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biopet.biopet
Commits
9e1bc3d0
Commit
9e1bc3d0
authored
Oct 13, 2014
by
Peter van 't Hof
Browse files
Fix args
parent
1d3bd651
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/CheckAllelesVcfInBam.scala
View file @
9e1bc3d0
...
...
@@ -38,15 +38,15 @@ object CheckAllelesVcfInBam extends ToolCommand {
case
class
Args
(
inputFile
:
File
=
null
,
outputFile
:
File
=
null
,
samples
:
List
[
String
]
=
Nil
,
bamFiles
:
List
[
File
]
=
Nil
,
minMapQual
:
Int
=
1
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
opt
[
File
](
'I'
,
"inputFile"
)
unbounded
()
required
()
maxOccurs
(
1
)
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
opt
[
File
](
'I'
,
"inputFile"
)
required
()
maxOccurs
(
1
)
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
inputFile
=
x
)
}
opt
[
File
](
'o'
,
"outputFile"
)
unbounded
()
required
()
maxOccurs
(
1
)
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
opt
[
File
](
'o'
,
"outputFile"
)
required
()
maxOccurs
(
1
)
valueName
(
"<file>"
)
action
{
(
x
,
c
)
=>
c
.
copy
(
outputFile
=
x
)
}
opt
[
String
](
's'
,
"sample"
)
unbounded
()
action
{
(
x
,
c
)
=>
opt
[
String
](
's'
,
"sample"
)
unbounded
()
minOccurs
(
1
)
action
{
(
x
,
c
)
=>
c
.
copy
(
samples
=
x
::
c
.
samples
)
}
opt
[
File
](
'b'
,
"bam"
)
unbounded
()
action
{
(
x
,
c
)
=>
opt
[
File
](
'b'
,
"bam"
)
unbounded
()
minOccurs
(
1
)
action
{
(
x
,
c
)
=>
c
.
copy
(
bamFiles
=
x
::
c
.
bamFiles
)
}
opt
[
Int
](
'm'
,
"min_mapping_quality"
)
unbounded
()
maxOccurs
(
1
)
action
{
(
x
,
c
)
=>
opt
[
Int
](
'm'
,
"min_mapping_quality"
)
maxOccurs
(
1
)
action
{
(
x
,
c
)
=>
c
.
copy
(
minMapQual
=
c
.
minMapQual
)
}
}
...
...
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