Duplex-tools

Fixed
- Bug where aligned BAMs would be used as inputs to filter_pairs. This meant running `filter_pairs` on a guppy directory would report an incorrect duplex rate

Fixed
- Bug where an incorrect tag was used to get sequence lengths from .bam files (for dorado)
Changed
- ProcessPoolExecutor -> ThreadPoolExecutor in filter_pairs for faster filtering
- Reporting duplex rate in duplex_tools pair

Added
- Ability to use an unmapped bam (output from dorado) as input to pairs_from_summary
- Ability to use an unmapped bam (output from dorado) as input to filter_pairs
- Convenience script (`duplex_tools pair unmapped.bam`) to call both pairs_from_summary and filter_pairs on a bam
- usage: duplex_tools pair unmapped.bam

Fixed
- Bug where template/complement pairs with small negative time between them would not be chosen (rounding error).
Added
- Option to set --no_end_penalties in filter_pairs. This option favours partial matches and avoids unbounded negative pairing scores

Fixed
- Bug where template/complement pairs with no time between them would not be chosen

Added
- Option to set --threads in filter_pairs
Updated
- Updated defaults in readme for duplex basecalling (`chunks_per_runner` 16 -> 416)