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Merge branch 'develop' into feature-extract_aligned_fastq
Conflicts: biopet-framework/BiopetFramework.iml biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
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- .idea/libraries/Maven__com_baqend_bloom_filter_1_02.xml 0 additions, 13 deletions.idea/libraries/Maven__com_baqend_bloom_filter_1_02.xml
- .idea/libraries/Maven__com_google_code_gson_gson_2_2_4.xml 0 additions, 13 deletions.idea/libraries/Maven__com_google_code_gson_gson_2_2_4.xml
- .idea/libraries/Maven__com_google_guava_guava_18_0.xml 4 additions, 4 deletions.idea/libraries/Maven__com_google_guava_guava_18_0.xml
- .idea/libraries/Maven__org_apache_commons_commons_pool2_2_2.xml 0 additions, 13 deletions...libraries/Maven__org_apache_commons_commons_pool2_2_2.xml
- .idea/libraries/Maven__redis_clients_jedis_2_5_1.xml 0 additions, 13 deletions.idea/libraries/Maven__redis_clients_jedis_2_5_1.xml
- .idea/misc.xml 1 addition, 1 deletion.idea/misc.xml
- biopet-framework/BiopetFramework.iml 3 additions, 6 deletionsbiopet-framework/BiopetFramework.iml
- biopet-framework/pom.xml 4 additions, 8 deletionsbiopet-framework/pom.xml
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala 6 additions, 2 deletions...ain/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala 66 additions, 72 deletions...l/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/BreakdancerVCF.scala 36 additions, 0 deletions...umc/sasc/biopet/extensions/svcallers/BreakdancerVCF.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala 7 additions, 3 deletions.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala 5 additions, 6 deletions...n/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala 8 additions, 6 deletions.../main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala 17 additions, 15 deletions.../nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala 22 additions, 20 deletions...main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala 44 additions, 37 deletions...n/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala 35 additions, 33 deletions...scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala 175 additions, 166 deletions.../src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
- biopet-framework/src/main/scripts/nl/lumc/sasc/biopet/extensions/svcallers/breakdancer2vcf.py 153 additions, 0 deletions.../lumc/sasc/biopet/extensions/svcallers/breakdancer2vcf.py
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