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biopet.biopet
Commits
d7b0ecdc
Commit
d7b0ecdc
authored
Apr 27, 2016
by
Peter van 't Hof
Browse files
Move gatk variantcallers to correct package
parent
d5c8751d
Changes
5
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public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/
gatk
/variantcallers/HaplotypeCaller.scala
→
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/
shiva
/variantcallers/HaplotypeCaller.scala
View file @
d7b0ecdc
...
...
@@ -3,11 +3,10 @@
* 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.pipelines.
gatk
.variantcallers
package
nl.lumc.sasc.biopet.pipelines.
shiva
.variantcallers
import
nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad
import
nl.lumc.sasc.biopet.utils.config.Configurable
/** Default mode for the haplotypecaller */
class
HaplotypeCaller
(
val
root
:
Configurable
)
extends
Variantcaller
{
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/
gatk
/variantcallers/HaplotypeCallerAllele.scala
→
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/
shiva
/variantcallers/HaplotypeCallerAllele.scala
View file @
d7b0ecdc
...
...
@@ -3,11 +3,10 @@
* 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.pipelines.
gatk
.variantcallers
package
nl.lumc.sasc.biopet.pipelines.
shiva
.variantcallers
import
nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad
import
nl.lumc.sasc.biopet.utils.config.Configurable
/** Allele mode for Haplotypecaller */
class
HaplotypeCallerAllele
(
val
root
:
Configurable
)
extends
Variantcaller
{
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/
gatk
/variantcallers/HaplotypeCallerGvcf.scala
→
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/
shiva
/variantcallers/HaplotypeCallerGvcf.scala
View file @
d7b0ecdc
...
...
@@ -3,11 +3,10 @@
* 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.pipelines.
gatk
.variantcallers
package
nl.lumc.sasc.biopet.pipelines.
shiva
.variantcallers
import
nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad
import
nl.lumc.sasc.biopet.utils.config.Configurable
/** Gvcf mode for haplotypecaller */
class
HaplotypeCallerGvcf
(
val
root
:
Configurable
)
extends
Variantcaller
{
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/
gatk
/variantcallers/UnifiedGenotyper.scala
→
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/
shiva
/variantcallers/UnifiedGenotyper.scala
View file @
d7b0ecdc
...
...
@@ -3,11 +3,10 @@
* 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.pipelines.
gatk
.variantcallers
package
nl.lumc.sasc.biopet.pipelines.
shiva
.variantcallers
import
nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad
import
nl.lumc.sasc.biopet.utils.config.Configurable
/** Default mode for UnifiedGenotyper */
class
UnifiedGenotyper
(
val
root
:
Configurable
)
extends
Variantcaller
{
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/
gatk
/variantcallers/UnifiedGenotyperAllele.scala
→
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/
shiva
/variantcallers/UnifiedGenotyperAllele.scala
View file @
d7b0ecdc
...
...
@@ -3,11 +3,10 @@
* 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.pipelines.
gatk
.variantcallers
package
nl.lumc.sasc.biopet.pipelines.
shiva
.variantcallers
import
nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad
import
nl.lumc.sasc.biopet.utils.config.Configurable
/** Allele mode for GenotyperAllele */
class
UnifiedGenotyperAllele
(
val
root
:
Configurable
)
extends
Variantcaller
{
...
...
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