Vcfvalidator

This release includes 2 changes:
- Added a new flag `--require-evidence` to check the presence of genotypes, allele frequencies or allele counts.
- Fix a bug where number parsing and validation was not as strict as expected.

This is a patch release that includes just 2 important fixes:

- There was an error about locales when running in Ubuntu 18: https://github.com/EBIvariation/vcf-validator/issues/184
- Bgzipped VCFs had a small chance of being read incompletely.

We recommend everyone to use this version instead of the previous ones.

Note that **everything except these new features is equally stable** as in the previous release v0.9.1. Using the latest version is recommended.

This release adds 2 new experimental features to the assembly checker

The 2 new features were not present in v0.9.1 and might change its behaviour in the future.

1) Possibility of checking a VCF against a FASTA file, where they use a different chromosome naming system.

For instance, your VCF uses chromosome numbers:

CHROM POS...
1 100 ...

but you have a FASTA with chromosome accessions:

>CM000001.3 chromosome 1
ATCG...


Now you can use the `-a` parameter to provide the path to a file with the mapping. The file structure expected is that of NCBI's assembly reports such as ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/285/GCA_000002285.2_CanFam3.1/GCA_000002285.2_CanFam3.1_assembly_report.txt

For each chromosome, the assembly checker will try to find in the FASTA any synonym under the columns "Sequence-Name", "GenBank-Accn", "RefSeq-Accn" and "UCSC-style-name".

2) Remote sequence retrieval.
If no FASTA file is provided, [EBI-ENA](https://www.ebi.ac.uk/ena) will be queried to download the sequence of each chromosome used in the VCF to check every reference allele.

This small release contains only small fixes and the next improvements:

If the header line in a VCF file contains several samples with the same name, it is now flagged as an error, as recently clarified in the VCF specification.

Warnings are now logged if there are unused parameters in the command used to run any of the tools. Thanks srbcheema1 for the contributions!

A new tool has been added to the suite! This one checks that the REF column in a VCF matches the sequence contained in a FASTA file, and reports any mismatches in a summary or plain text file, in a similar fashion to the VCF validator reporting. A new report type that only outputs the valid lines is also included in this tool.

We have also added support for Windows, making the suite compatible with the 3 major operating systems. Please be aware that you will need to decompress your files before validating them on Windows due to a [known issue](https://github.com/EBIvariation/vcf-validator/issues/160).

You can find the binaries for all versions, ready for direct download, attached to these notes.

MacOS users can now run the validation suite in their favorite OS, without needing Docker or admin permissions. Just copy the executable in the link into your machine and run it in exactly the same way as in Linux. Please let us know if you find any compatibility issues by [creating a bug report](https://github.com/EBIvariation/vcf-validator/issues/new).

The validator can also read files compressed in multiple formats without the need of a pipe. You can find instructions in the updated [README file](https://github.com/EBIvariation/vcf-validator/tree/v0.8#run).

Thanks to srbcheema1 for these contributions!