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test-vcf-reader.R
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library(testthat)
bcffile <- system.file("extdata", "test.bcf", package="vcfppR")
vcffile <- system.file("extdata", "raw.gt.vcf.gz", package="vcfppR")
svfile <- system.file("extdata", "sv.vcf.gz", package="vcfppR")
test_that("vcfreader: constructor with vcfffile only", {
br <- vcfreader$new(vcffile)
expect_true(br$variant())
expect_identical(br$chr(), "chr21")
expect_identical(br$pos(), 5030082L)
expect_identical(br$id(), "chr21:5030082:G:A")
expect_identical(br$ref(), "G")
expect_identical(br$alt(), "A")
})
test_that("vcfreader: constructor with vcfffile and region", {
br <- vcfreader$new(vcffile, "chr21:5030082-")
expect_true(br$variant())
expect_identical(br$chr(), "chr21")
expect_identical(br$pos(), 5030082L)
expect_identical(br$id(), "chr21:5030082:G:A")
expect_identical(br$ref(), "G")
expect_identical(br$alt(), "A")
})
test_that("vcfreader: constructor with vcfffile, region and samples", {
br <- vcfreader$new(vcffile, "chr21:5030082-", "HG00097,HG00099")
expect_identical(br$samples(), c("HG00097", "HG00099"))
expect_true(br$variant())
expect_identical(br$genotypes(F), rep(0L, 4))
expect_identical(br$chr(), "chr21")
expect_identical(br$pos(), 5030082L)
expect_identical(br$id(), "chr21:5030082:G:A")
expect_identical(br$ref(), "G")
expect_identical(br$alt(), "A")
})
test_that("vcfreader: get FORMAT item with Float type", {
br <- vcfreader$new(vcffile, "chr21:5030347-", "HG00097,HG00099")
expect_identical(br$samples(), c("HG00097", "HG00099"))
expect_true(br$variant())
expect_identical(br$pos(), 5030347L)
expect_identical(all(is.na(br$formatFloat("AB"))), TRUE)
})
test_that("vcfreader: get FORMAT item with Integer type", {
br <- vcfreader$new(vcffile, "chr21:5030347-", "HG00097,HG00099")
expect_identical(br$samples(), c("HG00097", "HG00099"))
expect_true(br$variant())
expect_identical(br$pos(), 5030347L)
expect_identical(br$formatInt("AD"), c(4L, 0L, 16L, 0L))
})
test_that("vcfreader: get FORMAT item with String type", {
br <- vcfreader$new(svfile, "chr21:5114000-", "HG00096,HG00097")
expect_identical(br$samples(), c("HG00096", "HG00097"))
expect_true(br$variant())
expect_identical(br$pos(), 5114000L)
expect_identical(br$formatStr("EV"), c("RD","RD"))
})
test_that("vcfreader: get FORMAT item for the unexpected and error", {
br <- vcfreader$new(vcffile, "chr21:5030347-", "HG00097,HG00099")
br$variant()
expect_identical(br$pos(), 5030347L)
expect_error(br$formatInt("AA")) ## AA not exists
expect_identical(br$formatInt("AD"), c(4L, 0L, 16L, 0L))
## use formatFloat will return unexpected values if AD in FORMAT if Integer
expect_error(expect_identical(br$formatFloat("AD"), c(4L, 0L, 16L, 0L))) ## AA exists but of Integer type
})
test_that("vcfreader: get variants type", {
br <- vcfreader$new(vcffile)
i <- 0
s <- 0
m <- 0
ms <- 0
while(br$variant()) {
if(br$isIndel()) i <- i + 1
if(br$isSV()) s <- s + 1
if(br$isMultiAllelics()) m <- m + 1
if(br$isMultiAllelicSNP()) ms <- ms + 1
}
expect_identical(i, 1)
