Commit bec375ba authored 10 years ago by bow

Merge branch 'feature-unittest_core' into 'develop'

Flexiprep unit test + fix for small bugs

See subject

See merge request !94

parents faa0baaf d04c7f03

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public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala 1 addition, 1 deletion

...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
public/bam2wig/src/test/resources/log4j.properties 25 additions, 0 deletions

public/bam2wig/src/test/resources/log4j.properties
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala 2 additions, 4 deletions

...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
public/bammetrics/src/test/resources/log4j.properties 25 additions, 0 deletions

public/bammetrics/src/test/resources/log4j.properties
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala 13 additions, 0 deletions

.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala 59 additions, 17 deletions

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala 15 additions, 4 deletions

...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala 33 additions, 18 deletions

...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala 10 additions, 0 deletions

...ork/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala 3 additions, 0 deletions

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

...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala 11 additions, 0 deletions

...main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala 8 additions, 2 deletions

...src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala 14 additions, 11 deletions

...c/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala 6 additions, 0 deletions

...n/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala 2 additions, 1 deletion

.../scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala 5 additions, 3 deletions

...lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala 2 additions, 2 deletions

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala 2 additions, 2 deletions

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.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

with 240 additions and 69 deletions

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