Fgpyo

Features

- Allow `lineterminator` specification in `MetricWriter` (220) by znorgaard
- Overload `SeqDict.from_sam()` method to support SAM files (183) by TimD1
- Trim flanking whitespace when reading a Metric (217) by nh13
- Add methods to fix mate info on non-primaries and templates (204) by clintval

Chores

- Fix website link in README (227)

CI

- Rename `pythonpackage` to `tests`, update action versions (223)

What's Changed
* chore: exclude `site/` and `docs/` from mypy checks by msto in https://github.com/fulcrumgenomics/fgpyo/pull/195
* feat: remove python 3.8 support by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/197
* Add all_r1 and all_r2 methods on Template by clintval in https://github.com/fulcrumgenomics/fgpyo/pull/200
* Template to treat 'secondary supplemental' as supplemental by clintval in https://github.com/fulcrumgenomics/fgpyo/pull/203
* Add a function for determining read pair orientation by clintval in https://github.com/fulcrumgenomics/fgpyo/pull/201
* Deprecate set_pair_info and _set_mate_info for set_mate_info by clintval in https://github.com/fulcrumgenomics/fgpyo/pull/202
* Allow insert size calculation to work on 1 read only by clintval in https://github.com/fulcrumgenomics/fgpyo/pull/205
* Add a method for progress logging multiple alignments by clintval in https://github.com/fulcrumgenomics/fgpyo/pull/199
* Make sure VcfHeaderNumber.value is called in VariantBuilder. by tfenne in https://github.com/fulcrumgenomics/fgpyo/pull/215
* Add tabix indexing of gzipped VCFs in VariantBuilder by tfenne in https://github.com/fulcrumgenomics/fgpyo/pull/214
* fix: `sum_of_base_qualities()` returns zero when a record has no base qualities by msto in https://github.com/fulcrumgenomics/fgpyo/pull/212
* doc: add fulcrum genomics more prominently by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/218
* chore: Move numpy to docs dependency group by msto in https://github.com/fulcrumgenomics/fgpyo/pull/221


**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.8.0...1.0.0

What's Changed

* Add `assert_fasta_indexed` by msto in https://github.com/fulcrumgenomics/fgpyo/pull/186
* Add clintval to CODEOWNERS by clintval in https://github.com/fulcrumgenomics/fgpyo/pull/189
* Update `pyproject.toml` (137) by TimD1 in https://github.com/fulcrumgenomics/fgpyo/pull/184
* Require error codes on `type: ignore` pragmas by msto in https://github.com/fulcrumgenomics/fgpyo/pull/190
* MetricWriter by msto in https://github.com/fulcrumgenomics/fgpyo/pull/123
* Add cigar utility method `query_alignment_offsets` by yfarjoun in https://github.com/fulcrumgenomics/fgpyo/pull/188

New Contributors
* TimD1 made their first contribution in https://github.com/fulcrumgenomics/fgpyo/pull/184

**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.7.1...0.8.0

What's Changed
* fix: longest homopolymer needs to be case insensitive by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/181


**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.7.0...0.7.1

What's Changed
* ci: remove the use of github-actions-ci environment by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/179
* feat: add methods for computing run lengths of repeats in a sequence by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/162


**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.6.0...0.7.0

What's Changed
* feat: Add methods for UMI extraction from read name by emmcauley in https://github.com/fulcrumgenomics/fgpyo/pull/118
* fix: RTD needs an `__init__.py` in `fgpyo/platform/` by emmcauley in https://github.com/fulcrumgenomics/fgpyo/pull/174
* fix: fgpyo.fasta.sequence_dictionary incorrect StrEnum import by nh13 in https://github.com/fulcrumgenomics/fgpyo/pull/175


**Full Changelog**: https://github.com/fulcrumgenomics/fgpyo/compare/0.5.0...0.6.0