[BioC] VariantAnnotation's predictCoding (via getTranscriptSeqs) calls makeUCSCTxListFromGRangesList with wrong function signature?

[Valerie Obenchain]

Hi SangChul,

Thanks for the bug report. You are correct, the problem was due to an 
update to .makeUCSCTxListFromGRangesList()  in GenomicFeatures. The 
'reorder.exons.on.minus.strand' argument has been replaced by 
'decreasing.rank.on.minus.strand'.  Now fixed in release 1.2.4 and devel 
1.3.4. These versions should be available through 
biocLite("VariantAnnotation") tomorrow.

Valerie


On 04/04/2012 06:14 PM, Sang Chul Choi wrote:
> Hi,
>
> I found out that getTranscriptSeqs calls makeUCSCTxListFromGRangesList of GenomicFeatures with a wrong function signature; lines 16-17 of VariantAnnotation/R/methods-getTranscriptSeqs.R.
> reorder.exons.on.minus.strand might need to be changed to decreasing.rank.on.minus.strand because of changes in GenomicFeatures. I do not know whether FALSE or TRUE is given to that argument.  I will appreciate if this can be corrected if this is a simple bug.  If this is not bug, I will appreciate if anyone could give me clue about the following error.
>
> I have the following error (I am using the development version of R and BioC packages).
>> aacoding<- predictCoding(vcf, txdb1, seqSource=FaFile)
> Error in GenomicFeatures:::.makeUCSCTxListFromGRangesList(query, reorder.exons.on.minus.strand = FALSE) :
>    unused argument(s) (reorder.exons.on.minus.strand = FALSE)
>
> Thank you,
>
> SangChul
>
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