From 8d6bb0f12cbe0cd64cda2b7774f9895d1a359bcc Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 13 Sep 2015 12:56:04 +0200
Subject: [PATCH] Moved to other package
---
.../sasc/biopet/{ => extensions}/tools/BastyGenerateFasta.scala | 2 +-
.../lumc/sasc/biopet/{ => extensions}/tools/BedToInterval.scala | 2 +-
.../{ => extensions}/tools/BedtoolsCoverageToCounts.scala | 2 +-
.../sasc/biopet/{ => extensions}/tools/BiopetFlagstat.scala | 2 +-
.../lumc/sasc/biopet/{ => extensions}/tools/FastqSplitter.scala | 2 +-
.../nl/lumc/sasc/biopet/{ => extensions}/tools/FastqSync.scala | 2 +-
.../lumc/sasc/biopet/{ => extensions}/tools/MergeAlleles.scala | 2 +-
.../lumc/sasc/biopet/{ => extensions}/tools/MergeTables.scala | 2 +-
.../lumc/sasc/biopet/{ => extensions}/tools/MpileupToVcf.scala | 2 +-
.../lumc/sasc/biopet/{ => extensions}/tools/PrefixFastq.scala | 2 +-
.../sasc/biopet/{ => extensions}/tools/SageCountFastq.scala | 2 +-
.../sasc/biopet/{ => extensions}/tools/SageCreateLibrary.scala | 2 +-
.../biopet/{ => extensions}/tools/SageCreateTagCounts.scala | 2 +-
.../nl/lumc/sasc/biopet/{ => extensions}/tools/SeqStat.scala | 2 +-
.../nl/lumc/sasc/biopet/{ => extensions}/tools/SquishBed.scala | 2 +-
.../nl/lumc/sasc/biopet/{ => extensions}/tools/VcfFilter.scala | 2 +-
.../nl/lumc/sasc/biopet/{ => extensions}/tools/VcfStats.scala | 2 +-
.../nl/lumc/sasc/biopet/{ => extensions}/tools/VcfWithVcf.scala | 2 +-
.../lumc/sasc/biopet/{ => extensions}/tools/VepNormalizer.scala | 2 +-
.../nl/lumc/sasc/biopet/{ => extensions}/tools/WipeReads.scala | 2 +-
20 files changed, 20 insertions(+), 20 deletions(-)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/BastyGenerateFasta.scala (98%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/BedToInterval.scala (97%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/BedtoolsCoverageToCounts.scala (96%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/BiopetFlagstat.scala (97%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/FastqSplitter.scala (97%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/FastqSync.scala (98%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/MergeAlleles.scala (97%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/MergeTables.scala (98%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/MpileupToVcf.scala (98%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/PrefixFastq.scala (97%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/SageCountFastq.scala (96%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/SageCreateLibrary.scala (97%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/SageCreateTagCounts.scala (97%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/SeqStat.scala (98%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/SquishBed.scala (94%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/VcfFilter.scala (97%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/VcfStats.scala (98%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/VcfWithVcf.scala (97%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/VepNormalizer.scala (97%)
rename public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/{ => extensions}/tools/WipeReads.scala (97%)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
similarity index 98%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
index 45b93f4f0..aa86cbbd8 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
similarity index 97%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
index 74e3beb1e..97b1e8bac 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
similarity index 96%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
index e18e411f4..1776b316e 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
similarity index 97%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
index 7053fd9ec..b7917e8f4 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
similarity index 97%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
index bcaafbd0e..b775b75e7 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
similarity index 98%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
index 4e8ec8dfe..7c35abfc9 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
similarity index 97%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
index 849ca8218..b967fdcc6 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
similarity index 98%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
index 9d939d0b5..9976d11d2 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
similarity index 98%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
index bc89f96fe..cf6104625 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
similarity index 97%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
index 4ef7693c5..623af27ca 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
similarity index 96%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
index 95a708a9a..621daabc3 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
similarity index 97%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
index dab1f3b87..f6c885750 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
similarity index 97%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
index 59f34b2b2..ddea61d9d 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
similarity index 98%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
index f34e0530f..8abd3ee88 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
similarity index 94%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
index a32fd1012..2de74b174 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
similarity index 97%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
index d8e71e5e6..f1c6bb85b 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
similarity index 98%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
index 8eede6f85..e5a45b446 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
similarity index 97%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
index ea8a7a611..73e73c113 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
similarity index 97%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
index 9ca92cbf4..78ea95d10 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
similarity index 97%
rename from public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
index 9290f5169..f3a548361 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.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.tools
+package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
--
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