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biopet.biopet
Commits
af88febc
Commit
af88febc
authored
Apr 11, 2017
by
Peter van 't Hof
Committed by
GitHub
Apr 11, 2017
Browse files
Merge pull request #65 from biopet/fix-BIOPET-642
Fixing nullpointer
parents
625bb514
1a99be40
Changes
2
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
af88febc
...
...
@@ -99,7 +99,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
beforeGraph
()
internalBeforeGraph
()
this
.
commandDirectory
=
this
.
jobOutputFile
.
getParentFile
if
(
jobOutputFile
!=
null
)
this
.
commandDirectory
=
this
.
jobOutputFile
.
getAbsoluteFile
.
getParentFile
super
.
freezeFieldValues
()
}
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
View file @
af88febc
...
...
@@ -23,13 +23,13 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class
BedtoolsIntersect
(
val
parent
:
Configurable
)
extends
Bedtools
{
@Input
(
doc
=
"Input file (bed/gff/vcf/bam)"
)
var
input
:
File
=
null
var
input
:
File
=
_
@Input
(
doc
=
"Intersect file (bed/gff/vcf)"
)
var
intersectFile
:
File
=
null
var
intersectFile
:
File
=
_
@Output
(
doc
=
"output File"
)
var
output
:
File
=
null
var
output
:
File
=
_
@Argument
(
doc
=
"Min overlap"
,
required
=
false
)
var
minOverlap
:
Option
[
Double
]
=
config
(
"minoverlap"
)
...
...
@@ -46,7 +46,8 @@ class BedtoolsIntersect(val parent: Configurable) extends Bedtools {
}
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
"intersect"
)
+
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
"intersect"
)
+
required
(
inputTag
,
input
)
+
required
(
"-b"
,
intersectFile
)
+
optional
(
"-f"
,
minOverlap
)
+
...
...
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