Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / fulcrumgenomics/fgpyo issues and pull requests
#188 - feat: add cigar utility method get_alignment_offsets
Pull Request -
State: open - Opened by yfarjoun 14 days ago
- 3 comments
#187 - Drop support for Python 3.8 after EOL
Issue -
State: open - Opened by msto 14 days ago
#186 - feat: Add `assert_fasta_is_indexed`
Pull Request -
State: open - Opened by msto 20 days ago
- 1 comment
#185 - feat: DataSubclassMixin
Pull Request -
State: open - Opened by msto 22 days ago
- 1 comment
#184 - Update pyproject.toml (#137)
Pull Request -
State: open - Opened by TimD1 28 days ago
- 2 comments
#183 - feat: overloaded 'SeqDict.from_sam()' method to support SAM files (#176)
Pull Request -
State: open - Opened by TimD1 28 days ago
- 1 comment
#182 - feat: added template.fixmate() (#83)
Pull Request -
State: open - Opened by TimD1 29 days ago
- 1 comment
#181 - fix: longest homopolymer needs to be case insensitive
Pull Request -
State: closed - Opened by nh13 about 1 month ago
- 1 comment
#180 - chore: remove the github-actions-ci environment
Issue -
State: open - Opened by nh13 about 2 months ago
#179 - ci: remove the use of github-actions-ci environment
Pull Request -
State: closed - Opened by nh13 about 2 months ago
- 1 comment
#178 - feat: support metric custom column ordering and sub-setting
Pull Request -
State: open - Opened by nh13 about 2 months ago
- 1 comment
#177 - Metric.write should support alternate ordering of fields
Issue -
State: open - Opened by ameynert about 2 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 about 2 months ago
Labels: good first issue, help wanted
#175 - fix: fgpyo.fasta.sequence_dictionary incorrect StrEnum import
Pull Request -
State: closed - Opened by nh13 about 2 months ago
- 1 comment
#174 - fix: RTD needs an `__init__.py` in `fgpyo/platform/`
Pull Request -
State: closed - Opened by emmcauley 2 months ago
- 1 comment
#173 - Revert "fix: Add return type hint to Metric.read()"
Pull Request -
State: closed - Opened by msto 2 months ago
- 1 comment
#172 - Bug: Incompatible types in assignment with `Metric.read`
Issue -
State: closed - Opened by nh13 2 months ago
- 1 comment
#171 - fixme: demonstrates typing bug with Metric.read
Pull Request -
State: closed - Opened by nh13 2 months ago
- 1 comment
#170 - Expand Levenshtein distance calculation functionality
Issue -
State: closed - Opened by znorgaard 2 months ago
Labels: enhancement
#169 - Should __get_item__() be reverted since it is confusing as to what the i-th entry of a Cigar is?
Issue -
State: open - Opened by yfarjoun 2 months ago
- 1 comment
#168 - feat: support PEP604 syntax `str | None`
Pull Request -
State: open - Opened by nh13 2 months ago
- 3 comments
#167 - feat: add hamming and levenshtein distance functions
Pull Request -
State: closed - Opened by znorgaard 3 months ago
- 5 comments
#166 - feat: move docs out of extras into their own group
Pull Request -
State: closed - Opened by nh13 3 months ago
- 2 comments
#165 - `mkdocs` dependencies should be declared as a dependency group, not extras
Issue -
State: closed - Opened by msto 3 months ago
- 1 comment
#164 - doc: Add installation of `mkdocs` dependencies to README
Pull Request -
State: closed - Opened by msto 3 months ago
- 1 comment
#163 - feat: Lint tests directory
Pull Request -
State: closed - Opened by msto 3 months ago
- 1 comment
#162 - feat: add methods for computing run lengths of repeats in a sequence
Pull Request -
State: closed - Opened by nh13 3 months ago
- 1 comment
#161 - Adds support for running doctest as part of pytest
Pull Request -
State: open - Opened by nh13 3 months ago
- 2 comments
#160 - feat: adds classes and methods for sequence dictionaries
Pull Request -
State: closed - Opened by nh13 3 months ago
- 1 comment
#159 - Add a lazy is_sorted function to collections
Pull Request -
State: closed - Opened by clintval 3 months ago
- 1 comment
#158 - feat: speed up longest_homopolymer
Pull Request -
State: closed - Opened by nh13 3 months ago
