Commit 3a13df98 authored 9 years ago by Peter van 't Hof

Merge branch 'feature-varda' into 'develop'

Feature varda

fixes #208 

This is to track this branch in jenkins

See merge request !245

parents 27236df5 9fbc2376

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public/biopet-extensions/pom.xml 7 additions, 0 deletions

public/biopet-extensions/pom.xml
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala 184 additions, 0 deletions

...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala 28 additions, 0 deletions

.../lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala 83 additions, 0 deletions

...in/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala 32 additions, 0 deletions

.../lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala 32 additions, 0 deletions

.../lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala 27 additions, 0 deletions

...sc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesDownload.scala 19 additions, 0 deletions

...sc/biopet/extensions/manwe/ManweDataSourcesDownload.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala 23 additions, 0 deletions

...c/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala 22 additions, 0 deletions

...c/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala 22 additions, 0 deletions

...c/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala 30 additions, 0 deletions

...l/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAnnotateVariations.scala 26 additions, 0 deletions

...pet/extensions/manwe/ManweSamplesAnnotateVariations.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala 62 additions, 0 deletions

...umc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala 38 additions, 0 deletions

.../sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala 41 additions, 0 deletions

.../sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala 29 additions, 0 deletions

.../lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala 22 additions, 0 deletions

.../lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala
public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BcfToolsTest.scala 35 additions, 0 deletions

...t/scala/nl/lumc/sasc/biopet/extensions/BcfToolsTest.scala
public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala 372 additions, 0 deletions

...test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala

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