Fix mpileup to vcf

Fix MpileupToVcf to handle multi-nuclitides char better.

Also some refactoring in mapping and flexiprep. R2 should now be a Option[File], also for #133

See merge request !160

Feature improved bammetrics

see #127

See merge request !158

Fix flag handling and add some logging

See merge request !159

Patch rscript

See merge request !156

Fixed style

Auto style plugin keep changing this files in develop.

See merge request !154

Fix Picard metrics parsing to use the correct types

Work in progress: don't merge yet.

This merge request is for #151. I implemented a general utility function that should be able to handle arbitrarily large numbers. The trade off is that it loses the type information. Maybe there is some clever way to retain it, based on the return types of the supplied conversion function(s). But for now, this should be sufficient for the fix of issue #151 (there, we pattern match to check the actual type).

There are still some todos:

- [x] Update Picard parsing to handle this
- [x] Add unit tests for the conversion functions
- [ ] Add BigInt and BigDecimal support for the `anyToJson` function (this is optional, I think)

See merge request !148

Tsv mod

This fixes/closes #73

Changes:
* Use VCF naming conventions for default fields
* Spelling/typos
* Adding the option to change the separator
* Adding option to change amount of decimals for numeric values
* Fixes sorting function
* adding tests

See merge request !153