enforce min bound on flanked region; skip empty gff3 lines

igvteam / igv-reports

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

MIT License

352 stars 53 forks source link

Closed tomkinsc closed 3 years ago

tomkinsc commented 4 years ago

Some gff3 files from genbank can have blank lines at the end. This adds a check that each line in a gff file has enough tokens to have start and end coords, and skips the line if not.
On short genomes such as viral, the start coord can go negative for variants near position 1 with sizable flank sizes (or not so sizable, depending). This enforces a min start coord of 1. The end coord fix is TBD

jrobinso commented 3 years ago

Apologies that this too so long, and thanks for the PR