Feature toolcommands

See merge request !18

Feature metrics on bam input

Added metrics when pipeline starts with bamfile

See merge request !16

Add IntelliJ project files

Two commits here:

* Adding IntelliJ project files (so anybody else could still use IntelliJ ;) + we have the Netbeans configs after all)
* .gitignore update to exclude personal IntelliJ project files

See merge request !15

Feature version

Fix for #10

See merge request !13

Waiyi

merge for ticket #54

See merge request !12

Sander

for #54 and #40

See merge request !11

Bow

Per #54

See merge request !10

Peter

First merge to start new branching, see also #54

See merge request !9