Commit d5906682 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Make prefix required

parent e77963db
...@@ -5,7 +5,7 @@ import java.io.File ...@@ -5,7 +5,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, ToolCommand } import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, ToolCommand }
import htsjdk.samtools.fastq.{ FastqRecord, AsyncFastqWriter, FastqReader, BasicFastqWriter } import htsjdk.samtools.fastq.{ FastqRecord, AsyncFastqWriter, FastqReader, BasicFastqWriter }
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input } import org.broadinstitute.gatk.utils.commandline.{ Argument, Output, Input }
import scala.collection.JavaConversions._ import scala.collection.JavaConversions._
/** /**
...@@ -17,10 +17,11 @@ class PrefixFastq(val root: Configurable) extends BiopetJavaCommandLineFunction ...@@ -17,10 +17,11 @@ class PrefixFastq(val root: Configurable) extends BiopetJavaCommandLineFunction
@Input(doc = "Input fastq", shortName = "I", required = true) @Input(doc = "Input fastq", shortName = "I", required = true)
var inputFastq: File = _ var inputFastq: File = _
@Output(doc = "Output fastq", shortName = "o", required = false) @Output(doc = "Output fastq", shortName = "o", required = true)
var outputFastq: File = _ var outputFastq: File = _
var prefixSeq = config("prefix_seq", default = "CATG") @Argument(doc = "Prefix seq", required = true)
var prefixSeq: String = _
override def commandLine = super.commandLine + override def commandLine = super.commandLine +
required("-i", inputFastq) + required("-i", inputFastq) +
...@@ -36,7 +37,7 @@ object PrefixFastq extends ToolCommand { ...@@ -36,7 +37,7 @@ object PrefixFastq extends ToolCommand {
return prefixFastq return prefixFastq
} }
case class Args(input: File = null, output: File = null, seq: String = "CATG") extends AbstractArgs case class Args(input: File = null, output: File = null, seq: String = null) extends AbstractArgs
class OptParser extends AbstractOptParser { class OptParser extends AbstractOptParser {
opt[File]('i', "input") required () maxOccurs (1) valueName ("<file>") action { (x, c) => opt[File]('i', "input") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
...@@ -45,7 +46,7 @@ object PrefixFastq extends ToolCommand { ...@@ -45,7 +46,7 @@ object PrefixFastq extends ToolCommand {
opt[File]('o', "output") required () maxOccurs (1) valueName ("<file>") action { (x, c) => opt[File]('o', "output") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
c.copy(output = x) c.copy(output = x)
} }
opt[String]('s', "seq") maxOccurs (1) valueName ("<prefix seq>") action { (x, c) => opt[String]('s', "seq") required () maxOccurs (1) valueName ("<prefix seq>") action { (x, c) =>
c.copy(seq = x) c.copy(seq = x)
} }
} }
......
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