- 1 comment
#157 - Feat: add longest_hp_len() to fgpyo/sequence.py
Pull Request -
State: closed - Opened by emmcauley 3 months ago
- 1 comment
#156 - Feat: add gc_content() calculation method to fgpyo/sequence.py
Pull Request -
State: closed - Opened by emmcauley 3 months ago
- 1 comment
#155 - feat: add len, iter, and getitem dunder methods to Cigar
Pull Request -
State: closed - Opened by msto 3 months ago
- 1 comment
#154 - - Added __getitem__ ~and __len__~ to the Cigar class, pulling the answer…
Pull Request -
State: closed - Opened by yfarjoun 3 months ago
- 1 comment
#153 - Feature request: add __get_item__() to Cigar class
Issue -
State: closed - Opened by yfarjoun 3 months ago
- 3 comments
#152 - Feature request: better modeling of a pysam sequence dictionary
Issue -
State: closed - Opened by nh13 3 months ago
- 1 comment
#151 - feat: Add `find_illumina_fastq`
Pull Request -
State: open - Opened by msto 3 months ago
- 9 comments
#150 - ci: update code-cov in GHA to use a token
Pull Request -
State: closed - Opened by nh13 3 months ago
- 1 comment
#149 - chore: ignore existing C901 violations
Pull Request -
State: closed - Opened by msto 4 months ago
- 2 comments
#148 - chore: fix B010 violations
Pull Request -
State: closed - Opened by nh13 4 months ago
- 3 comments
#147 - chore: fix B904 violations
Pull Request -
State: closed - Opened by nh13 4 months ago
#146 - chore: fix B028 violations
Pull Request -
State: closed - Opened by msto 4 months ago
#145 - chore: fix B007 violations
Pull Request -
State: closed - Opened by msto 4 months ago
#144 - chore: fix B017 violations
Pull Request -
State: closed - Opened by msto 4 months ago
#143 - `inspect._get_parser()` requires the now-deprecated `typing.*` collection types
Issue -
State: open - Opened by msto 4 months ago
- 1 comment
Labels: good first issue
#142 - chore: Add usual lints
Pull Request -
State: closed - Opened by msto 4 months ago
- 1 comment
#141 - Add lint checks for C901, bugbear, and quotes
Issue -
State: closed - Opened by msto 4 months ago
#140 - chore: Switch to ruff
Pull Request -
State: closed - Opened by msto 4 months ago
#139 - Move to `ruff`
Issue -
State: closed - Opened by msto 4 months ago
#138 - Add a `CONTRIBUTING.md`
Issue -
State: closed - Opened by msto 4 months ago
- 1 comment
#137 - Update `pyproject.toml`
Issue -
State: open - Opened by msto 4 months ago
#136 - Move code out of `__init__.py` and into `{submodule}.py` files
Issue -
State: open - Opened by msto 4 months ago
#135 - Move to mkdocs from Sphinx
Pull Request -
State: closed - Opened by nh13 4 months ago
- 5 comments
#134 - chore: Update mypy config
Pull Request -
State: closed - Opened by msto 4 months ago
#133 - Clean up `type: ignore`s
Issue -
State: open - Opened by msto 4 months ago
Labels: good first issue
#132 - Add `require`
Issue -
State: open - Opened by msto 4 months ago
- 1 comment
Labels: good first issue
#131 - Lock stdin/stdout so only one file handle may use either at a time
Issue -
State: open - Opened by msto 4 months ago
#130 - Add code coverage report
Issue -
State: open - Opened by msto 4 months ago
- 1 comment
#129 - feat: Add assertions to support `MetricWriter`
Pull Request -
State: open - Opened by msto 4 months ago
#128 - Use tox so we can test multiple python versions locally
Issue -
State: open - Opened by msto 4 months ago
- 3 comments
#127 - Use ruff (or flake8 plugins) to expand the range of lint checks
Issue -
State: closed - Opened by msto 4 months ago
- 1 comment
#126 - Use stricter mypy config
Issue -
State: closed - Opened by msto 4 months ago
#125 - refactor: Narrow typing on `to_reader` and `to_writer`
Pull Request -
State: closed - Opened by msto 4 months ago
- 1 comment
#124 - feat: Add `read_header()`
Pull Request -
State: closed - Opened by msto 4 months ago
#123 - feat: MetricWriter
Pull Request -
State: open - Opened by msto 4 months ago
#122 - Add function(s) to set the 5' most alignment on a read as primary
Issue -
State: open - Opened by msto 4 months ago
