Fix issue sequence filtering required alignment files.

New Features

• Filter sequences based on gaps or sequence length.
• Add a proportion of missing data parameter to the alignment filtering.

API Breaking Changes

• Rename classes and methods to improve clarity and consistency.
• Remove unnecessary mutability for conversion modules.
• Partition conversion moved to align module.
• Output directory and output format arguments for extraction are now required in the new instance of the extraction struct.

1. Instead of in the log file, alignment summary is now in a separate output file with alignment-summary suffix.
2. Read summary with complete option now writes per read position results to compressed zip file.
3. Prefix option for read, contig summary, and ID extraction.
4. CSV headers now use snake_case and more consistent across all features that output CSV.

ID parsing result is now in a directory consistent with other subcommands.