Re: vcflib does not install scripts - missing bgziptabix
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_moeller@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_moeller@gmx.de
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