[Bioc-devel] Bugfixes for VariantAnnotation::write_vcf

[Valerie Obenchain]

Not sure my first reply made it through ...

Hi Richard,

Thanks for the bug reports. Yes, I will have these fixed for the next 
release.

Valerie



On 03/29/2012 07:02 AM, Richard Pearson wrote:
> Hi
>
> I recognise that writeVcf is currently "under construction", but I've 
> rather come to rely on it, so have made a few bug fixes to get it 
> working for me. Could the following (rather clumsy) patches, or some 
> other work around, be included in time for the next release?
>
> 1) In .makeVcfMatrix, the case where ALT is a CompressedCharacterList 
> is not correctly handled. Adding the following gets around this:
>     if(is(ALT, "CompressedCharacterList")) {
>         ALT <- unlist(ALT)
>     }
>
> 2) In .makeVcfMatrix, the dat <- gsub("NA", ".", dat) can have the 
> effect of modifying names in the INFO field that contain the string 
> "NA" (e.g. "MYNAMES" gets changed to "MY.MES"). The following gets 
> around this:
>     dat <- gsub("^NA$", ".", dat)
>
> 3) In .makeVcfGeno, fields with mutliple values (e.g. GL) get split 
> into separate fields. The following got me round this (note use of 
> recursive=FALSE in unlist, plus extra cleaning up lines, plus changing 
> nsub to length(geno) in lst line which removes warnings about split):
>     subj <- lapply(seq_len(nsub),
>         function(i) {
>             dat <- unlist(lapply(geno, function(fld) fld[,i]), 
> use.names=FALSE, recursive=FALSE)
>             mat <- matrix(dat, ncol=length(geno))
>             mat <- gsub("^NA$", NA, mat)
>             lst <- split(mat, rep(seq_len(nrec), length(geno)))
>             rmna <- lapply(lst, na.omit)
>             collapsedText <- .pasteCollapse(CharacterList(rmna), 
> collapse=":")
>             rmc <- gsub("c\\(([^\\)]*)\\)", "\\1", collapsedText)
>             gsub(" ", "", rmc)
>         })
>
> Great package!
>
> Thanks
>
> Richard
>
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