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biopet.biopet
Commits
e58842e5
Commit
e58842e5
authored
Jul 27, 2015
by
Peter van 't Hof
Browse files
Fix args
parent
bcfaa188
Changes
2
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Inline
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
View file @
e58842e5
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.breakdancer
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
Reference
,
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
BiopetQScript
,
PipelineCommand
}
import
org.broadinstitute.gatk.queue.QScript
/// Breakdancer is actually a mini pipeline executing binaries from the breakdancer package
...
...
@@ -47,7 +47,6 @@ class Breakdancer(val root: Configurable) extends QScript with BiopetQScript wit
}
override
def
init
()
:
Unit
=
{
}
def
biopetScript
()
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
View file @
e58842e5
...
...
@@ -51,8 +51,8 @@ class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunctio
var
x
:
Option
[
Int
]
=
config
(
"x"
,
default
=
1000
)
var
b
:
Option
[
Int
]
=
config
(
"b"
,
default
=
100
)
var
t
:
Boolean
=
config
(
"t"
,
default
=
false
)
var
d
:
String
=
config
(
"d"
)
var
g
:
String
=
config
(
"g"
)
var
d
:
Option
[
String
]
=
config
(
"d"
)
var
g
:
Option
[
String
]
=
config
(
"g"
)
var
l
:
Boolean
=
config
(
"l"
,
default
=
false
)
var
a
:
Boolean
=
config
(
"a"
,
default
=
false
)
var
h
:
Boolean
=
config
(
"h"
,
default
=
false
)
...
...
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