Vcf-dedup

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* Major changes
- Adding support for a generic mode that relies on standard VCF annotations. QUAL column for variant calling quality and AF INFO annotation for the allele frequency.
- Platypus support now uses QUAL instead of QD as variant calling quality value.
* Minor changes
- Options not used for Platypus and generic modes `--sample-name` and `--sample-idx` are not required now. They are still required for Strelka and Starling.

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* Minor changes
- Making sure the writers are flushed and closed.

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* Major Changes:
- Option to sort the input VCF by chromosome, position, reference and alternate bases
- Platypus is now supported
- Additional selection method `allele_calls`. This selection method is not available as it does not report genotypes.

* Minor changes
- Duplicated variants are now written into file `${output_vcf}.duplicated.vcf`

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* Minor Changes:
- `duplication_finder` failed to write properly last set of duplicates.
- Fixed bug in calculation of allele frequencies for Starling. We were using AC, which did not exist, instead of AD.

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* Minor Changes:
- `duplication_finder` failed to write last set of duplicates.

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* Major Changes:
- `sample-name` parameter added in addition to `sample-idx`
- When output is not provdied it writes to standard output
- Fixed bug when calculating allele frequencies