NEWS.md

In knausb/vcfR: Manipulate and Visualize VCF Data

vcfR 2.0.0.

There is currently no plan to release vcfR 2.0.0. If and when this 'major' release occurs it will include changes that will break backward compatibility. At the present, this is simply a to-do list for ideas to include in the next major release.

• gzread needs us to tell it a maximum number of bytes to read in, so we need to make an arbitrary guess. I think I encountered a situation where 4-96 was not enough so I've bumped it to 16,384 B.
• Move 'FORMAT' column to its own slot. We can then cbind FORMAT and gt when passing to compiled code. This may have been addressed at 64a308ba50b9119108e8946737460de5997b805b by adding samples to vcfR method [.
• In issue #92 (vcfR2genlight big data #92), JimWhiting91 has documented that extract.gt() could be greatly improved with multithreading. While he used mclapply() I do not feel this is the best solution because it does not work on Windows. I think a better solution would be RCppParallel because this should work on all CRAN platforms.

vcfR 1.16.0

vcfR 1.15.0

Released on CRAN 2023-12-07 * Ran usethis::use_package_doc()

vcfR 1.14.0

Released on CRAN 2023-02-10 Compile time 'nodiscard' attribute: changed 'col_vec.size()' to 'sizeof(col_vec)' in ad_frequency.cpp and masplit.cpp vcfR_to_tidy handles no INFO in meta

vcfR 1.13.0

Released on CRAN 2022-07-16 * Added vcfR2hapmap() to convert data for use in GAPIT

vcfR 1.12.0

Released on CRAN 2020-09-01 Added PKGTYPE: both to appveyor.yml so Windows packages can be built from source Omitted configure file that unnecessarily tried to invoke checkbashisms * Incorporated help from https://stackoverflow.com/a/62721142 to use checkbashisms when checking on Debian flavors of Linux (ended up omitting this change but left this here to document it and the link)

vcfR 1.11.0

Released on CRAN 2020-06-05 * Now compatible with R 4.0.0 and dplyr 1.0.0

vcfR 1.10.0

Released on CRAN 2020-02-06 Handled deprecated "dplyr::verb_" function in vcfR2tidy Omitted unused elipses from proc.chromR()

vcfR 1.9.0

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.

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.

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).

vcfR 1.6.0

Released on CRAN 2017-12-08. vcf_field_names() now handles keys that are out of order and multiple optional keys. 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 . 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. Thanks Javier!

vcfR 1.5.0

Released on CRAN 2017-05-18.

• Created genetic_diff() to calculate fixation indicies.
• Addressed symbol recognition NOTE: https://github.com/RcppCore/Rcpp/issues/636#issuecomment-280985661.
• 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.

vcfR 1.4.0

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.
• Prof Brian Ripley brought to my attention that I have new memory access issues: The memory-access errors are new this version, and there is also undefined behavour (trying to coerce NaN to integer).

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.

vcfR 1.2.0

Released on CRAN 2016-07-25.

• 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.

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.

vcfR 1.0.0

Released on CRAN 2016-02-22. This release was used to prepare the manuscript that was submitted to Molecular Ecology Resources.

knausb/vcfR documentation built on Jan. 14, 2024, 1:56 a.m.