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biopet.biopet
Commits
a4fd6fcd
Commit
a4fd6fcd
authored
Apr 16, 2015
by
Peter van 't Hof
Browse files
Added a deprecated message
parent
d49e8e65
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
View file @
a4fd6fcd
...
...
@@ -24,6 +24,9 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import
java.io.PrintWriter
import
scala.io.Source
/**
* @deprecated Use picard.util.BedToIntervalList instead
*/
class
BedToInterval
(
val
root
:
Configurable
)
extends
BiopetJavaCommandLineFunction
{
javaMainClass
=
getClass
.
getName
...
...
@@ -41,6 +44,9 @@ class BedToInterval(val root: Configurable) extends BiopetJavaCommandLineFunctio
override
def
commandLine
=
super
.
commandLine
+
required
(
"-I"
,
input
)
+
required
(
"-b"
,
bamFile
)
+
required
(
"-o"
,
output
)
}
/**
* @deprecated Use picard.util.BedToIntervalList instead
*/
object
BedToInterval
extends
ToolCommand
{
def
apply
(
root
:
Configurable
,
inputBed
:
File
,
inputBam
:
File
,
output
:
File
)
:
BedToInterval
=
{
val
bedToInterval
=
new
BedToInterval
(
root
)
...
...
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