Ecosyste.ms: Issues

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GitHub / fulcrumgenomics/fgpyo issues and pull requests

#202 - Deprecate set_pair_info and _set_mate_info for set_mate_info

Pull Request - State: open - Opened by clintval 25 days ago - 1 comment

#201 - Add a function for determining read pair orientation

Pull Request - State: open - Opened by clintval 26 days ago - 1 comment

#200 - Add all_r1 and all_r2 methods on Template

Pull Request - State: closed - Opened by clintval 26 days ago - 2 comments

#199 - Add a method for progress logging templates

Pull Request - State: open - Opened by clintval 26 days ago - 4 comments

#198 - ci: add CI support for python 3.13

Pull Request - State: open - Opened by nh13 about 1 month ago - 1 comment

#197 - feat: remove python 3.8 support

Pull Request - State: closed - Opened by nh13 about 1 month ago - 2 comments

#196 - ci: migrate ubuntu-latest to ubuntu-24.04

Pull Request - State: closed - Opened by nh13 about 2 months ago - 2 comments

#195 - chore: exclude `site/` and `docs/` from mypy checks

Pull Request - State: closed - Opened by msto 2 months ago - 2 comments

#194 - feat: Add sorted Cartesian product

Pull Request - State: closed - Opened by msto 2 months ago - 1 comment

#193 - Add a function to extract the sort order from an `AlignmentHeader`

Issue - State: open - Opened by msto 2 months ago - 8 comments

#192 - Clean up our documentation

Issue - State: closed - Opened by msto 3 months ago
Labels: help wanted

#191 - chore: Add docstring lints

Pull Request - State: closed - Opened by msto 3 months ago - 2 comments
Labels: help wanted

#190 - chore: Require error codes on `type: ignore` pragmas

Pull Request - State: closed - Opened by msto 3 months ago - 2 comments

#189 - Add @clintval to CODEOWNERS

Pull Request - State: closed - Opened by clintval 4 months ago - 1 comment

#188 - feat: add cigar utility method get_alignment_offsets

Pull Request - State: closed - Opened by yfarjoun 4 months ago - 5 comments

#187 - Drop support for Python 3.8 after EOL

Issue - State: open - Opened by msto 4 months ago

#186 - feat: Add `assert_fasta_indexed`

Pull Request - State: closed - Opened by msto 4 months ago - 1 comment

#185 - feat: DataSubclassMixin

Pull Request - State: closed - Opened by msto 4 months ago - 1 comment

#184 - Update pyproject.toml (#137)

Pull Request - State: closed - Opened by TimD1 5 months ago - 2 comments

#183 - feat: overloaded 'SeqDict.from_sam()' method to support SAM files (#176)

Pull Request - State: open - Opened by TimD1 5 months ago - 1 comment

#182 - feat: added template.fixmate() (#83)

Pull Request - State: open - Opened by TimD1 5 months ago - 1 comment

#181 - fix: longest homopolymer needs to be case insensitive

Pull Request - State: closed - Opened by nh13 5 months ago - 1 comment

#180 - chore: remove the github-actions-ci environment

Issue - State: open - Opened by nh13 5 months ago

#179 - ci: remove the use of github-actions-ci environment

Pull Request - State: closed - Opened by nh13 5 months ago - 1 comment

#178 - feat: support metric custom column ordering and sub-setting

Pull Request - State: open - Opened by nh13 5 months ago - 1 comment

#177 - Metric.write should support alternate ordering of fields

Issue - State: open - Opened by ameynert 5 months ago
Labels: enhancement

#176 - Add a class/module method to read in a `.dict` file to a `SequenceDictionary`

Issue - State: open - Opened by nh13 5 months ago
Labels: good first issue, help wanted

#175 - fix: fgpyo.fasta.sequence_dictionary incorrect StrEnum import

Pull Request - State: closed - Opened by nh13 5 months ago - 1 comment

#174 - fix: RTD needs an `__init__.py` in `fgpyo/platform/`

Pull Request - State: closed - Opened by emmcauley 6 months ago - 1 comment

#173 - Revert "fix: Add return type hint to Metric.read()"

