add vcfreader@samples()

NEWS.md

@@ -1,3 +1,7 @@
+# vcfppR 0.3.7
+
+* add `vcfreader@samples()`
+
 # vcfppR 0.3.6
 
 * add `vcfreader::line`

R/RcppExports.R

@@ -61,6 +61,7 @@ heterozygosity <- function(vcffile, region = "", samples = "-", pass = FALSE, qu
 #' @field hasOTHER Test if current variant has a OTHER or not
 #' @field hasOVERLAP Test if current variant has a OVERLAP or not
 #' @field nsamples Return the number of samples
+#' @field samples Return a vector of samples id
 #' @field header Return the raw string of the vcf header
 #' @field string Return the raw string of current variant including newline
 #' @field line Return the raw string of current variant without newline

src/vcf-reader.cpp

@@ -51,6 +51,7 @@ using namespace std;
 //' @field hasOTHER Test if current variant has a OTHER or not
 //' @field hasOVERLAP Test if current variant has a OVERLAP or not
 //' @field nsamples Return the number of samples
+//' @field samples Return a vector of samples id
 //' @field header Return the raw string of the vcf header
 //' @field string Return the raw string of current variant including newline
 //' @field line Return the raw string of current variant without newline
@@ -245,6 +246,7 @@ class vcfreader {
         return v.size() / nsamples();
     }
     inline std::string header() const { return br.header.asString(); }
+    inline std::vector<std::string> samples() const { return br.header.getSamples(); }
     inline std::string string() const { return var.asString(); }
     inline std::string line() {
         std::string s = var.asString();
@@ -363,6 +365,7 @@ RCPP_MODULE(vcfreader) {
         .method("hasOTHER", &vcfreader::hasOTHER)
         .method("hasOVERLAP", &vcfreader::hasOVERLAP)
         .method("nsamples", &vcfreader::nsamples)
+        .method("samples", &vcfreader::samples)
         .method("header", &vcfreader::header)
         .method("string", &vcfreader::string)
         .method("line", &vcfreader::line)

tests/testthat/test-vcf-reader.R

@@ -5,7 +5,7 @@ svfile <- system.file("extdata", "sv.vcf.gz", package="vcfppR")
 
 test_that("vcfreader: constructor with vcfffile only", {
   br <- vcfreader$new(vcffile)
-  br$variant()
+  expect_true(br$variant())
   expect_identical(br$chr(), "chr21")
   expect_identical(br$pos(), 5030082L)
   expect_identical(br$id(), "chr21:5030082:G:A")
@@ -15,7 +15,7 @@ test_that("vcfreader: constructor with vcfffile only", {
 
 test_that("vcfreader: constructor with vcfffile and region", {
   br <- vcfreader$new(vcffile, "chr21:5030082-")
-  br$variant()
+  expect_true(br$variant())
   expect_identical(br$chr(), "chr21")
   expect_identical(br$pos(), 5030082L)
   expect_identical(br$id(), "chr21:5030082:G:A")
@@ -25,7 +25,8 @@ test_that("vcfreader: constructor with vcfffile and region", {
 
 test_that("vcfreader: constructor with vcfffile, region and samples", {
   br <- vcfreader$new(vcffile, "chr21:5030082-", "HG00097,HG00099")
-  br$variant()
+  expect_identical(br$samples(), c("HG00097", "HG00099"))
+  expect_true(br$variant())
   expect_identical(br$genotypes(F), rep(0L, 4))
   expect_identical(br$chr(), "chr21")
   expect_identical(br$pos(), 5030082L)
@@ -36,20 +37,23 @@ test_that("vcfreader: constructor with vcfffile, region and samples", {
 
 test_that("vcfreader: get FORMAT item with Float type", {
   br <- vcfreader$new(vcffile, "chr21:5030347-", "HG00097,HG00099")
-  br$variant()
+  expect_identical(br$samples(), c("HG00097", "HG00099"))
+  expect_true(br$variant())
   expect_identical(br$pos(), 5030347L)
   expect_identical(all(is.na(br$formatFloat("AB"))), TRUE)
 })
 
 test_that("vcfreader: get FORMAT item with Integer type", {
   br <- vcfreader$new(vcffile, "chr21:5030347-", "HG00097,HG00099")
-  br$variant()
+  expect_identical(br$samples(), c("HG00097", "HG00099"))
+  expect_true(br$variant())
   expect_identical(br$pos(), 5030347L)
   expect_identical(br$formatInt("AD"), c(4L, 0L, 16L, 0L))
 })
 
 test_that("vcfreader: get FORMAT item with String type", {
   br <- vcfreader$new(svfile, "chr21:5114000-", "HG00096,HG00097")
+  expect_identical(br$samples(), c("HG00096", "HG00097"))
   expect_true(br$variant())
   expect_identical(br$pos(), 5114000L)
   expect_identical(br$formatStr("EV"), c("RD","RD"))