Feature add ids to filter

Added options to vcf filter tool for @s.a.j.van_der_zeeuw and @j.f.j.laros

See merge request !88

Feature fix raxml

Small fix for basty pipeline

See merge request !87

Patch flexiprep mapping flags

@wyleung and @p.j.van_t_hof

This is what we discussed earlier. The temporary solution is to expose it in the command line. I've also added some notes there and did some small refactoring. It's all in the commit messages :).

See merge request !80

Patch doc fixes

Part of the docs in develop are still in there old setup. Should be added to dev.

See merge request !86

Feature igvtools

Using IGVtools `count` to create TDF or WIG files...

Need some more work - in next commits..

See merge request !73

Feature fix gatk

Small fix on gatk pipeline

Branch can be removed

See merge request !85

Feature vcf stats

More functions can be added but this is a first version that is ready to use in the gatk pipeline.

is also fix for #93

See merge request !84