Fix warns

Going to try to fix most of the code warnings from the IDE
Also going to optimise imports for the whole repository

See merge request !187

Conflicts:
	public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

Extract checkDict and checkFai in a public method

Fix for #173

Still needs testing.

See merge request !190

Report links fix - minor update

Fix the link to sasc.lumc.nl (don't point to the https version, redirect is automatic from http version)

See merge request !189

# Conflicts:
#	public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
#	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
#	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
#	public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
#	public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
#	public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala

https is working now, revert the change but keep the new layout and abbr tag. (second try). IDE was replacing the tag in an incorrect way.

Fix the link to sasc.lumc.nl (don't point to the https version, redirect is automatic from http version)

Feature report

second phase for reporting

Adding report to all general pipelines

See merge request !184

Issue164

See #164

See merge request !186

Fix the test of seqstat, so that develop can build again

See merge request !188

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

Working dir for unit tests is now the target folder

Fix for #150

See merge request !176

Small fixes

Fixes two small issues

1. Extra docs for target beds/regions of interest for Shiva
2. Fixes integer overflow on WGS coverage statistics for report (Size of human genome > 2^31 -1 bases)

See merge request !177