Dear Steffen, 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? Pj. 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 >
