/usr/lib/R/site-library/VariantAnnotation/unitTests/test_writeVcf-methods.R is in r-bioc-variantannotation 1.24.2-1.
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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 | test_writeVcf_connection_increment <- function()
{
fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
vcf1 <- readVcf(fl, "hg19")
outfl <- tempfile()
con <- file(outfl, open="a")
writeVcf(vcf1[1:2,], con)
writeVcf(vcf1[-(1:2),], con)
close(con)
vcf2 <- readVcf(outfl, "hg19")
checkIdentical(dim(vcf1), dim(vcf2))
}
test_writeVcf_tags <- function()
{
fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
dest <- tempfile()
vcf1 <- readVcf(fl, "hg19")
hd1 <- metadata(vcf1)$header
writeVcf(vcf1, dest)
vcf2 <- readVcf(dest, "hg19")
hd2 <- metadata(vcf2)$header
checkTrue(names(meta(hd1)) %in% names(meta(hd2)))
checkIdentical(names(geno(vcf1)), names(geno(vcf2)))
checkIdentical(colnames(mcols(info(vcf1))), colnames(mcols(info(vcf2))))
}
test_writeVcf_flatgeno <- function()
{
fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
dest <- tempfile()
vcf1 <- readVcf(fl, "hg19")
writeVcf(vcf1, dest)
vcf2 <- readVcf(dest, "hg19")
}
test_writeVcf_geno <- function()
{
fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
dest <- tempfile()
## empty
vcf1 <- readVcf(fl, "hg19", param=ScanVcfParam(geno=NA))
writeVcf(vcf1, dest)
vcf2 <- readVcf(dest, "hg19")
checkTrue(length(geno(vcf2)$GT) == 0L)
## Rle
vcf1 <- readVcf(fl, "hg19", param=ScanVcfParam(geno="GT"))
writeVcf(vcf1, dest)
vcf2 <- readVcf(dest, "hg19")
checkIdentical(geno(vcf1)$GT, geno(vcf2)$GT)
checkIdentical(geno(header(vcf1)), geno(header(vcf2)))
## matrix
vcf1 <- readVcf(fl, "hg19", param=ScanVcfParam(geno="GT"))
writeVcf(vcf1, dest)
vcf2 <- readVcf(dest, "hg19")
checkIdentical(geno(vcf1)$GT, geno(vcf2)$GT)
checkIdentical(geno(header(vcf1)), geno(header(vcf2)))
param=ScanVcfParam(geno="GT", samples="NA00003")
vcf1 <- readVcf(fl, "hg19", param=param)
writeVcf(vcf1, dest)
vcf2 <- readVcf(dest, "hg19")
checkIdentical(geno(vcf1)$GT, geno(vcf2)$GT)
checkIdentical(geno(header(vcf1)), geno(header(vcf2)))
checkTrue(samples(header(vcf2)) == "NA00003")
## array
vcf1 <- readVcf(fl, "hg19", param=ScanVcfParam(geno="HQ"))
writeVcf(vcf1, dest)
vcf2 <- # FORMAT descriptors for GENO fields
tryCatch(readVcf(dest, "hg19"), error=conditionMessage,
warning=conditionMessage)
checkIdentical(geno(vcf1)$HQ, geno(vcf2)$HQ)
checkIdentical(geno(header(vcf1)), geno(header(vcf2)))
param=ScanVcfParam(geno="HQ", sample="NA00003")
vcf1 <- readVcf(fl, "hg19", param=param)
suppressWarnings(writeVcf(vcf1, dest))
vcf2 <- readVcf(dest, "hg19")
checkIdentical(geno(vcf1)$HQ, geno(vcf2)$HQ)
checkIdentical(geno(header(vcf1)), geno(header(vcf2)))
checkTrue(samples(header(vcf2)) == "NA00003")
## matrix and array
param=ScanVcfParam(geno=c("GT", "HQ"), samples="NA00002")
vcf1 <- readVcf(fl, "hg19", param=param)
writeVcf(vcf1, dest)
vcf2 <- readVcf(dest, "hg19")
checkIdentical(geno(vcf1)$GT, geno(vcf2)$GT)
checkIdentical(geno(vcf1)$HQ, geno(vcf2)$HQ)
checkTrue(samples(header(vcf2)) == "NA00002")
vcf3 <- vcf1
geno(vcf3) <- geno(vcf3)[c("HQ", "GT")]
writeVcf(vcf3, dest)
vcf2 <- readVcf(dest, "hg19", param=param)
checkIdentical(geno(vcf1), geno(vcf2))
## list
fl <- system.file("extdata", "gl_chr1.vcf", package="VariantAnnotation")
hdr <- scanVcfHeader(fl)
param <- ScanVcfParam(samples=samples(hdr)[1:2])
vcf1 <- readVcf(fl, "", param=param)
writeVcf(vcf1, dest)
vcf2 <- readVcf(dest, "")
checkIdentical(geno(vcf1)$GL, geno(vcf2)$GL)
}
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