Release notes Biopet version 0.4.0

A reporting framework has been added for most pipelines
This framework produces a static HTML report which can be viewed in your browser
The framework contains lots of quality control and downstream analyses plots (genome coverage, transcript coverage etc etc.)
An issue where a NullPointerException was being thrown when output_dir was not set in the config was fixed. This now gives a nice error message which points to the missing key in the config
Pipelines now automatically write a log file if none is specified on command line
Tools writing to VCF will no longer fail when the output is not a gzipped VCF
Pipelines now support passing config options directly into the commandline prompt
Pipelines now support a more readable config file format YAML
Memlimit and vmem memory issues are solved by automatically increasing the amount of available memory when a job fails. --retry 5 should do the trick
BamMetrics pipeline is updated to work with newest version of Picard
A bug in VcfStats in comparing samples alleles is fixed. Now each allele can only be used once in the comparison.
VcfStats is now capable of summarizing stats per bin (bin size is changeable)
There is now a module which checks for the present of correct reference files if not it automatically builds the appropriate ref files

Some pipelines were updated as well: