v0.4.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: vcfppR
 Title: Rapid Manipulation of the Variant Call Format (VCF)
-Version: 0.3.8
+Version: 0.4.0
 Authors@R: c(
     person("Zilong", "Li", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5859-2078")),
@@ -11,7 +11,7 @@ Description: The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an ea
 Encoding: UTF-8
 Depends: R (>= 3.6.0)
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests: 
     testthat (>= 3.0.0)
 Config/testthat/edition: 3

NEWS.md

@@ -1,3 +1,8 @@
+# vcfppR 0.4.0
+
+* add `setid` option for vcftable
+* patches for upcoming Rtools on windows
+
 # vcfppR 0.3.8
 
 * fix issues on M1 Mac

R/vcf-tables.R

@@ -36,6 +36,8 @@
 #'                 If the FORMAT to extract is not "GT", then with collapse=TRUE it will try to turn a list of the extracted vector into a matrix.
 #'                 However, this raises issues when one variant is mutliallelic resulting in more vaules than others.
 #'
+#' @param setid logical. reset ID column as CHR_POS_REF_ALT.
+#'
 #' @return Return a list containing the following components:
 #'\describe{
 #'\item{samples}{: character vector; \cr
@@ -87,7 +89,7 @@
 #' str(res)
 #' @export
 vcftable <- function(vcffile, region = "", samples = "-", vartype = "all", format = "GT", ids = NULL,
-                     qual = 0, pass = FALSE, info = TRUE, collapse = TRUE) {
+                     qual = 0, pass = FALSE, info = TRUE, collapse = TRUE, setid = FALSE) {
   snps <- FALSE
   indels <- FALSE
   svs <- FALSE
@@ -117,6 +119,7 @@ vcftable <- function(vcffile, region = "", samples = "-", vartype = "all", forma
     res <- tableFormat(vcffile, region, samples, format, ids, qual, pass, info, snps, indels, multiallelics, multisnps, svs)
     if(is.list(res[[10]]) && collapse) res[[10]] <- do.call("rbind", res[[10]])
   }
+  if(setid) res$id <- paste(res$chr, res$pos, res$ref, res$alt, sep = "_")
   return(res)
 }
 

cran-comments.md

@@ -1,4 +1,2 @@
-Fix issues on M1 Mac 
-
-https://cran.r-project.org/web/checks/check_results_vcfppR.html
+Fix issue for upcoming Rtools on windows
 

tests/testthat/test-vcf-table.R

@@ -14,6 +14,11 @@ test_that("extract GT for all SNPs", {
   expect_identical(sum(res$alt!=""), length(res$alt))
 })
 
+test_that("extract SNPs by ID and reset ID afterwards", {
+  res <- vcftable(vcffile, vartype = "snps", id = c("chr21:5030516:G:A"), setid = TRUE)
+  expect_identical(res$id, "chr21_5030516_G_A")
+})
+
 test_that("extract GT for a indel with FILTER not displaying PASS", {
   res <- vcftable(vcffile, id = c("chr21:5030240:AC:A"), vartype = "indels", pass = TRUE)
   expect_equal(length(res$gt), 0)