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biopet.biopet
Commits
1c419d6e
Commit
1c419d6e
authored
Mar 27, 2017
by
Peter van 't Hof
Browse files
Fixing pipe command
(cherry picked from commit
e4baa723
)
parent
3019cf79
Changes
1
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
View file @
1c419d6e
...
...
@@ -34,17 +34,19 @@ class SamtoolsView(val root: Configurable) extends Samtools {
var
F
:
List
[
String
]
=
config
(
"F"
,
default
=
List
.
empty
[
String
])
def
cmdBase
=
required
(
executable
)
+
@Input
(
required
=
false
)
var
L
:
Option
[
File
]
=
None
def
cmdLine
=
required
(
executable
)
+
required
(
"view"
)
+
optional
(
"-q"
,
q
)
+
optional
(
"-L"
,
L
)
+
repeat
(
"-f"
,
f
)
+
repeat
(
"-F"
,
F
)
+
conditional
(
b
,
"-b"
)
+
conditional
(
h
,
"-h"
)
def
cmdPipeInput
=
cmdBase
+
"-"
def
cmdPipe
=
cmdBase
+
required
(
input
)
/** Returns command to execute */
def
cmdLine
=
cmdPipe
+
" > "
+
required
(
output
)
conditional
(
h
,
"-h"
)
+
(
if
(
inputAsStdin
)
"-"
else
required
(
input
))
+
(
if
(
outputAsStsout
)
""
else
" > "
+
required
(
output
))
}
object
SamtoolsView
{
...
...
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