Commit 0f4c6e15 authored 8 years ago by Sander Bollen

Merge branch 'develop' into fix-gvcfs-extract

Conflicts:
	shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala

parents 2491e655 f963bb6e

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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala 63 additions, 14 deletions

.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala 2 additions, 2 deletions

.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala 2 additions, 2 deletions

.../lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala 4 additions, 7 deletions

...lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BamGatherFunction.scala 2 additions, 3 deletions

.../lumc/sasc/biopet/extensions/gatk/BamGatherFunction.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala 3 additions, 4 deletions

...l/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala 41 additions, 43 deletions

...ala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariantsGather.scala 1 addition, 1 deletion

.../lumc/sasc/biopet/extensions/gatk/CatVariantsGather.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala 3 additions, 3 deletions

...la/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala 112 additions, 64 deletions

...nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CommandLineGATK.scala 1 addition, 1 deletion

...nl/lumc/sasc/biopet/extensions/gatk/CommandLineGATK.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ContigScatterFunction.scala 4 additions, 3 deletions

...c/sasc/biopet/extensions/gatk/ContigScatterFunction.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala 0 additions, 76 deletions

...main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkScatterFunction.scala 4 additions, 4 deletions

...umc/sasc/biopet/extensions/gatk/GatkScatterFunction.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala 67 additions, 42 deletions

...umc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala 3 additions, 3 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/IndelRealigner.scala 3 additions, 3 deletions

.../nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/LocusScatterFunction.scala 4 additions, 3 deletions

...mc/sasc/biopet/extensions/gatk/LocusScatterFunction.scala
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala 2 additions, 2 deletions

...cala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala

with 323 additions and 282 deletions

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