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
>>>>
>>>> _______________________________________________
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>>>>
>>>
>>> --
>>> 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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>>
>
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