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Merge remote-tracking branch 'remotes/origin/develop' into biopet-bios
# Conflicts: # flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
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- bam2wig/pom.xml 12 additions, 0 deletionsbam2wig/pom.xml
- bam2wig/src/test/resources/empty.bam 0 additions, 0 deletionsbam2wig/src/test/resources/empty.bam
- bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala 30 additions, 0 deletions...sc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala
- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala 5 additions, 7 deletions...in/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
- biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala 60 additions, 0 deletions...cala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala 135 additions, 134 deletions.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala 7 additions, 2 deletions...ala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala 1 addition, 1 deletion...la/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala 2 additions, 6 deletions...a/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala 2 additions, 2 deletions...nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala 2 additions, 2 deletions.../nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala 3 additions, 3 deletions...l/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala 2 additions, 2 deletions...l/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala 2 additions, 2 deletions...ala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala 4 additions, 3 deletions...src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala 29 additions, 19 deletions.../main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
- biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala 20 additions, 6 deletions...s/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala
- biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala 7 additions, 0 deletions...s/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
- biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala 2 additions, 2 deletions...ain/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala
- biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/SummaryValue.scala 0 additions, 1 deletion...cala/nl/lumc/sasc/biopet/utils/summary/SummaryValue.scala
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