Re: Any volunter to write a test for bamclipper?
Hi Steffen,
On 26 March 2021 6:35:13 am IST, "Steffen Möller" <steffen_moeller@gmx.de> wrote:
>
>> I found those files here[1] inside examples/ dir -- it also has
>> outputted *.primer.bam* files, so I think it is sensible
>> to assume that these files work.
>> I follow this in other packages as well, when on adding certain bam
>or
>> sam files, "something" happens which is good for
>> at least a preliminary functioning test :-)
>>
>> I added a autopkgtest to the salsa repo, please take in a look.
>>
>> PS: Please consider enabling salsa CI for any new packages that you
>> might push. I did so for this one for now.
>>
>> [1]: https://github.com/tommyau/bamclipper
>
>https://software.broadinstitute.org/software/igv/BAM
>
>One of the many reads from a high-throughput sequencing machine
>(pre-Nanopore this was 30, 70 or 144 nucleotides in length, since the
>nanopore we are talking about 10^6 "basepairs" that are continuously
>sequenced) is just a series of characters. For every such read you want
>to know where in the reference genome it likely was sequenced from, how
>the quality was at different parts of the read and how well it matches
>against a reference genome.
>
>bowtie http://bowtie-bio.sourceforge.net/manual.shtml gets reads as
>input, writes SAM which are converted to BAM via "samtools view".
I read it, and yes.
>There is loads of public data out there that we could use for testing
>purposes. As long as we can automate the generation of such a Debian
>Med
>Testing Environment from public data
How do we do that?
> - there is no need to have
>everything that we test on as a Debian package, right?
I admit, I do not get you here. The data to test on is inside the package, and it isn't the package itself.
What do I miss?
Nilesh
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