diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala new file mode 100644 index 0000000000000000000000000000000000000000..2faef859c3780ae842b24e478950be065f45a1cb --- /dev/null +++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala @@ -0,0 +1,36 @@ +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.{Output, Input} + +/** + * Created by pjvan_thof on 4/15/15. + */ +class BedToIntervalList(val root: Configurable) extends Picard { + javaMainClass = new picard.util.BedToIntervalList().getClass.getName + + @Input(doc = "Input bed file", required = true) + var input: File = null + + @Input(doc = "Reference dict file", required = true) + var dict: File = new File(config("reference").asString.stripSuffix(".fa").stripSuffix(".fasta") + ".dict") + + @Output(doc = "Output interval list", required = true) + var output: File = null + + override def commandLine = super.commandLine + + required("SEQUENCE_DICTIONARY=", dict, spaceSeparated = false) + + required("INPUT=", input, spaceSeparated = false) + + required("OUTPUT=", output, spaceSeparated = false) +} + +object BedToIntervalList { + def apply(root:Configurable, input:File, output:File): BedToIntervalList = { + val bi = new BedToIntervalList(root) + bi.input = input + bi.output = output + bi + } +} \ No newline at end of file