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 <[email protected]> +Cory McLean <[email protected]> . Thanks for your help with the cleanup! On Sun, Feb 21, 2021 at 4:23 AM Yoshiki Obata <[email protected]> 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 >
