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biopet.biopet
Commits
672a25a8
Commit
672a25a8
authored
Mar 03, 2015
by
bow
Browse files
Add -f and -F flags to samtools view wrapper
parent
2b26dc69
Changes
1
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Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
View file @
672a25a8
...
...
@@ -29,10 +29,14 @@ class SamtoolsView(val root: Configurable) extends Samtools {
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"
)
def
cmdBase
=
required
(
executable
)
+
required
(
"view"
)
+
optional
(
"-q"
,
quality
)
+
optional
(
"-f"
,
f
)
+
optional
(
"-F"
,
F
)
+
conditional
(
b
,
"-b"
)
+
conditional
(
h
,
"-h"
)
def
cmdPipeInput
=
cmdBase
+
"-"
...
...
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