Fix basecounter

Some small fixes

See merge request !373

Fixed bug in vcffilter

Fixes #313 

See merge request !370

Fix report, the logic to display SE or PE from flexiprep stats is deprecated since we always use flexiprep->cutadapt in SE mode. So only SE mode variables are generated and should be displayed in the report.

Set default htseq-count sorting order to pos



See merge request !364

Release 0.6.0

This is to merge back changes on the release branch to develop again. First !362  should be done

See merge request !363

Added wigle and tdf files to summary



See merge request !361

Fix names

When jenkins find no issues here we can merge this

See merge request !359

Fix small fixes



See merge request !357

General refactor Biopet



See merge request !358

Fix: Show a message for those plot, which were not created by FastQC. Some stati…

…stics cannot be collected by FastQC such as Kmer when the sequences are clean.

See merge request !355

Fix small fixes

Fixes #299 and #300 

See merge request !353

add amplicon bed file documentation

Added documentation about amplicon_bed and regions_of_interest bed files.

closes #297 

See merge request !356

Fix bug when bowtie2 is not able to find reference files ending with .bt2l



See merge request !354