Enhance Alignment Accuracy for Short Reads by Integrating `map-ont` and `splice` Options

📋 Description

When aligning short reads of approximately 350bp, there are cases where the map-ont option better represents the actual read alignment than the sr option.

Therefore, while currently only processing reads below 500bp with sr, we will modify it to include alignments with map-ont (and splice), and change it to select the optimal preset using extract_best_preset.

(This is more dependent on the behavior of mappy/minimap2 rather than a bug in DAJIN2.)

💬 Current Behavior

No response

🎯 Expected Behavior

No response

⚠️ Error message

No response

🔍 Environment

- OS: WSL2 Ubuntu
- DAJIN2 version: 0.5.2
- Python version: 3.10

📎 Anything else?

No response

akikuno / DAJIN2