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biopet.biopet
Commits
9ca827e9
Commit
9ca827e9
authored
Jul 27, 2015
by
Peter van 't Hof
Browse files
Fix add method
parent
5d834e35
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
View file @
9ca827e9
...
...
@@ -18,11 +18,14 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import
java.io.File
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
BiopetQScript
,
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
import
nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import
nl.lumc.sasc.biopet.extensions.delly.Delly
import
nl.lumc.sasc.biopet.tools.VcfStats
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.utils.commandline.Input
import
scala.collection.JavaConversions._
...
...
@@ -31,9 +34,11 @@ import scala.collection.JavaConversions._
*
* Created by pjvan_thof on 2/26/15.
*/
class
ShivaSvCalling
extends
SummaryQScript
with
SampleLibraryTag
with
Reference
{
class
ShivaSvCalling
(
val
root
:
Configurable
)
extends
QScript
with
SummaryQScript
with
SampleLibraryTag
with
Reference
{
qscript
=>
def
this
()
=
this
(
null
)
@Input
(
doc
=
"Bam files (should be deduped bams)"
,
shortName
=
"BAM"
,
required
=
true
)
protected
var
inputBamsArg
:
List
[
File
]
=
Nil
...
...
@@ -73,6 +78,8 @@ class ShivaSvCalling extends SummaryQScript with SampleLibraryTag with Reference
require
(
inputBams
.
nonEmpty
,
"No input bams found"
)
require
(
callers
.
nonEmpty
,
"must select at least 1 SV caller, choices are: "
+
callersList
.
map
(
_
.
name
).
mkString
(
", "
))
callers
.
foreach
(
_
.
addJobs
())
addSummaryJobs
()
}
...
...
@@ -113,7 +120,7 @@ class ShivaSvCalling extends SummaryQScript with SampleLibraryTag with Reference
//TODO: check double directories
for
((
sample
,
bamFile
)
<-
inputBams
)
{
val
cleverDir
=
new
File
(
outputDir
,
sample
)
val
clever
=
CleverCaller
(
qscript
,
bamFile
,
qscript
.
reference
,
cleverDir
,
cleverDir
)
val
clever
=
CleverCaller
(
qscript
,
bamFile
,
cleverDir
,
cleverDir
)
add
(
clever
)
}
}
...
...
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