1.5.0

[1.5.0] - 2026-02-17

🚀 Features

• (test) Add doctest support to pytest (#268)
• Calculate MD and NM tags (#229)
• Add FastaBuilder.to_fasta_file_handle() (#271)
• Implementation of cigar truncation methods ported from fgbio (#273)
• Add Cigar.coalesce() method (#275)

💼 Other

• Modernize pyproject.toml (#258)

🚜 Refactor

• Make to_fasta_file_handle a context manager (#272)

⚙️ Miscellaneous Tasks

• (ci) Update orhun/git-cliff-action from v3 to v4 (#267)
• (release) Bump to 1.5.0 (#276)

1.4.0

[1.4.0] - 2025-11-27

Chore

• Add __version__ attribute (#248)
• Update ci/check.sh and CONTRIBUTING.md to use primary uv interface (#237)
• (release) Bump to 1.4.0 (#266)

Docs

• Updates to various docs and error messages; speed up hamming (#265)

Feat

• Make FastxZipped error for mismatched read names deterministic (#252)
• require() (#246)
• SamBuilder can output SAM/BAM/CRAM (#257)

Fix

• Support PEP604 syntax str | None (#251)
• Issue #253 sam.reader fails silently

1.3.0

What's Changed

• New Feature: support multi-threaded reading and writing of gzip files by @nh13 in #240
• Bug Fix: Make it easier to set the END on records using VariantBuilder. by @tfenne in #241

Full Changelog: 1.2.0...1.3.0

1.2.0

[1.2.0] - 2025-05-20

Chore

• (release) Bump to 1.2.0

Doc

• Fix links to logo (#233)

Feat

• Support PEP604 syntax str | None (#168)

Fix

• Typing_extensions needed for @deprecated up until python 3.12 (#231)
• Publish sdist output directory argument

1.1.0

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)

1.0.0

What's Changed

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

Full Changelog: 0.8.0...1.0.0

0.8.0

What's Changed

• Add assert_fasta_indexed by @msto in #186
• Add @clintval to CODEOWNERS by @clintval in #189
• Update pyproject.toml (#137) by @TimD1 in #184
• Require error codes on type: ignore pragmas by @msto in #190
• MetricWriter by @msto in #123
• Add cigar utility method query_alignment_offsets by @yfarjoun in #188

New Contributors

• @TimD1 made their first contribution in #184

Full Changelog: 0.7.1...0.8.0

0.7.1

What's Changed

• fix: longest homopolymer needs to be case insensitive by @nh13 in #181

Full Changelog: 0.7.0...0.7.1

0.7.0

What's Changed

• ci: remove the use of github-actions-ci environment by @nh13 in #179
• feat: add methods for computing run lengths of repeats in a sequence by @nh13 in #162

Full Changelog: 0.6.0...0.7.0

0.6.0

What's Changed

• feat: Add methods for UMI extraction from read name by @emmcauley in #118
• fix: RTD needs an __init__.py in fgpyo/platform/ by @emmcauley in #174
• fix: fgpyo.fasta.sequence_dictionary incorrect StrEnum import by @nh13 in #175

Full Changelog: 0.5.0...0.6.0