Re: packages for analyses of DNA structural variations
Hi,
>
> I went a bit over packages listed in the "genome structure" tab
> https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=701092179
>
> and have surpyvor and tandem-genotypes considered worthy for sponsoring.
>
> npInv gives me
>
> $ lintian -i ../npinv_1.24+ds-1*changes
> W: npinv: bad-jar-name usr/share/java/npInv-1.24.jar
> N:
> W: bad-jar-name
> N:
> N: The package ships the specified "public" Jar file under
> N: /usr/share/java/, but the name does not correspond to Java policy
> N: guidelines. This can cause tools in the Debian Java toolchain to fail.
> N:
> N: Refer to Debian policy for Java section 2.4 (Java libraries) for
> N: details.
> N:
> N: Severity: warning
> N:
> N: Check: languages/java
>
> but I have cross-checked that but did not find anything weird except for the capital "I". Ideas are welcome.
I think it actually is the fact that capital letters are not nice per
Java policy guidelines. I admit I've personally ignored this type of
warning.
> I also need to extend the package description. Anyone feeling creative - please go for it :)
>
> I got stuck with pbmm2 (https://salsa.debian.org/med-team/pbmm2) , which needs a library (C++ API) for minimap2.
> and pbsv misses the source tree in the repository (reported as https://github.com/PacificBiosciences/pbbioconda/issues/418).
I remember I worked on the library for minimap2 some time ago (> one
year ago). I do not remember the outcome but it was a bit tricky.
Would need to check but I have no time right now.
> These structural variations are of direct clinical interest - not so much for the viral side of the sequencing but for the patient side, e.g. when looking for reasons why some people are more succeptible to develop long covid. Such analyses were more difficult when reads where only short, but with the Nanopore or the PacBio HiFi, longer reads become increasingly available.
>
> Many thanks and kind regards,
> Steffen
Thanks a lot for your work on this
Andreas.
>
>
>
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