Commit b76ad0ad authored 9 years ago by Peter van 't Hof

Merge branch 'develop' into feature-report

Conflicts:
	public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

parents dee7eea1 2b7a4f2f

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docs/examples/gentrap_example.json 54 additions, 0 deletions

docs/examples/gentrap_example.json
docs/pipelines/gentrap.md 8 additions, 3 deletions

docs/pipelines/gentrap.md
docs/pipelines/shiva.md 2 additions, 0 deletions

docs/pipelines/shiva.md
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp 9 additions, 1 deletion

...umc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp 7 additions, 1 deletion

...s/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp 1 addition, 1 deletion

...nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala 14 additions, 7 deletions

...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala 2 additions, 2 deletions

...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala 4 additions, 3 deletions

...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala 11 additions, 4 deletions

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala 15 additions, 0 deletions

...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala 4 additions, 2 deletions

...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala 14 additions, 4 deletions

...asc/biopet/extensions/picard/CollectMultipleMetrics.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala 5 additions, 2 deletions

.../sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala 22 additions, 18 deletions

.../scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala 1 addition, 1 deletion

...main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala 5 additions, 5 deletions

...rc/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala 24 additions, 46 deletions

...rk/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/MergeTablesTest.scala 1 addition, 1 deletion

...est/scala/nl/lumc/sasc/biopet/tools/MergeTablesTest.scala
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala 6 additions, 6 deletions

...rc/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala

with 209 additions and 107 deletions

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