Added a option to not keep the last fastq file anymore

See also #185 

Can not remove the zip action completely, it's still needed for the final fastqc. It's now intermediate by default when running flexiprep in an other pipeline on default.

See merge request !212

No chunk_metrics when chunking is disabled

Small improvement.

There is a chance this is a fix for #195, this is to sure

See merge request !225

Martijnvermaat readme fixes

Resolving some old pull request from github

See merge request !226

Merge branch 'readme-fixes' of git://github.com/martijnvermaat/biopet into martijnvermaat-readme-fixes

Added picard R scipts as workaround till issue is resolved

Workaround for #194 

Will first test this before merge.

See merge request !221

Feature tool squish bed

see also #49 

See merge request !223

Feature region af count

This is a new tool made for SASC project 71. Tool will get sums af AF from a vcf file for a given set of regions. Also generates a scatter plot when more vcf files are given, first vcf file is always the ref set like gonl or 1000 Genomes.
Will become a fix for multiple issue:
- [x] BedFile reader, htsjdk bed reader is not fully supported scala
 - [x] Extraction of Exons
 - [x] Extraction of Introns
 - [x] Extraction of UTR regions
 - [x] Squish method, requires by #49 
 - [x] Combine overlapping records
 - [x] Scatter regions with a given approximate bin size 
- [x] #192 
 - [x] Use Biopet interval interface
 - [x] Extract features when given in a bed file
- [x] #148 (need for #171)
 - [x] Use Biopet interval interface
 - [x] Use general scatter method
- [x] #49 
 - [x] Use Biopet interval interface
 - [x] Use general Squish method

See merge request !218

Raised memory for star

This will fix 8 test for STAR, tested in Jenkins run 80.

Other 12 failing tests are from picard, see #194 

See merge request !222

Fixed tophat unittests

This should fix failing unit tests for tophat

See merge request !220

Fix aligners

Some aligner are failing in testing, this should fix those issues

See merge request !217

Adding index file as output file for queue

Small fix to add the index file as output file for queue

See merge request !219