fulcrumgenomics/fgpyo

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Quality of life improvements for Bioinformatics in Python.

Stars: 35
Forks: 4
Open beginner issues: 0
Indexed issues: 23

Dominant language: Python
License: No license data
Last GitHub push: Sep 15, 2026
Latest indexed: Sep 16, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: good first issue
PR merge metrics: No merged PRs in 30d

Open All

23 open issues indexed

Create methods and type stubs on pysam htslib C extension calls Open

enhancement

fulcrumgenomics/fgpyo#22 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Create an equivalent to scala's `Either` class Open

fulcrumgenomics/fgpyo#42 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Add function to combine headers from multiple AlignmentFiles Open

fulcrumgenomics/fgpyo#56 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Metric.read and Metric.write should be context managers Open

fulcrumgenomics/fgpyo#70 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 16, 2026
Generate code for `SamBuilder` based on an input SAM/BAM Open

enhancement

fulcrumgenomics/fgpyo#79 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Feature: SAM tag enum Open

fulcrumgenomics/fgpyo#102 · 8 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
`Metric` should require decoration with `dataclass` or `attr.s` Open

fulcrumgenomics/fgpyo#114 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
`Metric` should support comma-delimited files Open

fulcrumgenomics/fgpyo#115 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Add function(s) to set the 5' most alignment on a read as primary Open

fulcrumgenomics/fgpyo#122 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Use tox so we can test multiple python versions locally Open

fulcrumgenomics/fgpyo#128 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Lock stdin/stdout so only one file handle may use either at a time Open

fulcrumgenomics/fgpyo#131 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Move code out of `__init__.py` and into `{submodule}.py` files Open

fulcrumgenomics/fgpyo#136 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
`inspect._get_parser()` requires the now-deprecated `typing.*` collection types Open

good first issue

fulcrumgenomics/fgpyo#143 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Metric.write should support alternate ordering of fields Open

enhancement

fulcrumgenomics/fgpyo#177 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
chore: remove the github-actions-ci environment Open

fulcrumgenomics/fgpyo#180 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Add a function to extract the sort order from an `AlignmentHeader` Open

fulcrumgenomics/fgpyo#193 · 8 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Consider more advanced views into the alignments in Template Open

fulcrumgenomics/fgpyo#207 · 4 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Metric to support a counter attribute Open

fulcrumgenomics/fgpyo#239 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Writers to accept `Path | None` Open

fulcrumgenomics/fgpyo#249 · 2 comments · 1 reaction · 0 assignees · Indexed Sep 16, 2026
FASTQ builder Open

fulcrumgenomics/fgpyo#254 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Optimize FastxZipped.__next__ to use a single pass over records Open

fulcrumgenomics/fgpyo#281 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026
Replace deprecated readthedocs GHA with built-in PR build integration Open

fulcrumgenomics/fgpyo#283 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 16, 2026
Discussion: consider widening Metric._parsers() to accept TypeAnnotation keys Open

fulcrumgenomics/fgpyo#303 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 16, 2026

fulcrumgenomics/fgpyo

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