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biopet.biopet
Commits
dfc55377
Commit
dfc55377
authored
Jan 13, 2015
by
Peter van 't Hof
Browse files
Added scala docs
parent
64f71be7
Changes
2
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
View file @
dfc55377
...
...
@@ -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
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
View file @
dfc55377
...
...
@@ -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
=
{
...
...
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