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biopet.biopet
Commits
982c9348
Commit
982c9348
authored
Dec 12, 2016
by
Peter van 't Hof
Browse files
Format fixes
parent
68c080d8
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
View file @
982c9348
...
...
@@ -19,7 +19,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/** Wrapper for the bgzip command */
class
Bgzip
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
...
...
@@ -35,8 +35,8 @@ class Bgzip(val root: Configurable) extends BiopetCommandLineFunction {
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
if
(
input
.
isEmpty
&&
!
inputAsStdin
)
Logging
.
addError
(
"Input is missing in Bgzip"
)
if
(
output
==
null
&&
!
outputAsStsout
)
Logging
.
addError
(
"Output is missing in Bgzip"
)
if
(
input
.
isEmpty
&&
!
inputAsStdin
)
Logging
.
addError
(
"Input is missing in Bgzip"
)
if
(
output
==
null
&&
!
outputAsStsout
)
Logging
.
addError
(
"Output is missing in Bgzip"
)
}
def
cmdLine
=
required
(
executable
)
+
...
...
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