Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / marcelm/dnaio issues and pull requests

#145 - Ignore complex mypy issue

Pull Request - State: closed - Opened by rhpvorderman about 1 month ago - 1 comment

#144 - s/d/_core.pyx: pedantic typo caught by linting.

Pull Request - State: closed - Opened by emollier about 1 month ago - 3 comments

#141 - Allow chunking uBAM

Pull Request - State: open - Opened by rhpvorderman about 1 month ago - 3 comments

#140 - Chunking for uBAM

Issue - State: open - Opened by rhpvorderman about 1 month ago - 2 comments

#139 - Properly convert missing qualities in BAM

Pull Request - State: closed - Opened by rhpvorderman about 2 months ago - 9 comments

#138 - installation from source with `pip install` fails

Issue - State: closed - Opened by boegel 3 months ago - 2 comments

#137 - Update bioconda-recipe to support osx-arm64

Issue - State: closed - Opened by isaacovercast 3 months ago - 1 comment

#136 - dnaio.exceptions.UnknownFileFormat

Issue - State: open - Opened by wook2014 3 months ago - 3 comments

#134 - Build macOS arm64 wheels

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

#133 - Rewrite ascii check to allow compiler auto vectorization

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

#132 - _Py_NegativeRefcount error

Issue - State: closed - Opened by bistace 8 months ago - 7 comments

#131 - Use dispatch rather than rely on separate compile commands for SSSE3 bam parser

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

#130 - Run tests on the M1 macOS runner

Pull Request - State: closed - Opened by marcelm 10 months ago - 1 comment

#129 - Extended BAM support

Issue - State: open - Opened by rhpvorderman 10 months ago - 10 comments

#128 - Add citation info

Pull Request - State: closed - Opened by marcelm 10 months ago

#127 - How to cite dnaio in a manuscript?

Issue - State: closed - Opened by DongzeHE 10 months ago - 2 comments

#126 - Highlight BAM support

Pull Request - State: closed - Opened by rhpvorderman 11 months ago - 1 comment

#124 - Support chunking of paired-end FASTA

Pull Request - State: closed - Opened by marcelm 11 months ago - 3 comments

#123 - Highlight xopen's Zstandard support when optionally installed

Pull Request - State: closed - Opened by bede almost 1 year ago - 8 comments

#122 - Add asan tox environment for testing memory errors

Pull Request - State: closed - Opened by rhpvorderman about 1 year ago

#121 - Add some tests

Pull Request - State: closed - Opened by marcelm about 1 year ago - 1 comment

#120 - Improve type hints

Pull Request - State: closed - Opened by marcelm about 1 year ago - 1 comment

#119 - Bump cibuildwheel so that wheels for Python 3.12 get built

Pull Request - State: closed - Opened by marcelm about 1 year ago

#118 - Typing warnings from mypy

Issue - State: closed - Opened by fjossandon about 1 year ago - 7 comments

#117 - Bump various versions

Pull Request - State: closed - Opened by marcelm about 1 year ago - 1 comment

#116 - Add a simple BAM parser to dnaio

Pull Request - State: closed - Opened by rhpvorderman about 1 year ago - 14 comments

#115 - Simplify ASCII check

Pull Request - State: closed - Opened by rhpvorderman about 1 year ago - 2 comments

#114 - Version 1.0

Issue - State: closed - Opened by rhpvorderman about 1 year ago - 3 comments

#113 - Add build.os key to Read the Docs configuration

Pull Request - State: closed - Opened by marcelm about 1 year ago - 1 comment

#112 - Get rid of setup.cfg, use pyproject.toml instead

Pull Request - State: closed - Opened by marcelm about 1 year ago

#111 - check quality score integrity

Issue - State: closed - Opened by rhpvorderman about 1 year ago - 1 comment

#110 - Add id and comment

Pull Request - State: closed - Opened by rhpvorderman about 1 year ago - 2 comments

#109 - Add ubam support

Issue - State: closed - Opened by rhpvorderman about 1 year ago - 11 comments

#108 - Use a newline index for FastqIter

Issue - State: closed - Opened by rhpvorderman over 1 year ago - 10 comments
Labels: performance