Pull Request - State: closed - Opened by msto 6 months ago - 1 comment

#172 - Bug: Incompatible types in assignment with `Metric.read`

Issue - State: closed - Opened by nh13 6 months ago - 1 comment

#171 - fixme: demonstrates typing bug with Metric.read

Pull Request - State: closed - Opened by nh13 6 months ago - 1 comment

#170 - Expand Levenshtein distance calculation functionality

Issue - State: closed - Opened by znorgaard 6 months ago
Labels: enhancement

#168 - feat: support PEP604 syntax `str | None`

Pull Request - State: open - Opened by nh13 6 months ago - 3 comments

#167 - feat: add hamming and levenshtein distance functions

Pull Request - State: closed - Opened by znorgaard 6 months ago - 5 comments

#166 - feat: move docs out of extras into their own group

Pull Request - State: closed - Opened by nh13 6 months ago - 2 comments

#165 - `mkdocs` dependencies should be declared as a dependency group, not extras

Issue - State: closed - Opened by msto 6 months ago - 1 comment

#164 - doc: Add installation of `mkdocs` dependencies to README

Pull Request - State: closed - Opened by msto 6 months ago - 1 comment

#163 - feat: Lint tests directory

Pull Request - State: closed - Opened by msto 6 months ago - 1 comment

#162 - feat: add methods for computing run lengths of repeats in a sequence

Pull Request - State: closed - Opened by nh13 6 months ago - 1 comment

#161 - Adds support for running doctest as part of pytest

Pull Request - State: open - Opened by nh13 6 months ago - 2 comments

#160 - feat: adds classes and methods for sequence dictionaries

Pull Request - State: closed - Opened by nh13 6 months ago - 1 comment

#159 - Add a lazy is_sorted function to collections

Pull Request - State: closed - Opened by clintval 6 months ago - 1 comment

#158 - feat: speed up longest_homopolymer

Pull Request - State: closed - Opened by nh13 7 months ago - 1 comment

#157 - Feat: add longest_hp_len() to fgpyo/sequence.py

Pull Request - State: closed - Opened by emmcauley 7 months ago - 1 comment

#156 - Feat: add gc_content() calculation method to fgpyo/sequence.py

Pull Request - State: closed - Opened by emmcauley 7 months ago - 1 comment

#155 - feat: add len, iter, and getitem dunder methods to Cigar

Pull Request - State: closed - Opened by msto 7 months ago - 1 comment

#154 - - Added __getitem__ ~and __len__~ to the Cigar class, pulling the answer…

Pull Request - State: closed - Opened by yfarjoun 7 months ago - 1 comment

#153 - Feature request: add __get_item__() to Cigar class

Issue - State: closed - Opened by yfarjoun 7 months ago - 3 comments

#152 - Feature request: better modeling of a pysam sequence dictionary

Issue - State: closed - Opened by nh13 7 months ago - 1 comment

#151 - feat: Add `find_illumina_fastq`

Pull Request - State: closed - Opened by msto 7 months ago - 9 comments

#150 - ci: update code-cov in GHA to use a token

Pull Request - State: closed - Opened by nh13 7 months ago - 1 comment

#149 - chore: ignore existing C901 violations

Pull Request - State: closed - Opened by msto 7 months ago - 2 comments

#148 - chore: fix B010 violations

Pull Request - State: closed - Opened by nh13 7 months ago - 3 comments

#147 - chore: fix B904 violations

Pull Request - State: closed - Opened by nh13 7 months ago

#146 - chore: fix B028 violations

Pull Request - State: closed - Opened by msto 7 months ago

#145 - chore: fix B007 violations

Pull Request - State: closed - Opened by msto 7 months ago

#144 - chore: fix B017 violations

Pull Request - State: closed - Opened by msto 7 months ago

#143 - `inspect._get_parser()` requires the now-deprecated `typing.*` collection types

Issue - State: open - Opened by msto 7 months ago - 1 comment
Labels: good first issue

