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Commit d7b0ecdc authored by Peter van 't Hof's avatar Peter van 't Hof
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Move gatk variantcallers to correct package

parent d5c8751d
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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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