Fix script run time

Fixes #330 

See merge request !381

Fix samplenames qiime

Samples in qiime may not contain `_`, this now get replaces to `-` for qiime only.

Also fixed small bug in vcfstats summary.

See merge request !380

Feature fix star options



See merge request !368

Fixed vcffilter test

Fixed failing tests

See merge request !379

fix #329



See merge request !377

Force reference dict in vcf to check on unknown contigs

Fixes #179 

See merge request !378

Snp test pipeline



See merge request !360

Refactor some loops and remove warnings

Reimplement some .par, removing for-loops. 
Avoiding warnings from the compiler wining about version specific syntax.

Adding description to the report builder (it's own commandline arg)

See merge request !376

Adding SortVcf extension

This wrapper can be used to sort VCF files, whenever they have to be sorted (some variant callers generate non-sorted VCF).

See merge request !372

Reimplement some .par, removing for-loops. Avoiding warnings from the compiler wining about version specific syntax.

Fix an issue with HashMap which is not handled by ConfigUtils. Converting to Map before adding to the JSONMap instead.

BamUtils Insertsize estimation is more acurate by sampling from all over the contig.

Updated BamUtils to fix the insertsize estimation used in the PindelConfig tool.

See merge request !371