- 1 comment
#121 - fix: r/w assertions
Pull Request -
State: closed - Opened by msto 4 months ago
- 1 comment
#120 - Package code and tests should be organized in separate directories, to be more consistent with Python conventions
Issue -
State: closed - Opened by msto 4 months ago
- 3 comments
#119 - refactor: writeable -> writable
Pull Request -
State: closed - Opened by msto 4 months ago
#118 - feat: Add methods for UMI extraction from read name
Pull Request -
State: closed - Opened by emmcauley 4 months ago
#117 - `io.assert_path_is_writeable()` should return True for "/dev/stdout"
Issue -
State: closed - Opened by msto 5 months ago
- 1 comment
Labels: good first issue
#116 - Add isort check to Github Action
Pull Request -
State: closed - Opened by emmcauley 5 months ago
- 1 comment
#115 - `Metric` should support comma-delimited files
Issue -
State: open - Opened by msto 5 months ago
#114 - `Metric` should require decoration with `dataclass` or `attr.s`
Issue -
State: open - Opened by msto 5 months ago
#113 - chore: add CODEOWNERS
Pull Request -
State: closed - Opened by msto 5 months ago
#112 - Consider renaming modules which shadow stdlib modules
Issue -
State: open - Opened by msto 5 months ago
#111 - Add a CODEOWNERS
Issue -
State: closed - Opened by msto 5 months ago
#110 - fix: Add return type hint to Metric.read()
Pull Request -
State: closed - Opened by msto 5 months ago
#109 - feat: Add asdict()
Pull Request -
State: closed - Opened by msto 5 months ago
- 5 comments
#108 - fix: DataclassInstance and AttrInstance protocols
Pull Request -
State: closed - Opened by msto 5 months ago
#107 - feat: Add MetricWriter class
Pull Request -
State: open - Opened by msto 5 months ago
- 1 comment
#106 - Add `as_fastafile` method to `FastaBuilder`
Issue -
State: open - Opened by msto 5 months ago
Labels: good first issue
#105 - feat: Add end property on SupplementaryAlignment
Pull Request -
State: closed - Opened by msto 6 months ago
- 1 comment
#104 - Metric wishlist
Issue -
State: open - Opened by msto 6 months ago
- 4 comments
#103 - feat: Support reading Picard-style metrics files with comments above the header
Pull Request -
State: open - Opened by msto 7 months ago
- 5 comments
#102 - Feature: SAM tag enum
Issue -
State: open - Opened by msto 7 months ago
- 8 comments
#101 - Factor out functions for parsers for built-in collections
Pull Request -
State: closed - Opened by jdidion 7 months ago
- 2 comments
#100 - Expose built-in parsers for use in custom parsers
Issue -
State: closed - Opened by jdidion 7 months ago
#99 - Support python 3.11 and 3.12 in CI, update black, flake8, and poetry versions
Pull Request -
State: closed - Opened by jdidion 7 months ago
- 2 comments
#98 - Drop support for python 3.7
Pull Request -
State: closed - Opened by jdidion 7 months ago
- 4 comments
#97 - Drop support for python 3.7
Issue -
State: closed - Opened by jdidion 7 months ago
#96 - Fix the check for `None` type in `inspect._get_parser`
Pull Request -
State: closed - Opened by jdidion 7 months ago
- 1 comment
#95 - Incorrect check for `NoneType`
Pull Request -
State: closed - Opened by jdidion 7 months ago
- 2 comments
#94 - `from_attr` returns a `none_parser` rather than throw `ParserNotFound`
Issue -
State: closed - Opened by jdidion 7 months ago
Labels: bug
#93 - Feature request: support sequence distance functions
Issue -
State: closed - Opened by msto 7 months ago
- 1 comment
Labels: good first issue
#92 - Feature request: UMI extraction from read name
Issue -
State: open - Opened by msto 7 months ago
Labels: good first issue
#91 - Add futures module for clean parallelism
Issue -
State: closed - Opened by TedBrookings 8 months ago
- 1 comment
Labels: enhancement
#90 - Metric.write should support excluding attributes
Issue -
State: open - Opened by msto 8 months ago
- 1 comment
Labels: enhancement
#89 - Metric.read should support PEP 604 syntax for `Optional` types
Issue -
State: open - Opened by msto 8 months ago
Labels: enhancement