Allows specifying bam files directly

[LudvigOlsen]

Hi guys,

I thought it a little suboptimal to have to copy all the bam files into the same directory to run Fragle. So I added the option of specifying the bam file paths directly.

I wanted to change as little as possible, but to ensure it worked with all the "--mode"s, I did end up making significant changes to the code base.

Here are my changes:

• Allows specifying multiple --input paths. Then parses them for whether it's a single directory, a list of bam files, or the data.pkl file. NOTE: This actually breaks specifying the previous output directory as input directory for --mode 'F' (now you need to add data.pkl to the path. If you think this needs to be possible, I can quickly add it. I just think it's cleaner this way.
• Refactors the command running part in main.py to reduce repeated code.
• Uses argparse in feature_generation.py and predict.py (easier to pass multiple bam file paths this way and reduces bug risks).
• Adds a check in predict.py for whether the output directory exists (when --mode 'F' and --output != --input).
• Specifies argparse choices for --mode to have it check the value automatically.
• Removes unused imports.
• I accidentally used my autoformatter (check out the amazing ruff) to have consistent styling. I actually didn't want to do this but it's the reason for some of the changes. If you want me to revert the conversion of quotes (' -> "), let me know.

I have tested all but the targeted version (--mode 'T').

I would totally understand if there are too many changes in this PR. I do think there are some good improvements here even if you don't want to support specifying bam files directly though.

Best,
Ludvig