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Releases: knausb/vcfR

v1.15.0

08 Dec 19:50
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v1.15.0

  • Ran usethis::use_package_doc()

v1.13.0

25 Jul 18:41
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vcfR 1.13.0

Released on CRAN 2022-07-16

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

v1.12.0

01 Sep 18:17
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updated release info in NEWS.md

vcfR 1.11.0

05 Jun 22:29
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Released on CRAN 2020-06-05

  • Now compatible with R 4.0.0 and dplyr 1.0.0

vcfR v1.10.0

06 Feb 16:22
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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

10 Jan 16:43
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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

17 Apr 18:26
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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

08 Feb 00:11
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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

08 Dec 16:19
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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

18 May 14:53
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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.