fix

Zilong-Li · Mar 23, 2024 · a1100a5 · a1100a5
1 parent 77ab79d
commit a1100a5
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Showing 5 changed files with 6 additions and 7 deletions.
diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -186,8 +186,7 @@ tableFormat <- function(vcffile, region, samples, format, ids, qualval, pass, IN
 #' bw$addContig("chr20")
 #' bw$addFORMAT("GT", "1", "String", "Genotype");
 #' bw$addSample("NA12878")
-#' bw$addSample("NA12879")
-#' s1 <- "chr20\t2006060\trs146931526\tG\tC\t100\tPASS\t.\tGT\t1|0\t1|1"
+#' s1 <- "chr20\t2006060\t.\tG\tC\t100\tPASS\t.\tGT\t1|0"
 #' tryCatch((bw$writeline(s1)), error=function(e) e)
 #' bw$close()
 NULL

diff --git a/man/vcfwriter.Rd b/man/vcfwriter.Rd
diff --git a/src/vcf-writer.cpp b/src/vcf-writer.cpp
@@ -42,8 +42,7 @@ using namespace std;
 //' bw$addContig("chr20")
 //' bw$addFORMAT("GT", "1", "String", "Genotype");
 //' bw$addSample("NA12878")
-//' bw$addSample("NA12879")
-//' s1 <- "chr20\t2006060\trs146931526\tG\tC\t100\tPASS\t.\tGT\t1|0\t1|1"
+//' s1 <- "chr20\t2006060\t.\tG\tC\t100\tPASS\t.\tGT\t1|0"
 //' tryCatch((bw$writeline(s1)), error=function(e) e)
 //' bw$close()
 class vcfwriter {

diff --git a/tests/testthat/test-modify-vcf.R b/tests/testthat/test-modify-vcf.R
@@ -1,6 +1,7 @@
 library(testthat)
 
 test_that("modify the genotypes", {
+  skip_on_os(c("windows"), arch = NULL)
   outvcf <- paste0(tempfile(), ".vcf.gz")
   bw <- vcfwriter$new(outvcf, "VCF4.3")
   bw$addContig("chr20")
@@ -32,6 +33,7 @@ test_that("modify the genotypes", {
 })
 
 test_that("modify item in FORMAT", {
+  skip_on_os(c("windows"), arch = NULL)
   ## creat a VCF with GP in FORMAT
   outvcf <- paste0(tempfile(), ".vcf.gz")
   bw <- vcfwriter$new(outvcf, "VCF4.3")

diff --git a/tests/testthat/test-vcf-writer.R b/tests/testthat/test-vcf-writer.R
@@ -8,7 +8,7 @@ test_that("vcfwriter: writing variant works", {
   bw$addContig("chr20")
   bw$addFILTER("PASS", "All filters passed")
   bw$addINFO("AF", "A", "Float", "Estimated allele frequency in the range (0,1)");
-  s1 <- "chr20\t2006060\trs146931526\tG\tC\t100\tPASS\t."
+  s1 <- "chr20\t2006060\t.\tG\tC\t100\tPASS\t."
   bw$writeline(s1)
   bw$close()
   ## tests