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

Feature fix mapping

Fix for #108

See merge request !81