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biopet.biopet
Commits
3fc3e1c5
Commit
3fc3e1c5
authored
Apr 26, 2016
by
Peter van 't Hof
Browse files
Disable scattering
parent
7570f55a
Changes
1
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Inline
Side-by-side
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
View file @
3fc3e1c5
...
...
@@ -31,11 +31,13 @@ import org.broadinstitute.gatk.queue.extensions.gatk.{ GATKScatterFunction, Read
import
org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Output
,
_
}
class
BaseRecalibrator
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
//TODO: check gathering
class
BaseRecalibrator
(
val
root
:
Configurable
)
extends
CommandLineGATK
/* with ScatterGatherableFunction */
{
analysisName
=
"BaseRecalibrator"
analysis_type
=
"BaseRecalibrator"
scatterClass
=
classOf
[
ReadScatterFunction
]
setupScatterFunction
=
{
case
scatter
:
GATKScatterFunction
=>
scatter
.
includeUnmapped
=
false
}
//TODO: check gathering
//scatterClass = classOf[ReadScatterFunction]
//setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
/** A database of known polymorphic sites */
@Input
(
fullName
=
"knownSites"
,
shortName
=
"knownSites"
,
doc
=
"A database of known polymorphic sites"
,
required
=
false
,
exclusiveOf
=
""
,
validation
=
""
)
...
...
@@ -46,8 +48,8 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK with Scat
private
var
knownSitesIndexes
:
Seq
[
File
]
=
Nil
/** The output recalibration table file to create */
@Output
(
fullName
=
"out"
,
shortName
=
"o"
,
doc
=
"The output recalibration table file to create"
,
required
=
true
,
exclusiveOf
=
""
,
validation
=
""
)
@Gather
(
classOf
[
org.broadinstitute.gatk.engine.recalibration.BQSRGatherer
])
@Output
(
fullName
=
"out"
,
shortName
=
"o"
,
doc
=
"The output recalibration table file to create"
,
required
=
true
,
exclusiveOf
=
""
,
validation
=
""
)
//TODO: check gathering
//
@Gather(classOf[org.broadinstitute.gatk.engine.recalibration.BQSRGatherer])
var
out
:
File
=
_
/**
...
...
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