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biopet.biopet
Commits
a0573985
Commit
a0573985
authored
May 04, 2016
by
Peter van 't Hof
Browse files
Add deprication tag
parent
502bfac1
Changes
5
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
View file @
a0573985
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@@ -25,6 +25,8 @@ import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output }
* Extension for CombineVariants from GATK
*
* Created by pjvan_thof on 2/26/15.
*
* @deprecated
*/
class
CombineVariants
(
val
root
:
Configurable
)
extends
Gatk
{
val
analysisType
=
"CombineVariants"
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
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a0573985
...
...
@@ -24,6 +24,8 @@ import org.broadinstitute.gatk.utils.commandline.Input
* General extension for GATK module
*
* Created by pjvan_thof on 2/26/15.
*
* @deprecated
*/
abstract
class
Gatk
extends
BiopetJavaCommandLineFunction
with
Reference
with
Version
{
override
def
subPath
=
"gatk"
::
super
.
subPath
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala
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a0573985
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...
@@ -26,6 +26,8 @@ import org.broadinstitute.gatk.utils.report.{ GATKReportTable, GATKReport }
* Extension for CombineVariants from GATK
*
* Created by pjvan_thof on 2/26/15.
*
* @deprecated
*/
class
GenotypeConcordance
(
val
root
:
Configurable
)
extends
Gatk
with
Summarizable
{
val
analysisType
=
"GenotypeConcordance"
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
View file @
a0573985
...
...
@@ -25,6 +25,8 @@ import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output }
* Extension for CombineVariants from GATK
*
* Created by pjvan_thof on 2/26/15.
*
* @deprecated
*/
class
SelectVariants
(
val
root
:
Configurable
)
extends
Gatk
{
val
analysisType
=
"SelectVariants"
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
View file @
a0573985
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
nl.lumc.sasc.biopet.core._
import
org.broadinstitute.gatk.engine.phonehome.GATKRunReport
/**
* @deprecated
*/
trait
GatkGeneral
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
CommandLineGATK
with
CommandLineResources
with
Reference
with
Version
{
var
executable
:
String
=
config
(
"java"
,
default
=
"java"
,
namespace
=
"java"
,
freeVar
=
false
)
...
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