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biopet.biopet
Commits
9461ff47
Commit
9461ff47
authored
Jun 03, 2016
by
Peter van 't Hof
Browse files
Put scattering back in for baserecalibration
parent
f6bfca5d
Changes
1
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
View file @
9461ff47
...
...
@@ -16,17 +16,16 @@ package nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import
nl.lumc.sasc.biopet.utils.VcfUtils
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Output
,
_
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Output
,
Input
}
//TODO: check gathering
class
BaseRecalibrator
(
val
root
:
Configurable
)
extends
CommandLineGATK
/* with ScatterGatherableFunction */
{
class
BaseRecalibrator
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
def
analysis_type
=
"BaseRecalibrator"
//TODO: check gathering
//scatterClass = classOf[ContigScatterFunction]
//setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
scatterClass
=
classOf
[
ContigScatterFunction
]
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
=
""
)
...
...
@@ -38,7 +37,7 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with S
/** The output recalibration table file to create */
@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])
@Gather
(
classOf
[
org.broadinstitute.gatk.engine.recalibration.BQSRGatherer
])
var
out
:
File
=
_
/** One or more covariates to be used in the recalibration. Can be specified multiple times */
...
...
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