v1.15.0

v1.15.0

• Ran usethis::use_package_doc()

v1.13.0

vcfR 1.13.0

Released on CRAN 2022-07-16

• Added vcfR2hapmap() to convert data for use in GAPIT

v1.12.0

updated release info in NEWS.md

vcfR 1.11.0

Released on CRAN 2020-06-05

• Now compatible with R 4.0.0 and dplyr 1.0.0

vcfR v1.10.0

vcfR 1.10.0

Released on CRAN 2020-02-06

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

vcfR v1.9.0

Released on CRAN 2020-01-10

• Changed class(x) == "matrix" to inherited(x, "matrix")
• Changed license from GPL to GPL-3 (#144).
• extract.haps() reports the correct number of variants processed when verbose.
• The square brackets ([]) handle @gt slots with no samples.
• vcfR2loci() now has the option return.alleles = FALSE.
• vcfR2genind() now has the option retrun.alleles = FALSE.
• Error handling code moved into the C++ functions called by read.vcfR so that errors are thrown earlier when reading a VCF. read.vcfR no longer checks that a file is readable first, which solves issues sometimes seen with shared files. (Issue #109, reported and fixed by @NikNakk).
• extract.haps() did not include the parameter return.alleles = TRUE in it's call to extract.gt() in the haploid branch of the function. This parameter has now been added. This also affects vcfR2DNAbin() which calls this function.
• vcfR2genlight() includes the parameter ... to pass parameters to adegenet::df2genind().
• is.indel() returns logical vector to identify indels.
• gt.to.popsum now handles genotypes that include some, but not all, missing alleles.

v1.8.0

vcfR 1.8.0

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).

v1.6.0

vcfR 1.6.0

Released on CRAN 2017-12-08.

• vcfR2DNAbin() can include indels and maintains alignment.
• write.vcf() now handles tilde expansion.
• rePOS() attempts to create a non-overlapping coordinate system from POS and CHROM.
• vcfR2DNAbin() manages the asterisk allele.
• extract.indels() ignores GATK's <NON_REF>.
• Added support for chromR objects with no gt slot to proc.chromR().
• Created peak_to_ploid() to call peaks and calculate dfe from freq_peak() output.
• Created freq_peak_plot() to help visualize the output of freq_peak().
• .vcf_stats_gz now has nrows and skip parameters.
• removed .Call() statements to standardize style.
• Created vcfR2migrate() to output MigrateN format data.
• Addressed clang-UBSAN memory leak in freq_peak().
• Created pairwise_genetic_diff() to calculate pairwise differentiation.

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.