When using the -t (trim) flag, and providing a .bed file that indicates an entire scaffold to be removed, features that would normally be on that scaffold should also be removed. Currently their indices are being output as negative values instead. May also extend to partial trims such as removing a single CDS.
How to reproduce:
Command:
python gag.py --fasta genome.fasta --gff genome.gff -t trim.bed --out output_folder
Input:
input.zip
When using the -t (trim) flag, and providing a .bed file that indicates an entire scaffold to be removed, features that would normally be on that scaffold should also be removed. Currently their indices are being output as negative values instead. May also extend to partial trims such as removing a single CDS.
How to reproduce: Command: python gag.py --fasta genome.fasta --gff genome.gff -t trim.bed --out output_folder Input: input.zip
Output: genome.gff.txt genome.tbl.txt