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 45b93f4f029840984e12a57900928fb9368b3e8e..aa86cbbd813a3321cacf8d2bbc6ce5da828679e5 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 74e3beb1e2d079f7f4df0a152e593e29c279394c..97b1e8bac430e0a29780197a1e468b50e4c212ca 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 e18e411f429feace2ee87c9c8cf2a477df484ad0..1776b316e7e3d60c43bda2c2171ca945caddcc90 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 7053fd9ec674fcd67e6ba540ae0de3618e68bc31..b7917e8f44ec71d1022ca26c915b0c5112afd6f3 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 bcaafbd0ef75a1af91a0d5261434a59406279075..b775b75e75042ccc660da378c27f64afd1923c81 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 4e8ec8dfee9e4364f13f88f4fdf686590c93622f..7c35abfc909a50ad4f10550e71480385db9bc97f 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 849ca8218b4631e3dbe91e450f3a42df857cdc82..b967fdcc6ef03bf9ef681c4c718ad58e9b209f02 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 9d939d0b545f94d0514d4d98a92422bd124d33e8..9976d11d26a18ba2564f32e1153303b5213c58ff 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 bc89f96fecafad45b094167f4b78d275f317761d..cf6104625bfaeb95d8d8f15ac813a59afe8c3f3a 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 4ef7693c5767ef653db7cb12ea634855c556f85c..623af27ca81cc91a14b209362cd909f151fcd051 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 95a708a9adaed92528d15f6d5828faa03104e6e5..621daabc3e2ca0d3b71831296e4cc2356ba0a040 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 dab1f3b8725dbc16659af11adc769b203b626980..f6c8857501c4137a8f594b57287ce1bb8abab3f7 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 59f34b2b24ee569a445546967a22701d3b2bfeef..ddea61d9d8850e0e895d4dc9f69c6b7cf5cae238 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 f34e0530f08c92aa154674fa1a353668aa97090f..8abd3ee880094403cef9d7b2df7431cd736be043 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 a32fd1012ce10613bcd26f13e5316024ad218c36..2de74b174e9d8a424c87f03dd15ab79117ab21fb 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 d8e71e5e60ee564ad03c1f6b87e88b5fba071845..f1c6bb85bbf77a19f954addcea0e2dc35a55002e 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 8eede6f8569b6ba93180ed9d3040e71acd86fe27..e5a45b446d0487d088c68d55fdb11a6e635cc183 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 ea8a7a611418ff03566f0e7176f753c5017b82a1..73e73c113b6a364cfa4379a33c15d8a6ac607e4e 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 9ca92cbf406548ad2c1c6cc2fd4eab3da517c8fb..78ea95d102f85622c00f2227b8644eb6bdf9af9d 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 9290f516999e6de8ed134e23529a411dcd6a0ca1..f3a548361c1afe99701f903c70911b2e3976b03f 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