Re: vcflib does not install scripts - missing bgziptabix

2021-05-25 Thread Pjotr Prins
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

Re: vcflib does not install scripts - missing bgziptabix

2021-05-25 Thread Steffen Möller
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 th

Re: vcflib does not install scripts - missing bgziptabix

2021-05-25 Thread Pjotr Prins
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 05:02:0

Re: vcflib does not install scripts - missing bgziptabix

2021-05-23 Thread Steffen Möller
After a look at the CMakeLists.txt file, I very much get the impression that the current vcflib package also misses the BINs, not ony the SCRIPTs. Best, Steffen Am 23.05.21 um 17:02 schrieb Pjotr Prins: > The vcflib installer drops the R scripts > > https://github.com/vcflib/vcflib/blob/master/

Re: vcflib does not install scripts - missing bgziptabix

2021-05-23 Thread Pjotr Prins
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

Re: vcflib does not install scripts - missing bgziptabix

2021-05-23 Thread Steffen Möller
Hi Michael, I'd happily address this rightaway, but what do you suggest? A separate arch-indep package sounds appropriate to me. On a sidenote - the Nanopore Structural Variant pipeline also needs vcfsort. Best, Steffen Am 23.05.21 um 15:47 schrieb Michael R. Crusoe: > Thanks for catching this

Re: vcflib does not install scripts - missing bgziptabix

2021-05-23 Thread Michael R. Crusoe
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 wrote: > Hello, > > cudaSV needs bgziptabix to be happy, which is how I became aware fo all > the scripts in > > Med/libvcflib$

vcflib does not install scripts - missing bgziptabix

2021-05-23 Thread Steffen Möller
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