/usr/lib/R/site-library/Rsamtools/unitTests/test_BcfFile.R is in r-bioc-rsamtools 1.30.0-1.
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", "ex1.bcf", package="Rsamtools")
test_BcfFile_openclose <- function()
{
.normalizePath <- Rsamtools:::.normalizePath
bf <- BcfFile(fl, character(0)) # no index
checkTrue(!isOpen(bf))
open(bf)
checkTrue(isOpen(bf))
checkIdentical(.normalizePath(fl), path(bf))
checkIdentical(character(0), index(bf, asNA=FALSE))
checkIdentical(NA_character_, index(bf))
close(bf)
checkTrue(!isOpen(bf))
checkException(close(bf), silent=TRUE)
bf <- open(bf) # open a closed BcfFile
checkTrue(isOpen(bf))
bf1 <- open(bf) # (re)open BcfFile
checkTrue(isOpen(bf1))
checkTrue(identical(bf$.extptr, bf1$.extptr))
checkTrue(isOpen(bf))
checkIdentical(.normalizePath(fl), path(bf))
## checkIdentical(.normalizePath(fl), index(bf))
}
test_BcfFile_scanBcfHeader <- function()
{
.chk <- function(h) {
checkTrue(validObject(h))
checkEquals(3L, length(h))
checkEquals(2L, length(h[["Reference"]]))
checkEquals("ex1.bam", h[["Sample"]])
checkEquals(1L, length(h[["Header"]]))
checkEquals(c(0, 0), dim(h[["Header"]][["META"]]))
}
bf <- open(BcfFile(fl, character(0)))
.chk(scanBcfHeader(bf))
bf <- BcfFile(fl, character(0))
.chk(scanBcfHeader(bf))
checkTrue(!isOpen(bf))
header <-
structure(list(Reference = character(0), Sample =
character(0), Header =
"##FORMAT=<ID=GD,Number=1,Type=Float,Description=\"alleles [0,2]\">"),
.Names = c("Reference", "Sample", "Header"))
checkTrue(validObject(Rsamtools:::.bcfHeaderAsSimpleList(header)))
}
test_BcfFile_scanBcfHeader_no_SAMPLE_header <- function()
{
fl <- system.file(package="Rsamtools", "unitTests", "cases",
"no_SAMPLE_header.vcf")
bf <- open(BcfFile(fl, character(0)))
on.exit(close(bf))
sample <- scanBcfHeader(bf)[["Sample"]]
exp <- c("NA00001", "NA00002", "NA00003")
checkIdentical(exp, sample)
}
test_BcfFile_scanBcfHeader_remote <- function()
{
if ("windows" == .Platform$OS.type) {
DEACTIVATED("remote scanBcFHeader not supported on Windows")
return(TRUE)
}
fl <- "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr22.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz"
file <- tryCatch({
open(BcfFile(fl))
}, warning=function(w) {
message("'test_BcfFile_scanBcfHeader_remote' warning:\n ",
conditionMessage(w))
TRUE
})
if (is.logical(file))
return(file)
obs <- .Call(Rsamtools:::.scan_bcf_header, Rsamtools:::.extptr(file))
close(file)
exp <- setNames(c(0L, 1092L, 29L), c("Reference", "Sample", "Header"))
checkIdentical(exp, sapply(obs, length))
}
test_BcfFile_scanBcfHeader_no_header_line <- function()
{
fl <- system.file(package="Rsamtools", "unitTests", "cases",
"no_header_line.vcf")
msg <- NULL
tryCatch(scanBcfHeader(fl), error=function(err) {
msg <<- conditionMessage(err)
})
checkIdentical("no 'header' line \"#CHROM POS ID...\"?", msg)
}
test_BcfFile_scan_noindex <- function()
{
bf <- open(BcfFile(fl, character(0)))
checkTrue(isOpen(bf))
p <- ScanBcfParam()
res <- scanBcf(bf, param=p)
checkEquals(11L, length(res))
checkEquals(3065L, res[["RecordsPerRange"]])
checkEquals(3065L, unique(sapply(res[1:9], length)))
checkEquals(1, length(res[["GENO"]]))
checkEquals(3065L, length(res[["GENO"]][["PL"]]))
checkIdentical(res, scanBcf(bf))
}
test_BcfFile_scan_index <- function()
{
bf <- open(BcfFile(fl))
which <- RangesList(seq1=IRanges(c(1, 1000), width=10),
seq2=IRanges(c(100, 1000), width=10))
p <- ScanBcfParam(which=which)
res <- scanBcf(bf, param=p)
checkEquals(11L, length(res))
checkEquals(c(0, 10, 10, 20), res[["RecordsPerRange"]])
checkEquals(30L, unique(sapply(res[1:9], length)))
checkEquals(1, length(res[["GENO"]]))
checkEquals(30L, length(res[["GENO"]][["PL"]]))
}
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