Feature shiva

This will become a new version of the variantcalling pipeline.

See also issue #116 and #119

See merge request !110

Feature rcommandline

R commandline function cherry-picked

See merge request !121

Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala

Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala

Patch mapping

Fix for #122

See merge request !120

Patch summary versions

Fix for Some(versions) in summary

See merge request !118

Patch seqstat

Fix for #121

See merge request !119

bow authored 10 years ago and Peter van 't Hof committed 10 years ago

(cherry picked from commit 6ca9d8be)

Feature scaladocs

Added scala docs to all extensions, utils and pipeline template.

See also #37

See merge request !116

Patch carp summary fix

In the CARP pipeline we forgot to fill in the global summary file. So this had to be added. Tested and works fine now!

See merge request !115