packages for analyses of DNA structural variations

[Steffen Möller <steffen_moeller@gmx.de>]

Hello,

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 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).

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