Commit ba3725c3 authored by pjvan_thof's avatar pjvan_thof
Browse files

Fix compile errors

parent 3835e14b
......@@ -20,7 +20,7 @@ package nl.lumc.sasc.biopet.extensions.clever
import java.io.{File, PrintWriter}
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.utils.ToolCommand
import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
......@@ -48,9 +48,8 @@ class CleverFixVCF(val parent: Configurable) extends BiopetJavaCommandLineFuncti
object CleverFixVCF extends ToolCommand {
case class Args(inputVCF: File = null, sampleLabel: String = "", outputVCF: File = null)
extends AbstractArgs
class OptParser extends AbstractOptParser {
class OptParser extends AbstractOptParser[Args](commandName) {
opt[File]('i', "inputvcf") required () valueName "<vcffile/path>" action { (x, c) =>
c.copy(inputVCF = x)
} text "Please specify the input Clever VCF file"
......
......@@ -18,7 +18,7 @@ import java.io.{File, PrintWriter}
import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.{BamUtils, ToolCommand}
import nl.lumc.sasc.biopet.utils.{AbstractOptParser, BamUtils, ToolCommand}
import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
class PindelConfig(val parent: Configurable) extends BiopetJavaCommandLineFunction {
......@@ -46,9 +46,8 @@ object PindelConfig extends ToolCommand {
sampleLabel: Option[String] = None,
insertSize: Option[Int] = None,
output: Option[File] = None)
extends AbstractArgs
class OptParser extends AbstractOptParser {
class OptParser extends AbstractOptParser[Args](commandName) {
opt[File]('i', "inputbam") required () valueName "<bamfile/path>" action { (x, c) =>
c.copy(inputBam = x)
} text "Please specify the input bam file"
......
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