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fix: readVcfStack(param=ScanVcfParam()) reads all files when which= is empty (#50) #10

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fix: readVcfStack(param=ScanVcfParam()) reads all files when which= is empty (#50) #10

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7 changes: 6 additions & 1 deletion R/VcfStack-class.R
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Original file line number Diff line number Diff line change
Expand Up @@ -313,7 +313,12 @@ readVcfStack <- function(x, i, j=colnames(x), param=ScanVcfParam())
gr <- GRanges()
} else { # use param
gr <- GRanges(vcfWhich(param))
i = intersect(names(files(x)), as.character(seqnames(gr)))
if (length(gr)) {
i = intersect(names(files(x)), as.character(seqnames(gr)))
} else {
## param provided but no which= specified: read all files
i = names(files(x))
}
}
x = x[i]

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8 changes: 8 additions & 0 deletions inst/unitTests/test_VcfStack-class.R
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Expand Up @@ -223,6 +223,14 @@ test_VcfStack_readVcfStack <- function(){
Rstack = RangedVcfStack(stack, gr)
temp7 = readVcfStack(Rstack)
checkTrue(all(dim(temp7) == dim(temp5)))

# test param=ScanVcfParam() with no which= reads all variants (#50)
# Previously returned 0-row VCF because empty which= intersected to empty i
tempParam = readVcfStack(Rstack, param=ScanVcfParam())
checkTrue(all(dim(tempParam) == dim(temp7)))

tempParamStack = readVcfStack(stack, param=ScanVcfParam())
checkTrue(all(dim(tempParamStack) == dim(temp)))
}

test_VcfStack_vcfFields <- function(){
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