Hi Tim,

Glad to hear you find the package useful also for validation!

1) There is no implementation of scanVcf, because I didn't want the package
to depend on too many other packages. Didn't have problems with the scanBcf
myself, and therefore saw no reason to include scanVcf. That was the
reason, but of course I can add an scanVcf option in the import-method!

2)  Did you mean that the default argument for searchArea could include all
the ranges in the provided bcf/vcf-file? If so I agree; will include that
asap.

Expect the new features before next week.

/J.R.


On Mon, Jan 13, 2014 at 8:21 PM, Tim Triche, Jr. <tim.triche@usc.edu> wrote:

> Hi all,
>
> I'm looking to verify some RNAseq results using (in some cases phased) SNP
> calls from the CEU trio and from primary samples in-house (case and matched
> control).  AllelicImbalance looks like a terrific library for this, however
> my BCFs can't be read by Rsamtools::scanBcf.  (I get an error "Error:
> scanBcf: failed to find fmt encoded as '16977'  path:
> /scratch/BAMs/LIU1675A8.hg19.bcf")
>
> VariantAnnotation::scanVcf, on the other hand, works fine.
>
> So, is there any particular reason why I couldn't hack up
> the impBcfGL/impBcfGRL method to use VCFs?  Also, would it make sense to
> have a default argument for searchArea that falls back to the assembly in
> the metadata, if one is specified?
>
> The bizarre thing with the BCFs is that I can scan their headers just
> fine... !
>
> Thanks,
>
> Timothy J. Triche, Jr., PhD
> Jane Anne Nohl Division of Hematology
> USC/Norris Comprehensive Cancer Center
>

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