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biopet.biopet
Commits
566bfacd
Commit
566bfacd
authored
Mar 03, 2015
by
bow
Browse files
Supply default arguments to samtools view wrapper
parent
d205c898
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
View file @
566bfacd
...
...
@@ -21,16 +21,16 @@ import java.io.File
class
SamtoolsView
(
val
root
:
Configurable
)
extends
Samtools
{
@Input
(
doc
=
"Bam File"
)
var
input
:
File
=
_
var
input
:
File
=
null
@Output
(
doc
=
"output File"
)
var
output
:
File
=
_
var
output
:
File
=
null
var
quality
:
Option
[
Int
]
=
config
(
"quality"
)
var
b
:
Boolean
=
config
(
"b"
)
var
h
:
Boolean
=
config
(
"h"
)
var
f
:
List
[
String
]
=
config
(
"f"
)
var
F
:
List
[
String
]
=
config
(
"F"
)
var
b
:
Boolean
=
config
(
"b"
,
default
=
false
)
var
h
:
Boolean
=
config
(
"h"
,
default
=
false
)
var
f
:
List
[
String
]
=
config
(
"f"
,
default
=
List
.
empty
[
String
]
)
var
F
:
List
[
String
]
=
config
(
"F"
,
default
=
List
.
empty
[
String
]
)
def
cmdBase
=
required
(
executable
)
+
required
(
"view"
)
+
...
...
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