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

...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala 0 additions, 7 deletions

...c/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala 1 addition, 1 deletion

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala 7 additions, 2 deletions

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala 12 additions, 14 deletions

.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala 1 addition, 1 deletion

...rc/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala 2 additions, 2 deletions

...l/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala 3 additions, 3 deletions

.../lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala 1 addition, 1 deletion

.../nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala 1 addition, 1 deletion

...mc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala 1 addition, 1 deletion

...et/extensions/picard/CollectAlignmentSummaryMetrics.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala 2 additions, 2 deletions

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

...c/biopet/extensions/picard/CollectInsertSizeMetrics.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala 2 additions, 2 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/SortSam.scala 2 additions, 2 deletions

...scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/SquishBed.scala 1 addition, 1 deletion

...rc/main/scala/nl/lumc/sasc/biopet/scripts/SquishBed.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala 2 additions, 0 deletions

.../src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala 2 additions, 2 deletions

...c/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala 2 additions, 2 deletions

...c/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala

with 47 additions and 49 deletions

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