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MariaNattestad / Assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
http://assemblytics.com
MIT License
136 stars 28 forks source link

Error Running Assemblytics_within_alignment.py #56

Closed jiaanqiang closed 7 months ago

jiaanqiang commented 11 months ago

Hi Maria, Thank you for creating such a useful tool. I've been running it successfully for most samples, but some are giving me the following error:

Traceback (most recent call last): File "Assemblytics_within_alignment.py", line 101, in main() File "Assemblytics_within_alignment.py", line 98, in main args.func(args) File "Assemblytics_within_alignment.py", line 56, in run report = variants[-1] IndexError: list index out of range

I'm not sure what's causing it. Any ideas on how to fix this?

Waiting for your reply. Thanks

Jia

MariaNattestad commented 11 months ago

Sorry that's a bug. It should probably have been caught more gracefully. It looks like something that shouldn't happen given the delta file format, at least as far as I knew when I was coding Assemblytics, since there was no spec, so I was working it out based on example files. The bug you encountered doesn't appear to have ever popped up before in 8 years of usage, which is very odd. I'm curious what you used to generate the delta file that was input to Assemblytics.

jiaanqiang commented 11 months ago

Thank you for your response. The issue has been resolved.