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biopet.biopet
Commits
c347da53
Commit
c347da53
authored
Apr 14, 2017
by
rhpvorderman
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Fixed code warnings
parent
1a7d4610
Changes
1
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+2
-2
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
View file @
c347da53
...
...
@@ -33,7 +33,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
var
R2
:
File
=
_
@Input
(
doc
=
"The reference file for the bam files."
,
shortName
=
"R"
)
var
reference
:
File
=
null
var
reference
:
File
=
_
@Output
(
doc
=
"Output file SAM"
,
shortName
=
"output"
)
var
output
:
File
=
_
...
...
@@ -75,7 +75,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
def
cmdLine
=
{
def
cmdLine
:
String
=
{
required
(
executable
)
+
required
(
"mem"
)
+
optional
(
"-k"
,
k
)
+
...
...
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