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 old cooking
shows where the roast went into the oven before the commercial and came out
ready to eat after...
Martin
On 8/27/19, 12:38 PM, "Jonathon Hill" <jh...@byu.edu> wrote:
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 <jh...@byu.edu> wrote:
>
> 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),
> "-C 50",
> "--min-MQ", minMapQuality(param),
> "--min-BQ", minBaseQuality(param),
> "--region", as.character(chrRange, ignore.strand=TRUE))
>
> As you can see, we use the BAQ score to filter. We have tried to
implement it without BAQ (using Rsamtools) and found it negatively affected our
results.
>
>> On Aug 23, 2019, at 4:53 PM, Martin Morgan <mtmorgan.b...@gmail.com>
wrote:
>>
>> 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"
<bioc-devel-boun...@r-project.org on behalf of jh...@byu.edu> 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 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
a pileup command, the Rsamtools implementation does not include the ability to
retrieve the BAQ score as far as we can tell, so we had to fall back on making
a system call to Rsamtools and reading in the results. Using Rhtslib is
intriguing, but it looks like we would need several header files in Samtools as
opposed to htslib and then implement our own C function. Again, we do not have
anyone that could do this. We are scientists, not programmers. Am I correct on
what it would require? Do you know of any other alternatives?
>>
>> Jonathon
>>
>>> On Aug 23, 2019, at 12:22 PM, Pages, Herve <hpa...@fredhutch.org> wrote:
>>>
>>> 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 implement
features
>>> not implemented in Rsamtools.
>>>
>>> H.
>>>
>>> On 8/23/19 11:05, Jonathon Hill wrote:
>>>> 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 the policy
for system dependencies? We have samtools listed in the DESCRIPTION and
installation instructions in our README, but I am sure that is not enough to
get it installed on the Build and Check servers.
>>>>
>>>> Thanks,
>>>>
>>>> Jonathon Hill
>>>>
>>>> _______________________________________________
>>>> Bioc-devel@r-project.org mailing list
>>>>
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AEKZKMjjFTbu5U_zn0bacvzv69lx_S5s7Yb6dSOXbJs&s=s5EMLCdAbnqgXWs3_-Sxm52Zuc3pqFirWz7z3ymBruU&e=
>>>>
>>>
>>> --
>>> Hervé Pagès
>>>
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M1-B514
>>> P.O. Box 19024
>>> Seattle, WA 98109-1024
>>>
>>> E-mail: hpa...@fredhutch.org
>>> Phone: (206) 667-5791
>>> Fax: (206) 667-1319
>>
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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