NEWS

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vcfppR 0.8.3 (2026-03-31)

• bugfix: vcfcomp with truth being an vcftable object for stats = "r2"!
• update F1 score to allow for missing category

vcfppR 0.8.2 (2025-11-06)

• extend subset S3 function for vcftable
• vcfcomp: stats='gtgq'
• fix vcfplot
• more unit tests and examples

vcfppR 0.8.1 (2025-08-25)

• remove unused code in vcfpp.h
• vcfcomp: rename the col name "concordance" as "accuracy"

vcfppR 0.8.0 (2025-07-02)

• copy static libs into libs folder

vcfppR 0.7.6 (2025-03-31)

• fix CRAN notes

vcfppR 0.7.5

• fix issue #14 to handle libdeflate dependency on linux

vcfppR 0.7.4

• fix issue #13 to speedup setRegion

vcfppR 0.7.3

• enable libdeflate on linux

vcfppR 0.7.2

• make htslib available for including and linking by other packages

vcfppR 0.7.0 (2024-12-21)

• fix parsing BCF when subsetting sample ids and the genomic region at the same time
• fix vcfcomp with stats="nrc" when the input vectors have different length
• use the latest version of htslib v1.21
• reduce the size of installation

vcfppR 0.6.0 (2024-09-29)

• upgrade vcfpp.h to v0.6.0
• new API vcfreader$setRegion
• new API vcfreader$getStatus

vcfppR 0.5.0 (2024-09-22)

• upgrade vcfpp.h to v0.5.1
• add bcfreader$updateSamples() function
• vcfcomp: can take vcftable object as input
• vcfcomp: defaults changed setid=FALSE
• bug fix

vcfppR 0.4.6 (2024-05-24)

• add vcfplot function
• fix bug in vcftable when FORMAT has unaligned list
• add vignette on vcfcomp

vcfppR 0.4.5 (2024-04-08)

• add vcfcomp function
• fix memory leaks and pass ASAN check

vcfppR 0.4.0 (2024-02-26)

• add setid option for vcftable
• patches for upcoming Rtools on windows

vcfppR 0.3.8 (2024-01-14)

• fix issues on M1 Mac

vcfppR 0.3.7

• add vcfreader@rmFormatTag()
• add vcfreader@samples()
• vcftable supports vartype = 'sv'

vcfppR 0.3.6

• add vcfreader::line
• remove vcfreader::setVariant
• bug fix setFormatStr
• more units tests

vcfppR 0.3.5 (2023-12-14)

• add vcfreader and vcfwriter

vcfppR 0.3.4

• support filters by variant ID

vcfppR 0.3.3

• use API of vcfpp.h v0.3.1
• set missing vaules in FORMAT to NA
• support filters by QUAL, FILTER and INFO

vcfppR 0.3.0

• First release using vcfpp.h v0.3.0
• add vcftable function
• add vcfsummary function
• add vcfpopgen function