[Bioc-devel] Developing a package that handle BAM file

Vincent Carey @tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Mon Dec 19 01:18:09 CET 2022

On Sun, Dec 18, 2022 at 4:07 PM Hao Feng <hxf155 using case.edu> wrote:

> Hi Bioconductor team,
> We’re developing a package to analyze a `new` type of high-throughput
> sequencing data. We have some BAM files ready. We’d like the package to be
> able to take BAM files as the input. In addition, to maintain our method’s
> statistical rigor, we’d like to implement repeated sampling for multiple
> times (a large number).
> This brings concern to a package development, which I’d like to collect
> some feedback prior to proceed:
> 1. The best practice to use BAM files as the example data? BAM files are
> large in general. Although we can use a part of the BAM, instead of the BAM
> from the whole genome, as the example data, I still don’t think it’s
> feasible to include those external files in the package submission. And due
> to the novelty of this sequencing experiment, I don’t think the current
> experiment data packages have them. Would you suggest us submitting a new
> experiment data package (of several dozen MBs), along with our software
> package?


> 2. Deal with long example run time? Due to repeated sampling and the
> handling of BAM files, we suspect our software code examples may take a
> long running time. Do you have any suggestions on this so it can pass the
> software checking, which is time-bound?


We will be happy to help you through any technical obstacles you encounter
in preparing either
the experiment data submission or the long testing situation.

Thank you

> Thank you very much in advance.
> Regards,
> Hao
> ---
> Hao Feng, Ph.D.
> Assistant Professor in Biostatistics
> Department of Population and Quantitative Health Sciences
> Case Western Reserve University School of Medicine
> Harland Wood Building - Room WG-82T
> 10900 Euclid Avenue
> SOM / Room G82T
> Cleveland, OH 44106-4945
> Phone: 216-368-5510
> Lab website: https://hfenglab.org/
> Official website: http://epbiwww.case.edu/haofeng-phd/
> Email: hxf155 using case.edu <mailto:hxf155 using case.edu>
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