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biopet.biopet
Commits
4639bd35
Commit
4639bd35
authored
Jan 13, 2015
by
Peter van 't Hof
Browse files
Added scala docs
parent
faf89169
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
View file @
4639bd35
...
...
@@ -22,6 +22,15 @@ class AnnotateVcfWithBed {
object
AnnotateVcfWithBed
extends
ToolCommand
{
/**
* Args for the commandline tool
* @param inputFile input vcf file
* @param bedFile bed file to annotate to vcf file
* @param outputFile output vcf file
* @param fieldName Info field that should be used
* @param fieldDescription Description at field if needed
* @param fieldType Type of filed, can be: "Integer", "Flag", "Character", "Float"
*/
case
class
Args
(
inputFile
:
File
=
null
,
bedFile
:
File
=
null
,
outputFile
:
File
=
null
,
...
...
@@ -50,6 +59,11 @@ object AnnotateVcfWithBed extends ToolCommand {
}
text
(
"Description of field in new vcf file"
)
}
/**
* Program will Annotate a vcf file with the overlapping regions of a bed file, 4e column of the bed file we in a info tag in the vcf file
*
* @param args
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
sys
.
exit
(
1
)
...
...
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