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biopet.biopet
Commits
d45432ba
Commit
d45432ba
authored
Mar 27, 2015
by
Sander Bollen
Browse files
Change variables to proper camelCase
parent
4a553316
Changes
1
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Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VCFWithVCF.scala
View file @
d45432ba
...
...
@@ -18,7 +18,7 @@ object VCFWithVCF extends ToolCommand {
case
class
Args
(
inputFile
:
File
=
null
,
outputFile
:
File
=
null
,
secondaryV
CF
:
File
=
null
,
secondaryV
cf
:
File
=
null
,
fields
:
List
[
Fields
]
=
Nil
,
matchAllele
:
Boolean
=
true
)
extends
AbstractArgs
...
...
@@ -29,8 +29,8 @@ object VCFWithVCF extends ToolCommand {
opt
[
File
](
'O'
,
"outputFile"
)
required
()
maxOccurs
(
1
)
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
outputFile
=
x
)
}
opt
[
File
](
'S'
,
"SecondaryV
CF
"
)
required
()
maxOccurs
(
1
)
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
secondaryV
CF
=
x
)
opt
[
File
](
'S'
,
"SecondaryV
cf
"
)
required
()
maxOccurs
(
1
)
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
secondaryV
cf
=
x
)
}
opt
[
String
](
'f'
,
"field"
)
unbounded
()
valueName
(
"<input_field:output_field>"
)
action
{
(
x
,
c
)
=>
val
values
=
x
.
split
(
":"
)
...
...
@@ -47,7 +47,7 @@ object VCFWithVCF extends ToolCommand {
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
sys
.
exit
(
1
)
val
reader
=
new
VCFFileReader
(
commandArgs
.
inputFile
)
val
secondaryReader
=
new
VCFFileReader
(
commandArgs
.
secondaryV
CF
)
val
secondaryReader
=
new
VCFFileReader
(
commandArgs
.
secondaryV
cf
)
val
header
=
reader
.
getFileHeader
val
secondHeader
=
secondaryReader
.
getFileHeader
...
...
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