/usr/lib/R/site-library/VariantAnnotation/unitTests/test_scanVcf.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 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 | fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
scn <- scanVcf(fl)
test_FixedTypes <- function()
{
.vcf_map_fixed <- VariantAnnotation:::.vcf_map_fixed
exp <- exp0 <- list(rowRanges=NULL, REF=NULL,
ALT=list("A", character()),
QUAL=list("1", numeric()),
FILTER=list("1", character()))
named <- names(exp)[-(1:2)]
checkIdentical(exp, .vcf_map_fixed(character(), FALSE))
checkIdentical(exp[1:2], .vcf_map_fixed(NA, FALSE))
exp <- exp0
exp[1] <- list(NULL)
checkIdentical(exp, .vcf_map_fixed(named, FALSE))
warn <- FALSE
obs <- withCallingHandlers({
.vcf_map_fixed("FOO", FALSE)
}, warning=function(w) {
warn <<- TRUE
invokeRestart("muffleWarning")
})
checkTrue(warn)
checkIdentical(exp[1:2], obs)
}
test_InfoTypes <- function()
{
fmt <- info(scanVcfHeader(fl))
info <- scn[[1]]$INFO
checkIdentical(as.integer(c(3, 3, 2, 3, 3)), info$NS)
checkIdentical(as.integer(c(14, 11, 10, 13, 9)), info$DP)
checkEquals(class(info$AF), "matrix")
checkIdentical(c(TRUE, FALSE, TRUE, FALSE, FALSE), info$DB)
checkIdentical(c(TRUE, rep(FALSE, 4)), info$H2)
}
test_GenoTypes <- function()
{
fmt <- geno(scanVcfHeader(fl))
geno <- scn[[1]]$GENO
checkEquals(typeof(unlist(geno$GT)), "character")
checkIdentical(lapply(geno, class), list(GT="matrix", GQ="matrix",
DP="matrix", HQ="array"))
mat <- matrix(c(1, 3, 6, 7, 4, 8, 5, 0, 4, 2, 5, 3, 4, 2, 3),
nrow=5, dimnames=list(NULL, c("NA00001", "NA00002", "NA00003")))
checkEquals(mat, geno$DP)
}
test_scanVcf_no_FORMAT_column <- function()
{
## no FORMAT -- don't parse GENO
fl <- system.file(package="VariantAnnotation", "unitTests",
"cases", "no_FORMAT_column.vcf")
geno <- scanVcf(fl)[[1]]$GENO
checkIdentical(setNames(list(), character()), geno)
}
test_scanVcf_FORMAT_header_no_SAMPLEs <- function()
{
## GENO tags, but no SAMPLE or actual samples
fl <- system.file(package="VariantAnnotation", "unitTests",
"cases", "FORMAT_header_no_SAMPLEs.vcf")
geno <- scanVcf(fl)[[1]]$GENO
checkIdentical(c("GT", "DS", "GL"), names(geno))
checkTrue(all(sapply(geno, nrow) == 5L))
checkTrue(all(sapply(geno, ncol) == 0L))
}
test_scanVcf_no_INFO_header <- function()
{
fl <- system.file(package="VariantAnnotation", "unitTests",
"cases", "no_INFO_header.vcf")
info <- suppressWarnings(scanVcf(fl)[[1]]$INFO$INFO)
checkIdentical(rep(".", 5L), info)
}
test_scanVcf_negative_Number <- function()
{
fl <- system.file(package="VariantAnnotation", "unitTests",
"cases", "negative_FORMAT_Number.vcf")
pl <- scanVcf(fl)[[1]]$GENO$PL
checkIdentical(3L, unique(sapply(pl, length)))
checkIdentical(761L, sum(sapply(pl, sum)))
}
test_scanVcf_crlf <- function()
{
writeLines(readLines(fl), xx <- tempfile(), sep="\r\n")
checkIdentical(scanVcfHeader(fl), scanVcfHeader(xx))
}
test_scanVcfHeader_VarScan <- function()
{
fl <- system.file("unitTests", "cases", "VarScan_header.vcf",
package="VariantAnnotation")
hd <- scanVcfHeader(fl)
checkIdentical(dim(info(hd)), c(7L, 3L))
checkIdentical(names(info(hd)), c("Number", "Type", "Description"))
expected <- paste0("Somatic status of variant ",
"(0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)")
checkIdentical(info(hd)["SS", "Description"], expected)
fl <- system.file("extdata", "ex2.vcf",
package="VariantAnnotation")
hd <- scanVcfHeader(fl)
checkIdentical(length(names(header(hd))), 7L)
checkIdentical(names(meta(hd)), c("META", "contig", "SAMPLE", "PEDIGREE"))
checkIdentical(header(hd)$contig[["assembly"]], "B36")
}
test_scan_row.names <- function()
{
fl <- system.file("extdata", "chr7-sub.vcf.gz", package="VariantAnnotation")
scn <- scanVcf(fl)[[1]]
checkTrue(!is.null(names(scn$rowRanges)))
scn <- scanVcf(fl, row.names=FALSE)
checkTrue(is.null(names(scn$rowRanges)))
param <- ScanVcfParam(which=GRanges("7", IRanges(55000723, 55000789)))
scn <- scanVcf(fl, param=param, row.names=FALSE)
checkTrue(is.null(names(scn$rowRanges)))
}
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