Pore-c-py

Added
- create-chunked-ubam: break an unaligned bam into chunks

Added
- bam: add PG tag to bam files produced
- export: add separate export subcommand
- paired-end-export: enable filtering paired end read export to cis only and distance bounds
- chromunity: add option to merge fragments colinear in the read and genome into a single 'monomer'
- cli.py: add option to remove SAM tags from input, rename and move subcommands
- digest: move digest to top-level command, add option to remove sam tags from output
- aligns.py: add functions to group alignments colinear in the genome
Fixed
- model.py: fix mixed up sam tags
Changed
- remove kw_only from dataclass (requires python 3.10 or higher)
- overlaps.py: remove fragment overlap code
- dataclasses: replace attrs uses with dataclasses
- mappy: remove genome index and mappy uses

Added
- io.py: write basic summary stats in json format
- io.py: write a chromunity-compatible parquet file
Fixed
- model.py: use read start,end coords as monomer id
- Snakefile: fix integration tests

Fixed
- aligns.py: fix bug caused by change in lru_cache signature
Changed
- sam_tags.py: rename to sam_utils to reflect broader functoin
- utils.py: remove utils.py put functionaliy into io and sam_tags
- sam_tags.py: move sam tag processing to separate module
- model.py: make pore-s-specific tags into global settings

Fixed
- variants.py: remove partial phasing code
- testing.py: fix phased vcf generation

Changed
- model.py: set paired end fields and add walk metadata
- model.py: downgrade mm tags to work with pysam, ease roundtrip of tag data
- cli.py: analyse the first n reads
Fixed
- hatch.toml: fix type