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fix: preserve '*' spanning deletion alleles at read time (#65) #104

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fix: preserve '*' spanning deletion alleles at read time (#65) #104

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ Type: Package
Title: Annotation of Genetic Variants
Description: Annotate variants, compute amino acid coding changes,
predict coding outcomes.
Version: 1.59.0
Version: 1.59.1
Authors@R: c(
person("Valerie", "Oberchain", role="aut"),
person("Martin", "Morgan", role="aut"),
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15 changes: 15 additions & 0 deletions NEWS
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@@ -1,3 +1,18 @@
CHANGES IN VERSION 1.59.1
-------------------------

BUG FIXES

o readVcf() now preserves '*' (spanning deletion) alleles instead of
converting them to empty strings. VCFs containing '*' alleles are
returned with a CharacterList ALT column (same as structural variant
VCFs), allowing faithful round-trip through writeVcf(). Previously,
'*' was erased at read time making it impossible to write valid VCF
output for files containing spanning deletions — IGV/htsjdk would
reject the output with "empty alleles are not permitted". VCFs
without '*' alleles continue to use DNAStringSetList as before.
(GitHub issue #65)

CHANGES IN VERSION 1.36.0
-------------------------

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6 changes: 4 additions & 2 deletions R/AllUtilities.R
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Expand Up @@ -110,20 +110,22 @@
CharacterList(x)
} else {
flat[grepl("I", flat, fixed=TRUE)] <- "."
flat[grepl("*", flat, fixed=TRUE)] <- ""
relist(DNAStringSet(flat), x)
}
}

## The grep for '.' here is looking for '.' as *part* of the ALT field.
## If the ALT were '.' only, with no other characters, it would have been
## converted to an empty string in the C code before it reached this point.
## '*' is the VCF spanning deletion allele — not valid DNA, treated as
## structural so it's preserved in a CharacterList (GitHub issue #65).
.isStructural <- function(x)
{
grepl("<", x, fixed=TRUE) |
grepl("[", x, fixed=TRUE) |
grepl("]", x, fixed=TRUE) |
grepl(".", x, fixed=TRUE)
grepl(".", x, fixed=TRUE) |
grepl("*", x, fixed=TRUE)
}

.formatInfo <- function(x, hdr, nrecords)
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