New Features and Bug Fixes

[alex-sandercock]

• Update polyRAD inputs
• Add SVG support throughout
• Update Cores selection slider
• Update VCF Filter Plots before user selections
• Add MADC example file to Convert to VCF
• Add warning for non-fixedAlleleID MADC
• Add user option to obtain ALT and REF information from MADC file for madcs2vcf()
• Export/Import bgzipped VCF files
• Prevent download of .html file if error occurs during Convert to VCF, or Dosage Calling
• Add user note below dosage ratio plot designating 0 as homozygous reference
• Add contamRate as a user option for polyRAD

[alex-sandercock]

I remembered why the VCF filtering plots do not populate until the user selects "Apply Filters" - This is because Updog will impute all sites, so the SNP and Sample histograms will appear as 0 missing data until the user selects the min read depth value to convert dosage calls to NA. To get around this, I am using the read depth value provided by the user, and displaying both pre- and post- filtered VCF plots after applying the filters.