Accepted pending minor revisions

vcfR 1.1.0

Released on CRAN 2016-05-26.

This release includes the incorporation of suggestions made by reviewers of the manuscript submitted to Molecular Ecology Resources.

• added is.het() to identify heterozygotes in a matrix of genotypes.
• Fixed one-off error in vcfR2DNAbin where a variant one position beyond the locus would attempt to be included but threw an error.
• Added examples to VCF input and output.
• Added vcfR_test as lightweight test VCF data.
• Changed chromR@name to chromR@names for consistency with other R objects.
• Added AD_frequency calculates allele frequencies from matrices of AD data.
• read.vcfR() handles VCF data with no GT region (ala LoFreq).
• gt2alleles handles missing data ('.').
• read.vcfR() checks for and removes carriage returns (Windows).
• vcfR2DNAbin converts 'NA' to 'n' prior to conversion to DNAbin.
• chromR2vcfR implements use.mask.
• extract.gt() converts "." to NA.
• Added tidyr compatibility - thank you Eric Anderson!
• write.vcf() now uses mask = TRUE.
• maf() provides counts and frequency for the minor (or other) allele.
• create.chromR() now handles instances with no seq and the annotation position exceeds the greatest VCF POS.
• read.vcfR() now handles tilde expansion.
• addID() populates the non-missing values in the ID column of VCF data by concatenating the chromosome and position.