expect_identical(s, 0)
expect_identical(m, 2)
expect_identical(ms, 2)
})
test_that("vcfreader: test variants type", {
br <- vcfreader$new(vcffile)
i1 <- 0
i2 <- 0
i3 <- 0
i4 <- 0
i5 <- 0
i6 <- 0
i7 <- 0
i8 <- 0
while(br$variant()) {
if(br$hasSNP()) i1 <- i1 + 1
if(br$hasINDEL()) i2 <- i2 + 1
if(br$hasINS()) i3 <- i3 + 1
if(br$hasDEL()) i4 <- i4 + 1
if(br$hasMNP()) i5 <- i5 + 1
if(br$hasBND()) i6 <- i6 + 1
if(br$hasOTHER()) i7 <- i7 + 1
if(br$hasOVERLAP()) i8 <- i8 + 1
}
expect_identical(i1, 14)
expect_identical(i2, 1)
expect_identical(i3, 0)
expect_identical(i4, 1)
expect_identical(i5, 0)
expect_identical(i6, 0)
expect_identical(i7, 0)
expect_identical(i8, 0)
})
test_that("vcfreader: reading variant only", {
br <- vcfreader$new(vcffile)
br$variant()
expect_identical(br$chr(), "chr21")
expect_identical(br$pos(), 5030082L)
expect_identical(br$id(), "chr21:5030082:G:A")
expect_identical(br$ref(), "G")
expect_identical(br$alt(), "A")
expect_equal(br$qual(), 70.06, tolerance = 1e-6)
expect_identical(br$filter(), "VQSRTrancheSNP99.80to100.00")
expect_identical(br$info(), "AC=2;AF=0.000616523;AN=3244;DP=2498;FS=0;MLEAC=1;MLEAF=0.0003083;MQ=17.07;MQ0=0;QD=17.52;SOR=3.258;VQSLOD=-32.6;culprit=MQ;AN_EUR=658;AN_EAS=548;AN_AMR=520;AN_SAS=624;AN_AFR=894;AF_EUR=0;AF_EAS=0;AF_AMR=0.00384615;AF_SAS=0;AF_AFR=0;AC_EUR=0;AC_EAS=0;AC_AMR=2;AC_SAS=0;AC_AFR=0;AC_Het_EUR=0;AC_Het_EAS=0;AC_Het_AMR=0;AC_Het_SAS=0;AC_Het_AFR=0;AC_Het=0;AC_Hom_EUR=0;AC_Hom_EAS=0;AC_Hom_AMR=2;AC_Hom_SAS=0;AC_Hom_AFR=0;AC_Hom=2;HWE_EUR=1;ExcHet_EUR=1;HWE_EAS=1;ExcHet_EAS=1;HWE_AMR=0.00192678;ExcHet_AMR=1;HWE_SAS=1;ExcHet_SAS=1;HWE_AFR=1;ExcHet_AFR=1;HWE=0.000308356;ExcHet=1;ME=0;AN_EUR_unrel=508;AN_EAS_unrel=448;AN_AMR_unrel=330;AN_SAS_unrel=484;AN_AFR_unrel=666;AF_EUR_unrel=0;AF_EAS_unrel=0;AF_AMR_unrel=0;AF_SAS_unrel=0;AF_AFR_unrel=0;AC_EUR_unrel=0;AC_EAS_unrel=0;AC_AMR_unrel=0;AC_SAS_unrel=0;AC_AFR_unrel=0;AC_Het_EUR_unrel=0;AC_Het_EAS_unrel=0;AC_Het_AMR_unrel=0;AC_Het_SAS_unrel=0;AC_Het_AFR_unrel=0;AC_Hom_EUR_unrel=0;AC_Hom_EAS_unrel=0;AC_Hom_AMR_unrel=0;AC_Hom_SAS_unrel=0;AC_Hom_AFR_unrel=0")
br$rmInfoTag("AC")
print(br$infoInt("AC")) ## TODO: AC value still exists
print(br$info())
af <- br$infoFloat("AF")
## expect_equal(0.00061652297, 0.00061652300, tolerance = 1e-6)
expect_equal(af, 0.000616523, tolerance = 1e-6)
dp <- br$infoInt("DP")
expect_identical(dp, 2498L)
gt <- br$genotypes(TRUE)
expect_identical(length(gt), 3202L)
gt <- br$genotypes(FALSE)
expect_identical(length(gt), 6404L)
pl <- br$formatInt("PL")
expect_identical(length(pl), 9606L)
})
test_that("vcfreader: read and output variant", {
br <- vcfreader$new(vcffile)
br$variant()
br$setCHR("chr22")
expect_identical(br$chr(), "chr22")
br$setPOS(9999L)
expect_identical(br$pos(), 9999L)
br$setID("rs122334")
expect_identical(br$id(), "rs122334")
expect_identical(br$ref(), "G")
expect_identical(br$alt(), "A")
br$setRefAlt("A,GA")
expect_identical(br$ref(), "A")
expect_identical(br$alt(), "GA")
expect_identical(br$infoInt("AC"), 2L)
br$setInfoInt("AC", 3L)
expect_identical(br$infoInt("AC"), 3L)
br$setInfoFloat("AF", 0.3)
