Commit 74077f92 authored 10 years ago by bow

Merge branch 'feature-fix_mapping' into 'develop'

Feature fix mapping

Fix for #108

See merge request !81

parents bfdd3e42 fa32164f

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protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala 1 addition, 1 deletion

...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala 1 addition, 1 deletion

...l/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala 2 additions, 2 deletions

...ala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala 1 addition, 2 deletions

...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala 0 additions, 3 deletions

.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala 3 additions, 3 deletions

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala 1 addition, 1 deletion

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala 2 additions, 2 deletions

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

...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala 7 additions, 7 deletions

...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala 2 additions, 2 deletions

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala 6 additions, 6 deletions

...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala 11 additions, 9 deletions

.../nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala 6 additions, 6 deletions

...l/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala 1 addition, 1 deletion

...nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala 2 additions, 2 deletions

.../scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala 2 additions, 2 deletions

...la/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala 1 addition, 1 deletion

...umc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala 2 additions, 2 deletions

...scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala 18 additions, 11 deletions

...rc/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala

with 71 additions and 66 deletions

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