diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/svcallers/breakdancer2vcf.py b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/svcallers/breakdancer2vcf.py
rename to public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
similarity index 92%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala
rename to public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
index 518c2dc0778619deddcaf24798533b5c31842b17..67a6943e21fdafbcd694008f611017b0ca1bcee2 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
@@ -13,16 +13,14 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions.svcallers
+package nl.lumc.sasc.biopet.extensions.breakdancer
import java.io.File
-import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
-
import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.BiopetQScript
-import nl.lumc.sasc.biopet.core.PipelineCommand
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.extensions.breakdancer.BreakdancerVCF
+import org.broadinstitute.gatk.queue.QScript
/// Breakdancer is actually a mini pipeline executing binaries from the breakdancer package
class Breakdancer(val root: Configurable) extends QScript with BiopetQScript {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/BreakdancerCaller.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/BreakdancerCaller.scala
rename to public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
index d125b1396947e5040faeb46cf5cb9adcff4b79a8..0613644979a36ef9e76c0772acd0e8652c5d4e3f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/BreakdancerCaller.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
@@ -1,11 +1,10 @@
-package nl.lumc.sasc.biopet.extensions.svcallers
+package nl.lumc.sasc.biopet.extensions.breakdancer
import java.io.File
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
-
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "breakdancer-max", freeVar = false)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/BreakdancerConfig.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/BreakdancerConfig.scala
rename to public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
index 81a6bc738393e53be4e514b41a8a579e15442b8b..88b8521ad37765c124a54a65427c649c02546e0c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/BreakdancerConfig.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
@@ -1,11 +1,10 @@
-package nl.lumc.sasc.biopet.extensions.svcallers
+package nl.lumc.sasc.biopet.extensions.breakdancer
import java.io.File
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
-
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BreakdancerConfig(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "bam2cfg.pl", freeVar = false)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/BreakdancerVCF.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/BreakdancerVCF.scala
rename to public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
index 4df187dd6a0d65509aaadf9949c2c8d2af12baac..986ace419440b62d59cf554b1f25c14e636c9c1c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/BreakdancerVCF.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
@@ -13,14 +13,13 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions.svcallers
+package nl.lumc.sasc.biopet.extensions.breakdancer
import java.io.File
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BreakdancerVCF(val root: Configurable) extends PythonCommandLineFunction {
setPythonScript("breakdancer2vcf.py")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Clever.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/Clever.scala
similarity index 89%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Clever.scala
rename to public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/Clever.scala
index cd5427c6edce4bca08cc489686bdb3818e375fef..a978cbef47aeae28bcbc656f4670545562e44b69 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Clever.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/Clever.scala
@@ -13,16 +13,13 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions.svcallers
+package nl.lumc.sasc.biopet.extensions.clever
import java.io.File
-import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
-
import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.BiopetQScript
-import nl.lumc.sasc.biopet.core.PipelineCommand
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import org.broadinstitute.gatk.queue.QScript
class Clever(val root: Configurable) extends QScript with BiopetQScript {
def this() = this(null)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/CleverCaller.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
similarity index 94%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/CleverCaller.scala
rename to public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
index 66ed9365ddafc8f6ddc57ffeb9eba2370a8d18f6..c070b709607f322576bbf72c52221b708ad4ff3b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/CleverCaller.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
@@ -1,11 +1,10 @@
-package nl.lumc.sasc.biopet.extensions.svcallers
+package nl.lumc.sasc.biopet.extensions.clever
import java.io.File
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
-
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "clever")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Delly.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Delly.scala
rename to public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
index 3a17375ad6244bad797fcdf3d5ce8c2de54a8c9a..cc403f383f6f7db2c29b2bcb0d6300737f476d78 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Delly.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.extensions.svcallers
+package nl.lumc.sasc.biopet.extensions.delly
import java.io.File
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/DellyCaller.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
similarity index 95%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/DellyCaller.scala
rename to public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
index a4f0490f6354d64aac921a032c384a2ee918161d..5956c31b4c05f253de1c4e344f942c01248c04f0 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/DellyCaller.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.extensions.svcallers
+package nl.lumc.sasc.biopet.extensions.delly
import java.io.File
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/pindel/Pindel.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/pindel/Pindel.scala
rename to public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
index cfcd31a2bf4a4f1e92fc9f520ffb882beea0d00f..0cb157d1e688d312128a79f95955551934f28e69 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/pindel/Pindel.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions.svcallers.pindel
+package nl.lumc.sasc.biopet.extensions.pindel
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import org.broadinstitute.gatk.queue.QScript
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/pindel/PindelCaller.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/pindel/PindelCaller.scala
rename to public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
index 6bcc620332a07722513ef66ad006ba789e00b47a..66a7cd256af53e3892db62add979ffc5f08293a4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/pindel/PindelCaller.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions.svcallers.pindel
+package nl.lumc.sasc.biopet.extensions.pindel
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/pindel/PindelConfig.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/pindel/PindelConfig.scala
rename to public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
index 85dc67905871883f8ca47a10e08bb8056f051520..f6845a1c784b8ca999184a2ec4456c7bd2780ecf 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/pindel/PindelConfig.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions.svcallers.pindel
+package nl.lumc.sasc.biopet.extensions.pindel
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.PipelineCommand
diff --git a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
index c57ce72d140cafab19d305730310372cdf001fe1..057379a33428f59c785d36f937e153fa55e2525b 100644
--- a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+++ b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
@@ -25,10 +25,12 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetQScript, MultiSampleQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.Ln
+import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
+import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaMerge, SambambaMarkdup }
-//import nl.lumc.sasc.biopet.extensions.svcallers.pindel.Pindel
-import nl.lumc.sasc.biopet.extensions.svcallers.{ Breakdancer, Delly, CleverCaller }
+//import nl.lumc.sasc.biopet.extensions.pindel.Pindel
+import nl.lumc.sasc.biopet.extensions.delly.Delly
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping