VADR breaks processing AY394999.1: "Use of uninitialized value $uapos" about vadr HOT 4 CLOSED

Another accession with the same issue: AY395000.1

from vadr.

Thanks, Tomer. I'm working on a fix and will update you when I have more to report.

from vadr.

Thanks for reporting this, @taltman. This was due to a bug that is demonstrated if an entire internal CDS feature is deleted, as is the case with AY34999 and AY35000 (the hypothetical protein sars8a CDS is deleted).

I've fixed this in the develop branch and the fix will go into the next release: v1.1.1 which should happen within the next few weeks. As a temporary workaround, using --skip_pv with v-annotate.pl to avoid vadr exiting in error, but note that the sars8a CDS will be incorrectly annotated in the .ftr table with a length of '0' (start coordinate is 1 more than stop coordinate, e.g for AY394999: 27702 to 27701). With the fix, deleted features are not annotated in the .ftr file, but a new DELETION_OF_FEATURE error is reported.

The iss21-delcds test in testfiles/github-issues/ exercises the fix for this bug.

from vadr.

Thanks for looking into this! I appreciate the work-around, and look forward to the upcoming version.

from vadr.