BcfTools View extension

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala

+package nl.lumc.sasc.biopet.extensions.bcftools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Argument, Output, Input}
+
+/**
+ * Created by ahbbollen on 12-10-15.
+ */
+class BcftoolsView(val root: Configurable) extends Bcftools {
+
+  @Input(doc = "Input VCF file")
+  var input: File = _
+
+  @Output(doc = "Output file")
+  var output: File = _
+
+  @Argument(doc = "drop individual genotypes")
+  var dropGenotype: Boolean = false
+
+  @Argument(doc = "header only")
+  var headerOnly: Boolean = false
+
+  @Argument(doc = "Compression level")
+  var compressionLevel: Int = 9
+
+  @Argument(doc = "output type")
+  var outputType: String = "z"
+
+  @Argument(doc = "regions")
+  var regions: String = _
+
+  @Argument(doc = "region file")
+  var regionFile: File = _
+
+  @Argument(doc = "targets")
+  var targets: String = _
+
+  @Argument(doc = "targets file")
+  var targetFile: File = _
+
+  @Argument(doc = "trim alt alleles")
+  var trimAltAlleles: Boolean = false
+
+  @Argument(doc = "no update")
+  var noUpdate: Boolean = false
+
+  @Argument(doc = "samples")
+  var samples: List[String] = Nil
+
+  @Argument(doc = "samples file")
+  var sampleFile: File = _
+
+  @Argument(doc = "minimum allele count")
+  var minAC: Int = _
+
+  @Argument(doc = "max allele count")
+  var maxAC: Int = _
+
+  @Argument(doc = "exclude (expression)")
+  var exclude: String = _
+
+  @Argument(doc = "apply filters")
+  var applyFilters: List[String] = Nil
+
+  @Argument(doc = "genotype")
+  var genotype: String = _
+
+  @Argument(doc = "include (expression)")
+  var include: String = _
+
+  @Argument(doc = "Known (ID field is not .) only")
+  var known: Boolean = false
+
+  @Argument(doc = "min alleles")
+  var minAlleles: Int = _
+
+  @Argument(doc = "max alleles")
+  var maxAlleles: Int = _
+
+  @Argument(doc = "novel (ID field is .) only")
+  var novel: Boolean = false
+
+  @Argument(doc = "phased only")
+  var phased: Boolean = false
+
+  @Argument(doc = "exclude phased (only)")
+  var excludePhased: Boolean = false
+
+  @Argument(doc = "min allele frequency")
+  var minAF: Int = _
+
+  @Argument(doc = "max allele frequency")
+  var maxAF: Int = _
+
+  @Argument(doc = "uncalled only")
+  var uncalled: Boolean = false
+
+  @Argument(doc = "exclude uncalled (only)")
+  var excludeUncalled: Boolean = false
+
+  @Argument(doc = "types")
+  var types: String = _
+
+  @Argument(doc = "exclude types")
+  var excludeTypes: String = _
+
+  @Argument(doc = "private (requires samples)")
+  var onlyPrivate: Boolean = false
+
+  @Argument(doc = "Exclude privates")
+  var excludePrivate: Boolean = false
+
+
+
+  override def beforeGraph() = {
+    super.beforeGraph()
+
+    require((compressionLevel <= 9) && (compressionLevel >= 0))
+    require(
+      (outputType.length == 1) &&
+        (outputType == "z" || outputType == "b" || outputType == "u" || outputType == "v")
+    )
+  }
+
+  def baseCmd = {
+    executable + conditional(dropGenotype, "-G") + conditional(headerOnly, "-h") +
+    required("-l", compressionLevel) + required("-O", outputType) +
+    optional("-r", regions) + optional("-R", regionFile) +
+    optional("-t", targets) + optional("-T", targetFile) +
+    conditional(trimAltAlleles, "-a") + conditional(noUpdate, "-I") +
+    repeat("-s", samples) + optional("-S", sampleFile) +
+    optional("-c", minAC) + optional("-C", maxAC) +
+    optional("-e", exclude) + optional("-f", applyFilters) +
+    optional("-g", genotype) + optional("-i", include) +
+    conditional(known, "-k") + optional("-m", minAlleles) +
+    optional("-M", maxAlleles) + conditional(novel, "-n") +
+    conditional(phased, "-p") + conditional(excludePhased, "-P") +
+    optional("-q", minAF) + optional("-Q", maxAF) +
+    conditional(uncalled, "-u") + conditional(excludeUncalled, "-U") +
+    optional("-v", types) + conditional(onlyPrivate, "-x") +
+    conditional(excludePrivate, "-X")
+  }
+
+  def cmdPipeInput = {
+    baseCmd + "-"
+  }
+
+  def cmdPipe = {
+    baseCmd + required(input)
+  }
+
+  def cmdLine = {
+    baseCmd + required("-o", output) + required(input)
+  }
+
+}