Thank you for your reply. Considering opinions, it would be better to remove VCF IO from the codebase for the present. When removing from codebase, removing description from the document Ahmet commented at https://issues.apache.org/jira/browse/BEAM-5628 is also needed.
On Wed, Feb 24, 2021 at 2:31 AM Cory McLean <c...@google.com> wrote: > > +1 to removing from the codebase, and if it becomes of interest again, > porting to cyvcf2. But most genomics workflows are not using Beam at the > moment. > > On Tue, Feb 23, 2021 at 1:12 AM Chamikara Jayalath <chamik...@google.com> > wrote: >> >> Given that we don't support Python 2 anymore, it sounds like this is just >> broken code and we cannot expect anybody to be using it (after Beam 2.24.0). >> If so +1 for removing it from the codebase. If we decide to add it back with >> Python3 support, we should be able to refer to (working) 2.24.0 >> implementation. >> >> Thanks, >> Cham >> >> On Mon, Feb 22, 2021 at 5:17 PM Valentyn Tymofieiev <valen...@google.com> >> wrote: >>> >>> Hi Yoshiki, >>> >>> If switching the code to a new version of VCF package is something easy to >>> do, I would keep the code, but keep the dependency on vcf packages >>> optional, since we know that this code is not in use. If you decide to try >>> this route, https://issues.apache.org/jira/browse/BEAM-5628 mentions >>> cyvcf2 as a possible replacement. >>> >>> If replacement is not trivial and/or nobody is interested in making it >>> work, I would remove this IO. >>> >>> CC'ing a few folks who may have an opinion: +Chamikara Jayalath +Cory >>> McLean . >>> >>> Thanks for your help with the cleanup! >>> >>> On Sun, Feb 21, 2021 at 4:23 AM Yoshiki Obata <yoshiki.ob...@gmail.com> >>> wrote: >>>> >>>> Hi all, >>>> >>>> I'm cleaning up Python 2 codepath now and find that VCF IO codes still >>>> remain though they might not work properly with latest Beam because >>>> they depend on PyVCF which does not support Python 3. >>>> According to comments in vcfio.py, migrating to Nucleus is expected, >>>> but it is concluded that the plan is not the right option at the >>>> comment of https://issues.apache.org/jira/browse/BEAM-5628 >>>> >>>> Now, it would be needed to decide which should we do for VCF IO - drop >>>> support or maintain support using another vcf package. >>>> Would anyone have a basis for the decision? >>>> >>>> Yoshiki
