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biopet.biopet
Commits
4a9966de
Commit
4a9966de
authored
Mar 27, 2017
by
Peter van 't Hof
Browse files
Fixing code warnings
parent
793b521d
Changes
1
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
View file @
4a9966de
...
...
@@ -16,9 +16,11 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetCommandLineFunction
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Version
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.util.matching.Regex
/**
* Wrapper for the cuffquant command line tool.
...
...
@@ -116,11 +118,11 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction with V
/** Disable SCV correction */
var
noScvCorrection
:
Boolean
=
config
(
"no_scv_correction"
,
default
=
false
)
def
versionRegex
=
"""cuffquant v(.*)"""
.
r
def
versionCommand
=
executable
def
versionRegex
:
Regex
=
"""cuffquant v(.*)"""
.
r
def
versionCommand
:
String
=
executable
override
def
versionExitcode
=
List
(
0
,
1
)
def
cmdLine
=
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
"--output-dir"
,
outputDir
)
+
optional
(
"--mask-file"
,
maskFile
)
+
...
...
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