/usr/lib/R/site-library/VariantAnnotation/unitTests/test_ScanVcfParam-class.R is in r-bioc-variantannotation 1.20.2-1+b1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 | test_ScanVcfParam_which <- function()
{
which <- RangesList(seq1=IRanges(1000, 2000),
seq2=IRanges(c(100, 1000), c(1000, 2000)))
svp <- ScanVcfParam(which=which)
checkIdentical(which, vcfWhich(svp))
checkException(vcfWhich(svp) <- DataFrame(), silent=TRUE)
checkException(vcfWhich(svp) <- SimpleList(), silent=TRUE)
}
test_ScanVcfParam_fixed <- function()
{
fx <- c("GT", "ALT")
svp <- ScanVcfParam(fixed=fx)
checkIdentical(fx, vcfFixed(svp))
checkException(vcfFixed(svp) <- DataFrame(), silent=TRUE)
checkException(vcfFixed(svp) <- 1:5, silent=TRUE)
fx <- NA_character_
svp <- ScanVcfParam(fixed=fx)
checkIdentical(fx, vcfFixed(svp))
}
test_ScanVcfParam_info <- function()
{
info <- c("NS", "DP")
svp <- ScanVcfParam(info=info)
checkIdentical(info, vcfInfo(svp))
checkException(vcfInfo(svp) <- DataFrame(), silent=TRUE)
checkException(vcfInfo(svp) <- 1:5, silent=TRUE)
info <- NA_character_
svp <- ScanVcfParam(info=info)
checkIdentical(info, vcfInfo(svp))
}
test_ScanVcfParam_geno <- function()
{
geno <- c("GT", "GQ")
svp <- ScanVcfParam(geno=geno)
checkIdentical(geno, vcfGeno(svp))
checkException(vcfGeno(svp) <- DataFrame(), silent=TRUE)
checkException(vcfGeno(svp) <- 1:5, silent=TRUE)
geno <- NA_character_
svp <- ScanVcfParam(geno=geno)
checkIdentical(geno, vcfGeno(svp))
}
test_ScanVcfParam_samples <- function()
{
samp <- c("GT", "GQ")
svp <- ScanVcfParam(samples=samp)
checkIdentical(samp, vcfSamples(svp))
checkException(vcfSamples(svp) <- DataFrame(), silent=TRUE)
checkException(vcfSamples(svp) <- 1:5, silent=TRUE)
checkException(ScanVcfParam(geno="DP", samples=NA), silent=TRUE)
checkException(ScanVcfParam(geno=NA, samples="foo"), silent=TRUE)
}
test_ScanVcfParam_trimEmpty <- function()
{
svp <- ScanVcfParam()
checkIdentical(TRUE, vcfTrimEmpty(svp))
vcfTrimEmpty(svp) <- FALSE
checkIdentical(FALSE, vcfTrimEmpty(svp))
checkException(vcfTrimEmpty(svp) <- "a", silent=TRUE)
checkException(vcfTrimEmpty(svp) <- 1:5, silent=TRUE)
## FIXME : should this work?
#checkException(vcfTrimEmpty(svp) <- NA, silent=TRUE)
}
test_ScanVcfParam_GRangesList <- function()
{
fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
compressVcf <- bgzip(fl, tempfile())
idx <- indexTabix(compressVcf, "vcf")
tab <- TabixFile(compressVcf, idx)
gr1 <- GRanges("1", IRanges(13219, 2827695, name="regionA"))
gr2 <- GRanges(rep("2", 2),
IRanges(c(321680, 14477080), c(321689, 14477090),
name=c("regionB", "regionC")))
grl <- GRangesList("1"=gr1, "2"=gr2)
vcf_grl <- readVcf(tab, "hg19", grl)
gr <- unlist(grl, use.names=FALSE)
vcf_gr <- readVcf(tab, "hg19", gr)
checkIdentical(rowRanges(vcf_grl), rowRanges(vcf_gr))
}
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