Isn't namespace pollution something that comes up when you have a conflict? What is the chance of vcfallelicprimitives getting into a conflict? It would have to be another VCF toolkit ;)
On Tue, May 25, 2021 at 07:41:46PM +0200, Steffen Möller wrote: > Dear Pjotr, > > Am 25.05.21 um 19:18 schrieb Pjotr Prins: > > I am looking at > > > > https://packages.debian.org/sid/amd64/libvcflib-tools/filelist > > > > and the R scripts are there. I think it is strange that many tools get > > installed in /usr/lib/vcflib/bin/ though. Is this policy? The man > > pages cover them all. > > > > wdyt? > > Thank you for spotting them. My hunch is that Michael wanted to avoid > name clashess - the vcftools package for instance also has vcf-sort, > just with a hypthen and there may be others forthcoming who then all > fight for their position in /usr/bin. > > The policy is to hide away those executables that are meant for > "internal use". So, I tend to think that this move was a bit too much on > the side of caution. > > So, I think that we should come up with yet another package, called > "vcflib" that drags in libvcflib-tools as an architecture-dependend > dependency and that ships the scripts in /usr/bin. For the moment I am > not sure about what to do about the binaries hidden away. I prefer > shipping them in /usr/bin but it is Michael's package and I would want > him to greenlight this first. > > Best, > Steffen > > > > > On Sun, May 23, 2021 at 05:02:01PM +0200, Pjotr Prins wrote: > >> The vcflib installer drops the R scripts > >> > >> https://github.com/vcflib/vcflib/blob/master/CMakeLists.txt#L189 > >> > >> not sure you'd want those? > >> > >> Pj. > >> > >> On Sun, May 23, 2021 at 03:47:02PM +0200, Michael R. Crusoe wrote: > >>> Thanks for catching this, Steffen! > >>> A bug report would be appreciated, so we don't lose track of this. > >>> -- > >>> Michael R. Crusoe > >>> > >>> On Sun, May 23, 2021, 14:51 Steffen Möller <[1]steffen_moel...@gmx.de> > >>> wrote: > >>> > >>> Hello, > >>> cudaSV needs bgziptabix to be happy, which is how I became aware fo > >>> all > >>> the scripts in > >>> Med/libvcflib$ ls scripts/ > >>> bed2region plotXPEHH.R vcfindelproximity > >>> vcfnulldotslashdot vcfregionreduce_and_cut > >>> bgziptabix vcf2bed.py vcfindels > >>> vcfplotaltdiscrepancy.r vcfregionreduce_pipe > >>> plotBfst.R vcf2sqlite.py vcfjoincalls > >>> vcfplotaltdiscrepancy.sh vcfregionreduce_uncompressed > >>> plotHaplotypes.R vcfbiallelic vcfmultiallelic > >>> vcfplotsitediscrepancy.r vcfremovenonATGC > >>> plotHapLrt.R vcfclearid vcfmultiway > >>> vcfplottstv.sh vcfsnps > >>> plotPfst.R vcfclearinfo vcfmultiwayscripts > >>> vcfprintaltdiscrepancy.r vcfsort > >>> plot_roc.r vcfcomplex vcfnobiallelicsnps > >>> vcfprintaltdiscrepancy.sh vcf_strip_extra_headers > >>> plotSmoothed.R vcffirstheader vcfnoindels > >>> vcfqualfilter vcfvarstats > >>> plotWCfst.R vcfgtcompare.sh vcfnosnps > >>> vcfregionreduce > >>> Med/libvcflib$ du -sh scripts/ > >>> 399K scripts/ > >>> being plain missing in libvcflib1 . Should there be a libvcflib-bin > >>> package? These scripts are expected to install together with vcflib, > >>> so > >>> maybe having them recommended is a good idea? The vcftools package > >>> is > >>> something independent. > >>> debian/rules removes *.R files, so someone on this list knows more > >>> about > >>> it all than me, please give some directions. > >>> Best, > >>> Steffen > >>> > >>> References > >>> > >>> 1. mailto:steffen_moel...@gmx.de >