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vcfR v1.9.0
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@knausb knausb released this 10 Jan 16:43
· 118 commits to master since this release
v1.9.0
fa551f6

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.
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