Commit 06c874ae authored 9 years ago by Wai Yi Leung

Merge with develop

parents 627f9574 911948ed

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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala 6 additions, 6 deletions

.../lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala 0 additions, 54 deletions

.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala 3 additions, 0 deletions

.../main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala 4 additions, 4 deletions

...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala 11 additions, 1 deletion

...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala 4 additions, 1 deletion

.../scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Version.scala 80 additions, 0 deletions

...ore/src/main/scala/nl/lumc/sasc/biopet/core/Version.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala 4 additions, 4 deletions

...in/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala 2 additions, 2 deletions

...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala 23 additions, 12 deletions

...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala 4 additions, 4 deletions

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala 4 additions, 4 deletions

...main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala 4 additions, 4 deletions

...main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala 4 additions, 4 deletions

.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala 4 additions, 4 deletions

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala 4 additions, 4 deletions

...main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala 4 additions, 4 deletions

...src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala 4 additions, 4 deletions

.../src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala 4 additions, 4 deletions

...ain/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala 4 additions, 4 deletions

...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala

with 177 additions and 124 deletions

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