v1.12.0

Merge remote-tracking branch 'upstream/master'

vcfR v1.10.0

Released on CRAN 2020-02-06

• Handled deprecated "dplyr::verb_" function in vcfR2tidy
• Omitted unused elipses from proc.chromR()

v1.8.0

Released on CRAN 2018-04-17

• Attempted to address CRAN's 'Note: break used in wrong context: no loop is visible' issue.
• .vcf_stats_gz() reports number of elements in header as well as the file's last line. This is used by read.vcfR() to check for poorly formed files.
• show method for vcfR now queries @fix instead of @gt.
• check_keys() checks key definitions in the meta section to make sure they are unique.
• freq_peak_plot() has parameter posUnits to adjust units of scatterplot.
• vcfR2migrate() manual discusses Unix and Windows line endings.

v1.7.0

This version was released to coincide with the submission of a manuscript on the subject of the inference of copy number variation.

vcfR 1.7.0

Released on CRAN 2018-02-07.

• vcf_field_names() now delimts on KEY= of key/value pairs, allows commas to be used within value.
• read.vcfR() will download files when provided with a link.
• Added example data from the Variant Effect Predictor (vep) data(vep).

v1.5.0

Released on CRAN 2017-05-18.

• Created genetic_diff() to calculate fixation indicies.
• Addressed symbol recognition NOTE: RcppCore/Rcpp#636 (comment).
• Moved pinfsc50.png to tools.
• Added samples parameter to vcfR method [.
• Deprecated the parameters 'chrom.s' and 'chrom.e' of 'chromo()', please use 'xlim' instead.
• Added length() method for chromR objects.
• [ method throws warning if FORMAT is omitted.
• plot() for signature 'chromR' handles INFO column when its all NA.
• create.chrom() subsets to first chromosome when more than one is provided.
• adegenet::nLoc(NULL) appears to generate an error when converting data types.

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.