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biopet.biopet
Commits
50feeba1
Commit
50feeba1
authored
Jan 13, 2015
by
Peter van 't Hof
Browse files
Added scala docs
parent
62b94624
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
View file @
50feeba1
...
...
@@ -23,6 +23,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
/**
* Queue extension for the FastqSplitter
* @param root Parent object
*/
class
FastqSplitter
(
val
root
:
Configurable
)
extends
BiopetJavaCommandLineFunction
{
javaMainClass
=
getClass
.
getName
...
...
@@ -35,10 +39,20 @@ class FastqSplitter(val root: Configurable) extends BiopetJavaCommandLineFunctio
override
val
defaultVmem
=
"8G"
memoryLimit
=
Option
(
4.0
)
/**
* Generate command to execute
* @return
*/
override
def
commandLine
=
super
.
commandLine
+
required
(
"-I"
,
input
)
+
repeat
(
"-o"
,
output
)
}
object
FastqSplitter
extends
ToolCommand
{
/**
* Arg for commandline program
* @param inputFile input fastq file
* @param outputFile output fastq files
*/
case
class
Args
(
inputFile
:
File
=
null
,
outputFile
:
List
[
File
]
=
Nil
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
...
...
@@ -51,6 +65,8 @@ object FastqSplitter extends ToolCommand {
}
/**
* Program will split fastq file in multiple fastq files
*
* @param args the command line arguments
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
...
...
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