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biopet.biopet
Commits
e07f79b0
Commit
e07f79b0
authored
Nov 18, 2016
by
Sander Bollen
Browse files
Merge branch 'fix-BIOPET-458' into 'develop'
Fixed nullpointer See merge request !474
parents
98890af0
f78b2c09
Changes
1
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
e07f79b0
...
...
@@ -38,8 +38,6 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
if
(
config
.
contains
(
"output_dir"
,
path
=
Nil
))
config
(
"output_dir"
,
path
=
Nil
).
asFile
else
new
File
(
"."
)
}
require
(
outputDir
.
canRead
,
s
"No premision to read outputdir: $outputDir"
)
require
(
outputDir
.
canWrite
,
s
"No premision to read outputdir: $outputDir"
)
@Argument
(
doc
=
"Disable all scatters"
,
shortName
=
"DSC"
,
required
=
false
)
var
disableScatter
:
Boolean
=
false
...
...
@@ -161,10 +159,10 @@ object BiopetQScript {
def
checkOutputDir
(
outputDir
:
File
)
:
Unit
=
{
// Sanity checks
require
(
outputDir
.
getParentFile
.
canRead
,
s
"No premision to read parent of outputdir: ${outputDir.getParentFile}"
)
require
(
outputDir
.
getParentFile
.
canWrite
,
s
"No premision to write parent of outputdir: ${outputDir.getParentFile}"
)
require
(
outputDir
.
getAbsoluteFile
.
getParentFile
.
canRead
,
s
"No premision to read parent of outputdir: ${outputDir.getParentFile}"
)
require
(
outputDir
.
getAbsoluteFile
.
getParentFile
.
canWrite
,
s
"No premision to write parent of outputdir: ${outputDir.getParentFile}"
)
outputDir
.
mkdir
()
require
(
outputDir
.
canRead
,
s
"No premision to read outputdir: $outputDir"
)
require
(
outputDir
.
canWrite
,
s
"No premision to write outputdir: $outputDir"
)
require
(
outputDir
.
getAbsoluteFile
.
canRead
,
s
"No premision to read outputdir: $outputDir"
)
require
(
outputDir
.
getAbsoluteFile
.
canWrite
,
s
"No premision to write outputdir: $outputDir"
)
}
}
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