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biopet.biopet
Commits
3ce0cd9f
Commit
3ce0cd9f
authored
Oct 12, 2016
by
Sander Bollen
Browse files
autostyle
parent
8e13d8ac
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala
View file @
3ce0cd9f
...
...
@@ -33,7 +33,7 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver
protected
var
script
:
File
=
new
File
(
"/nl/lumc/sasc/biopet/extensions/cnmops.R"
)
def
versionCommand
=
super
.
cmdLine
+
"--version"
def
versionRegex
=
"\\d+\\.\\d+\\.\\d+"
.
r
def
versionRegex
=
"\\d+\\.\\d+\\.\\d+"
.
r
private
def
stringToInt
(
s
:
String
)
:
Option
[
Int
]
=
{
try
{
...
...
@@ -44,10 +44,10 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver
}
/**
* Check whether version of cn mops is at least 1.18.0
*
* @return
*/
* Check whether version of cn mops is at least 1.18.0
*
* @return
*/
def
versionCheck
:
Boolean
=
{
getVersion
match
{
case
Some
(
version
)
=>
{
...
...
@@ -79,7 +79,7 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver
lazy
val
outputCnv
:
File
=
{
outputDir
match
{
case
Some
(
dir
)
if
dir
.
exists
=>
new
File
(
dir
,
"cnv.txt"
)
case
_
=>
throw
new
IllegalArgumentException
(
"Unexpected error when trying to set cn.MOPS CNV output"
)
case
_
=>
throw
new
IllegalArgumentException
(
"Unexpected error when trying to set cn.MOPS CNV output"
)
}
}
...
...
@@ -87,7 +87,7 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver
lazy
val
outputCnr
:
File
=
{
outputDir
match
{
case
Some
(
dir
)
if
dir
.
exists
=>
new
File
(
dir
,
"cnr.txt"
)
case
_
=>
throw
new
IllegalArgumentException
(
"Unexpected error when trying to set cn.MOPS CNR output"
)
case
_
=>
throw
new
IllegalArgumentException
(
"Unexpected error when trying to set cn.MOPS CNR output"
)
}
}
...
...
@@ -95,7 +95,7 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver
lazy
val
rawOutput
:
File
=
{
outputDir
match
{
case
Some
(
dir
)
if
dir
.
exists
=>
new
File
(
dir
,
"rawoutput.txt"
)
case
_
=>
throw
new
IllegalArgumentException
(
"Unexpected error when trying to set cn.MOPS raw output"
)
case
_
=>
throw
new
IllegalArgumentException
(
"Unexpected error when trying to set cn.MOPS raw output"
)
}
}
...
...
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