| ... | ... |
@@ -2,8 +2,8 @@ Package: PureCN |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Copy number calling and SNV classification using |
| 4 | 4 |
targeted short read sequencing |
| 5 |
-Version: 2.9.3 |
|
| 6 |
-Date: 2023-12-11 |
|
| 5 |
+Version: 2.9.4 |
|
| 6 |
+Date: 2024-01-12 |
|
| 7 | 7 |
Authors@R: c(person("Markus", "Riester",
|
| 8 | 8 |
role = c("aut", "cre"),
|
| 9 | 9 |
email = "[email protected]", |
| ... | ... |
@@ -46,16 +46,16 @@ test_that("M2 VCF with POP_AF flag is annotated with DB flag", {
|
| 46 | 46 |
vcf.m2.file <- system.file("extdata", "example_mutect2.vcf.gz", package = "PureCN")
|
| 47 | 47 |
vcf.m2 <- PureCN:::.readAndCheckVcf(vcf.m2.file, "hg38") |
| 48 | 48 |
expect_equal(c(TRUE, rep(FALSE, 10)), info(vcf.m2)$DB) |
| 49 |
- expect_equal(unlist(info(vcf.m2)$POP_AF>0.001), info(vcf.m2)$DB) |
|
| 49 |
+ expect_equal(unlist(info(vcf.m2)$POP_AF > 0.001), info(vcf.m2)$DB) |
|
| 50 | 50 |
|
| 51 |
- expect_output(filterVcfMuTect(vcf.m2, use.somatic.status=FALSE), |
|
| 52 |
- "Less than half of variants in dbSNP") |
|
| 51 |
+ expect_output(filterVcfMuTect(vcf.m2, use.somatic.status = FALSE), |
|
| 52 |
+ "Less than half of variants are annoted as germline database member") |
|
| 53 | 53 |
output.file <- tempfile(fileext = ".vcf") |
| 54 | 54 |
writeVcf(vcf.m2, file = output.file) |
| 55 | 55 |
expect_output(vcf.m2 <- PureCN:::.readAndCheckVcf(output.file, "hg38"), |
| 56 | 56 |
"Will ignore POP_AF") |
| 57 | 57 |
expect_equal(c(TRUE, rep(FALSE, 10)), info(vcf.m2)$DB) |
| 58 |
- expect_equal(unlist(info(vcf.m2)$POP_AF>0.001), info(vcf.m2)$DB) |
|
| 58 |
+ expect_equal(unlist(info(vcf.m2)$POP_AF > 0.001), info(vcf.m2)$DB) |
|
| 59 | 59 |
file.remove(output.file) |
| 60 | 60 |
|
| 61 | 61 |
vcf.m2 <- PureCN:::.readAndCheckVcf(vcf.m2.file, "hg38") |
