2-build.out")
+  }
+
+  def cmdLine = required(executable) +
+    optional("--bmax", bmax) +
+    optional("--bmaxdivn", bmaxdivn) +
+    optional("--dcv", dcv) +
+    optional("--offrate", offrate) +
+    optional("--ftabchars", ftabchars) +
+    optional("--localoffrate", localoffrate) +
+    optional("--localftabchars", localftabchars) +
+    optional("--seed", seed) +
+    optional("--snp", snp) +
+    optional("--haplotype", haplotype) +
+    optional("--ss", ss) +
+    optional("--exon", exon) +
+    conditional(large-index, "--large-index") +
+    conditional(dcv, "--dcv") +
+    conditional(memory-fitting, "--memory-fitting") +
+    conditional(nodc, "--nodc") +
+    conditional(noref, "--noref") +
+    conditional(justref, "--justref") +
+    conditional(quiet, "--quiet") +
+    required(inputFasta) +
+    required(hisat2IndexBase)
+
+}