Clint Valentine

Support the read structure operator `C` for cell barcodes

1

Upstream and related issue: - https://github.com/fulcrumgenomics/fgbio/pull/1103 Luckily the spec. and the `read-structure` crate already have such support: - https://github.com/fulcrumgenomics/read-structure/blob/295aa041621cd8d95ef88af4d30c03b5d2bb4348/src/segment_type.rs#L28

Remove support for Python3.9

2

Closes https://github.com/fulcrumgenomics/fgpyo/issues/247 Removes _**most**_ references to `Union[T]` and `Optional[T]`. There are still many old-style references to titlecase types (e.g. `List[T]` vs `list[T]`). I figured it would create too much code...

Nextflow linter errors on custom Groovy code in lib/ as not being defined

1

## Bug report ### Expected behavior and actual behavior Running `nextflow lint ./` on a project that has Groovy classes in `lib/` and using those classes in the Nextflow script...

Cache the mate cigar the first time it is parsed on SamRecord

3

I'm starting to think we should cache the mate cigar like we do with the record's cigar. It would require similar trickery to detect when a new mate cigar is...