#142 - chore: Add usual lints

Pull Request - State: closed - Opened by msto 7 months ago - 1 comment

#141 - Add lint checks for C901, bugbear, and quotes

Issue - State: closed - Opened by msto 7 months ago

#140 - chore: Switch to ruff

Pull Request - State: closed - Opened by msto 7 months ago

#139 - Move to `ruff`

Issue - State: closed - Opened by msto 7 months ago

#138 - Add a `CONTRIBUTING.md`

Issue - State: closed - Opened by msto 7 months ago - 1 comment

#137 - Update `pyproject.toml`

Issue - State: closed - Opened by msto 7 months ago

#135 - Move to mkdocs from Sphinx

Pull Request - State: closed - Opened by nh13 8 months ago - 5 comments

#134 - chore: Update mypy config

Pull Request - State: closed - Opened by msto 8 months ago

#133 - Clean up `type: ignore`s

Issue - State: closed - Opened by msto 8 months ago
Labels: good first issue

#132 - Add `require`

Issue - State: open - Opened by msto 8 months ago - 1 comment
Labels: good first issue

#130 - Add code coverage report

Issue - State: open - Opened by msto 8 months ago - 1 comment

#129 - feat: Add assertions to support `MetricWriter`

Pull Request - State: closed - Opened by msto 8 months ago

#128 - Use tox so we can test multiple python versions locally

Issue - State: open - Opened by msto 8 months ago - 3 comments

#127 - Use ruff (or flake8 plugins) to expand the range of lint checks

Issue - State: closed - Opened by msto 8 months ago - 1 comment

#126 - Use stricter mypy config

Issue - State: closed - Opened by msto 8 months ago

#125 - refactor: Narrow typing on `to_reader` and `to_writer`

Pull Request - State: closed - Opened by msto 8 months ago - 1 comment

#124 - feat: Add `read_header()`

Pull Request - State: closed - Opened by msto 8 months ago

#123 - feat: MetricWriter

Pull Request - State: closed - Opened by msto 8 months ago - 2 comments

#122 - Add function(s) to set the 5' most alignment on a read as primary

Issue - State: open - Opened by msto 8 months ago - 1 comment

#121 - fix: r/w assertions

Pull Request - State: closed - Opened by msto 8 months ago - 1 comment

#119 - refactor: writeable -> writable

Pull Request - State: closed - Opened by msto 8 months ago

#118 - feat: Add methods for UMI extraction from read name

Pull Request - State: closed - Opened by emmcauley 8 months ago

#117 - `io.assert_path_is_writeable()` should return True for "/dev/stdout"

Issue - State: closed - Opened by msto 8 months ago - 1 comment
Labels: good first issue

#116 - Add isort check to Github Action

Pull Request - State: closed - Opened by emmcauley 8 months ago - 1 comment

#115 - `Metric` should support comma-delimited files

Issue - State: open - Opened by msto 8 months ago

#113 - chore: add CODEOWNERS

Pull Request - State: closed - Opened by msto 9 months ago

#112 - Consider renaming modules which shadow stdlib modules

Issue - State: open - Opened by msto 9 months ago

#111 - Add a CODEOWNERS

Issue - State: closed - Opened by msto 9 months ago

#110 - fix: Add return type hint to Metric.read()

Pull Request - State: closed - Opened by msto 9 months ago

#109 - feat: Add asdict()

Pull Request - State: closed - Opened by msto 9 months ago - 5 comments

#108 - fix: DataclassInstance and AttrInstance protocols

Pull Request - State: closed - Opened by msto 9 months ago

#107 - feat: Add MetricWriter class

Pull Request - State: closed - Opened by msto 9 months ago - 1 comment

#106 - Add `as_fastafile` method to `FastaBuilder`

Issue - State: open - Opened by msto 9 months ago
Labels: good first issue

#105 - feat: Add end property on SupplementaryAlignment

Pull Request - State: closed - Opened by msto 9 months ago - 1 comment

#104 - Metric wishlist

Issue - State: open - Opened by msto 9 months ago - 4 comments

#103 - feat: Support reading Picard-style metrics files with comments above the header

Pull Request - State: closed - Opened by msto 10 months ago - 6 comments