EDGE_pro 1.3.1: crashes when resolving overlapping protein genes on the same strand
Submitted bug report:
SUBJECT: bugfix: edge-pro 1.3.1: crashes when resolving overlapping protein genes on the same strand
Folks
Running EDGE-pro 1.3.1 on NZ_CP010555.1, the edge.pl script crashed on line 455:
PREPROCESSING:
Getting sizes
Combining ptt and rnt files
Can't use string ("-") as an ARRAY ref while "strict refs" in use at /home/curtish/.conda/envs/edge-pro/bin/edge.pl line 455.
The problem is triggered by overlapping CDS on the same strang, and triggers code where it looks like a code re-write that switched from indexing into @combined to using @arr1 and @arr2 accidently left an [$j] index on @arr2. The fix is
455c459,460
< elsif(($arr2[5] eq "tRNA") || ($arr2[$j][5] eq "rRNA")){ #the second gene is tRNA/rRNA, so ignore the first gene
---
> elsif(($arr2[5] eq "tRNA") || ($arr2[5] eq "rRNA")){ #the second gene is tRNA/rRNA, so ignore the first gene
I would provide a pull request, but I don’t see EDGE-Pro code hosted on github or the like.
Regards,