Commit e44e7e62 authored 10 years ago by bow

Merge branch 'feature-merge_alleles' into 'develop'

Feature merge alleles

Extends from !44
Also added a tool MergeAlleles and implemented in the gatk-variantcalling pipeline

See merge request !46

parents 933194d3 c405c4bb

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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala 38 additions, 22 deletions

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala 11 additions, 0 deletions

...ain/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala 2 additions, 3 deletions

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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala 13 additions, 6 deletions

...ork/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala 2 additions, 2 deletions

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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala 2 additions, 2 deletions

...src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala 4 additions, 2 deletions

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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala 6 additions, 6 deletions

.../scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala 1 addition, 1 deletion

...nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala 1 addition, 1 deletion

...l/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala 0 additions, 1 deletion

...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala 2 additions, 5 deletions

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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala 2 additions, 5 deletions

.../sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala 2 additions, 4 deletions

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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala 6 additions, 12 deletions

...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala 12 additions, 31 deletions

.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala 1 addition, 2 deletions

...umc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala 1 addition, 1 deletion

...scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala 14 additions, 32 deletions

...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala 5 additions, 9 deletions

.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

with 125 additions and 147 deletions

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