I think you should proceed supposing that the build system will not install
samtools, and that an R-based implementation is 'in the future'. As such, you
should arrange in your examples / vignette to provide 'mock' output from
samtools that you then process in your package -- kind of like the
Hi,
I just wanted to check in, as I know we got interrupted by the weekend. Any
thoughts on the best way forward?
Thanks,
Jonathon
> On Aug 23, 2019, at 5:00 PM, Jonathon Hill wrote:
>
> Yes, gladly. Thank you for taking time to help me. Here is the exact line of
> R code where we build
Yes, gladly. Thank you for taking time to help me. Here is the exact line of R
code where we build the samtools command (the file to be tested is added later):
args <- paste("mpileup -ERI", #Redo Baq, ignore readgroups, and skip indels
"-f", refFasta(param),
can you provide an example of the samtools command line that you evaluate?
On 8/23/19, 6:11 PM, "Bioc-devel on behalf of Jonathon Hill"
wrote:
I had not until today. I spent the afternoon looking at the possibility,
and it looks like it would be beyond my lab’s skills. We do not have
I had not until today. I spent the afternoon looking at the possibility, and it
looks like it would be beyond my lab’s skills. We do not have anyone
comfortable in C, as we do everything in R. The problem is that we need to get
the results of the mpileup command with BAQ score. Although it has
Hi Jonathon,
Have you considered depending on Rhtslib? See
https://bioconductor.org/packages/Rhtslib
Rsamtools itself is implemented on top of Rhtslib. Note that other
Bioconductor packages (e.g. DiffBind, deepSNV, BitSeq, qrqc, QuasR,
seqbias, TransView, etc...) use Rhtslib internally to
Hi,
I am working through the process of submitting a new package (MMAPPR2). We are
having a problem with the build failing, because our package requires Samtools
installed. We cannot use Rsamtools, as we depend on features not implemented in
the package. How do we resolve the issue? What is
