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test_vcfFields <- function(){
## invalid
checkException(vcfFields(NA_character_), silent = TRUE)
checkException(vcfFields(tempfile()), silent = TRUE)
## empty
target <- CharacterList(
fixed = character(), info = character(), geno = character(),
samples = character()
)
checkIdentical(target, vcfFields())
## structure
fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
flds <- vcfFields(fl)
checkTrue(validObject(flds))
checkTrue(is(flds, "CharacterList"))
target <- c(fixed = 4L, info = 6L, geno = 4L, samples = 3L)
checkIdentical(target, lengths(flds))
## signatures
hdr <- scanVcfHeader(fl)
flds.hdr <- vcfFields(hdr)
vf <- VcfFile(fl)
flds.vf <- vcfFields(vf)
vcf <- readVcf(fl, genome = "hg19")
flds.vcf <- vcfFields(vcf)
checkIdentical(flds, flds.hdr)
checkIdentical(flds, flds.vf)
checkIdentical(flds, flds.vcf)
## VCFFileList
vfl <- VcfFileList(c(fl, fl))
checkIdentical(vcfFields(vfl[[1]]), vcfFields(vfl))
}
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