Discrepancy between get_organelle_from_reads and summary_get_organelle_output logs

[marcelglueck]

First check

• I used the GitHub search to find a similar issue and didn't find it.
• I searched GetOrganelle.wiki context, especially the FAQ and browsed the examples to confirm it is unexpected to happen.
• I have updated GetOrganelle to the latest version

Describe the bug
Run the summary_get_organelle_output.py script for assemblies that produced the warning "WARNING: Ambiguous base(s) used!". The summary file will not feature this information. Instead, it says "degnerate_base_used=no".

To Reproduce
assembly_log.txt
assembly_stats.csv

[JianjunJin]

Hi @marcelglueck, Thanks for pointing out this!
It was now fixed in the branch https://github.com/Kinggerm/GetOrganelle/tree/intermediate_graph, which largely differs from the main branch (v1.7).
It will take time to release a formal version.

I will leave it open until fully tested and the new version is released.