Alignment Mode and Parameter Adjustment in StainedGlass

[justdx]

Hi Mitchell,

I've been using StainedGlass on my sequences, but I've encountered an issue where the job ends quickly without producing any expected results. Upon investigation, I discovered that the alignment with "ava-ONT" doesn't align any sequences, whereas it aligns successfully with "asm5" in my test. I'm curious about why you selected this alignment mode and if there's a way to adjust this alignment parameter while running the software.

Thank you for your assistance.