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biopet.biopet
Commits
1df0636d
Commit
1df0636d
authored
Oct 06, 2015
by
Sander van der Zeeuw
Browse files
add BuildBamIndex to biopet
parent
95b665ed
Changes
1
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public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala
0 → 100644
View file @
1df0636d
package
nl.lumc.sasc.biopet.extensions.picard
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
/**
* Created by sajvanderzeeuw on 6-10-15.
*/
class
BuildBamIndex
(
val
root
:
Configurable
)
extends
Picard
{
javaMainClass
=
new
picard
.
sam
.
BuildBamIndex
().
getClass
.
getName
@Input
(
doc
=
"The input SAM or BAM files to analyze."
,
required
=
true
)
var
input
:
File
=
_
@Output
(
doc
=
"The output file to bam file to"
,
required
=
true
)
var
output
:
File
=
_
override
def
cmdLine
=
super
.
cmdLine
+
required
(
"INPUT="
,
input
,
spaceSeparated
=
false
)
+
required
(
"OUTPUT="
,
output
,
spaceSeparated
=
false
)
}
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