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biopet.biopet
Commits
7accfa72
Commit
7accfa72
authored
Dec 28, 2015
by
Peter van 't Hof
Browse files
Fixed traits
parent
00a7a89a
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
→
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping
Trait
.scala
View file @
7accfa72
...
...
@@ -8,6 +8,7 @@ import nl.lumc.sasc.biopet.extensions.Ln
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
MergeSamFiles
,
AddOrReplaceReadGroups
,
SamToFastq
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
import
MultisampleMapping.MergeStrategy
...
...
@@ -17,10 +18,8 @@ import scala.collection.JavaConversions._
/**
* Created by pjvanthof on 18/12/15.
*/
trait
MultisampleMapping
extends
QScript
with
MultiSampleQScript
with
Reference
{
qscript
=>
//def this() = this(null)
trait
MultisampleMappingTrait
extends
MultiSampleQScript
with
Reference
{
qscript
:
QScript
=>
def
mergeStrategy
:
MergeStrategy.Value
=
{
val
value
:
String
=
config
(
"merge_strategy"
,
default
=
"preprocessmarkduplicates"
)
...
...
@@ -190,6 +189,9 @@ trait MultisampleMapping extends QScript
}
}
}
class
MultisampleMapping
(
val
root
:
Configurable
)
extends
QScript
with
MultisampleMappingTrait
{
def
this
()
=
this
(
null
)
}
object
MultisampleMapping
extends
PipelineCommand
{
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
7accfa72
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import
nl.lumc.sasc.biopet.core.Reference
import
nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
import
nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMapping
import
nl.lumc.sasc.biopet.pipelines.mapping.
{
MultisampleMapping
Trait
}
import
nl.lumc.sasc.biopet.pipelines.toucan.Toucan
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.queue.QScript
*
* Created by pjvan_thof on 2/26/15.
*/
trait
ShivaTrait
extends
MultisampleMapping
with
Reference
with
TargetRegions
{
qscript
:
QScript
=>
trait
ShivaTrait
extends
MultisampleMapping
Trait
with
Reference
with
TargetRegions
{
qscript
:
QScript
=>
override
def
reportClass
=
{
val
shiva
=
new
ShivaReport
(
this
)
...
...
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