[Bioc-devel] Bugfixes for VariantAnnotation::write_vcf

[Valerie Obenchain]

Now fixed in devel 1.3.2 and release 1.2.2.

Valerie

On 03/29/12 10:20, Valerie Obenchain wrote:
> 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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>
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