Commit 07388f51 authored 9 years ago by Peter van 't Hof

Merge remote-tracking branch 'origin/develop' into feature-scoverage

Conflicts:
	protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala

parents c02fcacd 5555a57f

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protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala 12 additions, 6 deletions

.../scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala 7 additions, 1 deletion

.../sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala 1 addition, 0 deletions

...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala 2 additions, 1 deletion

...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala 5 additions, 1 deletion

...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala 2 additions, 0 deletions

...cala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala 18 additions, 1 deletion

...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
public/biopet-core/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-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala 40 additions, 0 deletions

...a/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala 1 addition, 0 deletions

...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala 21 additions, 3 deletions

...ala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala 3 additions, 2 deletions

...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala 1 addition, 1 deletion

...a/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala 1 addition, 0 deletions

...s/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala 3 additions, 0 deletions

...la/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala 1 addition, 0 deletions

.../scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala 2 additions, 1 deletion

...t/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala 1 addition, 0 deletions

...ala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala 3 additions, 0 deletions

...st/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala 2 additions, 0 deletions

...est/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala

with 128 additions and 19 deletions

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