Commit dfc55377 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added scala docs

parent 64f71be7
......@@ -30,6 +30,10 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
memoryLimit = config("memory_limit")
}
/**
* Creates command to execute extension
* @return
*/
override def commandLine: String = {
preCmdInternal
val cmd = super.commandLine
......
......@@ -9,6 +9,8 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Output, Input }
import scala.collection.JavaConversions._
/**
* Queue class for PrefixFastq tool
*
* Created by pjvan_thof on 1/13/15.
*/
class PrefixFastq(val root: Configurable) extends BiopetJavaCommandLineFunction {
......@@ -23,6 +25,10 @@ class PrefixFastq(val root: Configurable) extends BiopetJavaCommandLineFunction
@Argument(doc = "Prefix seq", required = true)
var prefixSeq: String = _
/**
* Creates command to execute extension
* @return
*/
override def commandLine = super.commandLine +
required("-i", inputFastq) +
required("-o", outputFastq) +
......@@ -30,6 +36,14 @@ class PrefixFastq(val root: Configurable) extends BiopetJavaCommandLineFunction
}
object PrefixFastq extends ToolCommand {
/**
* Create a PrefixFastq class object with a sufix ".prefix.fastq" in the output folder
*
* @param root parent object
* @param input input file
* @param outputDir outputFolder
* @return PrefixFastq class object
*/
def apply(root: Configurable, input: File, outputDir: String): PrefixFastq = {
val prefixFastq = new PrefixFastq(root)
prefixFastq.inputFastq = input
......@@ -37,6 +51,12 @@ object PrefixFastq extends ToolCommand {
return prefixFastq
}
/**
* Args for commandline program
* @param input input fastq file (can be zipper)
* @param output output fastq file (can be zipper)
* @param seq Seq to prefix the reads with
*/
case class Args(input: File = null, output: File = null, seq: String = null) extends AbstractArgs
class OptParser extends AbstractOptParser {
......@@ -52,6 +72,8 @@ object PrefixFastq extends ToolCommand {
}
/**
* Program will prefix reads with a given seq
*
* @param args the command line arguments
*/
def main(args: Array[String]): Unit = {
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment