v1.4.0

Released on CRAN 2017-01-07.

• masplit() converts '.' to NA.
• extract.indels() does not recognize NA as a deletion.
• Added parameter getINFO to getFIX() to suppress INFO column.
• CRAN brought to my attention that I have new memory access issues which have been addressed.

v1.3.0

vcfR 1.3.0

Released on CRAN 2016-12-08.

• extract.gt() no longer uses parameter allele.sep().
• Added more info to chromR show method.
• When annotation data include more than one chromosome in create.chromR() the data are subset to the first chromosome. Thank you Christian!
• added convertNA parameter to extract.gt() to allow preservation of VCF encoding of missing data. Thank you Thierry!
• added convertNA parameter to read.vcfR() to allow preservation of VCF encoding of missing data. Thank you Thierry!
• extract.haps omits gt.split and implements unphased_as_NA
• gtsplit handles a mixture of phased and unphased data
• Added 'getters' for vcfR and chromR slots. Thanks Zhian!
• Created freq_peak() to find peaks in allele balance frequency data.
• Created masplit() to parse matrices contains delimited strings.
• Created ordisample() to ordinate sample information.
• extract.gt() can now use the ID column from the fix region for rownames.
• Created INFO2df() and metaINFO2df().
• Prof Brian Ripley made me aware of memory leaks reported by valgrind.
  Conditional jump or move depends on uninitialised value(s) - write_vcf_body file initialization issue resolved.

v1.2.0 dplyr 0.5.0 compatibility

• vcfR2genind() greps genotypes containing a missing allele ('.') and sets to NA.
• dplyr v0.5.0 broke some vcfR2tidy functionality. This functionality should be fixed in this release.
• is_het() rapidly identifies heterozygotes.
• extract.info() scores missing elements as NA.

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.

v1.0.0

Released on CRAN on 2016-02-22.