expect_equal(br$infoFloat("AF"), 0.3, tolerance = 1e-6)
br$setInfoStr("VariantType", "indel")
expect_identical(br$infoStr("VariantType" ), "indel")
## output current variant to another vcf
s1 <- br$string()
outvcf <- file.path(tempdir(), "test.vcf.gz")
file.create(outvcf)
br$output(outvcf)
br$write()
br$close()
br <- vcfreader$new(outvcf)
br$variant()
s2 <- br$string()
expect_identical(s1, s2)
})
test_that("vcfreader: remove tag from FORMAT", {
br <- vcfreader$new(vcffile)
br$variant() ## first variant
s <- unlist(strsplit(br$line(), "\t"))
expect_identical(s[9], "GT:AD:DP:GQ:PL")
br$variant() ## second variant
br$rmFormatTag("AD")
br$rmFormatTag("AB")
br$rmFormatTag("PGT")
br$rmFormatTag("PID")
s <- unlist(strsplit(br$line(), "\t"))
expect_identical(s[9], "GT:DP:GQ:PL")
expect_identical(s[10], "1/1:2:6:64,6,0")
## AD was removed, so we get integer(0)
ad <- br$formatInt("AD")
expect_identical(length(ad),0L)
## output current variant to another vcf
outvcf <- file.path(tempdir(), "test.vcf.gz")
file.create(outvcf)
br$output(outvcf)
br$write()
br$close()
## check the output file
br <- vcfreader$new(outvcf)
br$variant()
s <- unlist(strsplit(br$line(), "\t"))
expect_identical(s[9], "GT:DP:GQ:PL")
expect_identical(s[10], "1/1:2:6:64,6,0")
## AD doesn't exist. so we get error, is this a bad design?
expect_error(br$formatInt("AD"))
})
test_that("can set genotypes for single sample", {
br <- vcfreader$new(svfile, "", "HG00096")
br$variant()
br$genotypes(F)
br$setGenotypes(c(1L,1L))
outfile <- paste0(tempfile(), ".vcf.gz")
br$output(outfile)
br$write()
br$close()
vcf <- vcftable(outfile)
expect_true(vcf$gt==2)
})
test_that("can change samples name and set genotypes for single sample", {
br <- vcfreader$new(svfile, "", "HG00096")
br$variant()
expect_identical(br$infoStr("SVTYPE"), "DUP")
expect_identical(br$genotypes(F), c(0L, 0L))
br$setGenotypes(c(1L,1L))
expect_identical(br$genotypes(F), c(1L, 1L))
outfile <- paste0(tempfile(), ".vcf.gz")
br$output(outfile)
br$updateSamples("ZZZZZ")
br$write()
br$close()
vcf <- vcftable(outfile)
expect_true(vcf$gt==2)
expect_true(vcf$samples=="ZZZZZ")
})
test_that("can getStatus of a region", {
br <- vcfreader$new(svfile)
expect_identical(br$getStatus("chr22"),-2L)
expect_identical(br$getStatus("XXX-1-9999"),-2L)
expect_identical(br$getStatus("chr21:5029001-5029100"), 0L)
expect_identical(br$getStatus("chr21"), 1L)
})
test_that("can set region back and forth", {
br <- vcfreader$new(svfile)
br$setRegion("chr21:5227411")
br$variant()
expect_identical(br$infoStr("SVTYPE"), "INS")
## set region back
br$setRegion("chr21:5114000")
br$variant()
expect_identical(br$infoStr("SVTYPE"), "DUP")
})
test_that("bcfreader: subset samples and region for BCF", {
br <- vcfreader$new(bcffile, "1:10000-13000", "I1,I10")
expect_true(br$variant())
expect_identical(br$genotypes(F), c(1L, 1L, 0L, 1L))
expect_true(br$variant())
expect_identical(br$genotypes(F), c(0L, 0L, 0L, 0L))
expect_true(br$variant())
expect_identical(br$genotypes(F), c(1L, 0L, 0L, 0L))
expect_true(br$variant())
expect_identical(br$genotypes(F), c(1L, 1L, 0L, 1L))
})