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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