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. > > > -- http://fam-tille.de