#107 - FastqFormatError, while reading in chunks

Issue - State: closed - Opened by arunhpatil almost 2 years ago - 5 comments

#106 - Fix buffer filling up on incomplete paired FASTQ

Pull Request - State: closed - Opened by marcelm almost 2 years ago - 1 comment

#105 - Check for most common case where there is no second header

Pull Request - State: closed - Opened by rhpvorderman about 2 years ago - 5 comments

#104 - Test detect format

Pull Request - State: closed - Opened by marcelm about 2 years ago - 2 comments

#103 - ResourceWarnings

Issue - State: closed - Opened by marcelm about 2 years ago - 3 comments

#102 - Bump cibuildwheel

Pull Request - State: closed - Opened by marcelm about 2 years ago

#101 - Avoid running CI jobs twice

Pull Request - State: closed - Opened by marcelm about 2 years ago - 1 comment

#100 - Let’s ignore __repr__ functions for coverage percentages

Pull Request - State: closed - Opened by marcelm about 2 years ago - 1 comment

#99 - Faster SequenceRecord initialization.

Pull Request - State: closed - Opened by rhpvorderman about 2 years ago - 3 comments

#98 - Avoid pytest 7.2 warnings

Pull Request - State: closed - Opened by marcelm about 2 years ago

#97 - Run tests on Python 3.11

Pull Request - State: closed - Opened by marcelm about 2 years ago

#96 - Allow setting open_threads and compression_level

Pull Request - State: closed - Opened by rhpvorderman about 2 years ago - 5 comments

#95 - Document SequenceRecord.reverse_complement

Pull Request - State: closed - Opened by marcelm about 2 years ago - 2 comments

#94 - Add better type hints for dnaio.open()

Issue - State: closed - Opened by marcelm about 2 years ago

#93 - Improve coverage

Pull Request - State: closed - Opened by marcelm about 2 years ago - 2 comments

#92 - Upload again code coverage reports to Codecov.io

Pull Request - State: closed - Opened by marcelm about 2 years ago

#91 - Fix mypy error: A function returning TypeVar should receive at least …

Pull Request - State: closed - Opened by marcelm about 2 years ago - 1 comment

#89 - Update various docstrings

Pull Request - State: closed - Opened by marcelm over 2 years ago - 2 comments

#88 - Consistently raise FastaFormatError on parse errors

Pull Request - State: closed - Opened by marcelm over 2 years ago - 1 comment

#87 - Multiple reader/writer api

Pull Request - State: closed - Opened by rhpvorderman over 2 years ago - 10 comments

#86 - Version 0.9.1

Pull Request - State: closed - Opened by rhpvorderman over 2 years ago - 4 comments

#85 - Also build wheels on MacOS X

Pull Request - State: closed - Opened by rhpvorderman over 2 years ago - 2 comments

#84 - Identifying bottlenecks

Issue - State: closed - Opened by rhpvorderman over 2 years ago - 4 comments

#83 - Compilation error

Issue - State: closed - Opened by stheil15 over 2 years ago - 3 comments

#82 - Switch single&paired API to single&multiple API.

Issue - State: closed - Opened by rhpvorderman over 2 years ago - 2 comments

#81 - API documentation improvements (and some other minor things)

Pull Request - State: closed - Opened by marcelm over 2 years ago - 1 comment

#80 - Eliminate extra type checking loop in records_are_mates

Pull Request - State: closed - Opened by rhpvorderman over 2 years ago

#79 - Add records_are_mates function

Pull Request - State: closed - Opened by rhpvorderman over 2 years ago - 7 comments

#78 - Three-way is mate comparison

Issue - State: closed - Opened by rhpvorderman over 2 years ago - 2 comments

#77 - SequenceRecord array class

Issue - State: closed - Opened by marcelm over 2 years ago - 6 comments

#76 - Does SequenceRecord need to support the buffer protocol?

Issue - State: closed - Opened by rhpvorderman over 2 years ago - 2 comments

#75 - Small pointer refactor and cleanup

Pull Request - State: closed - Opened by rhpvorderman over 2 years ago - 1 comment

#74 - Vectorize the ASCII check using SSE2 instructions

Pull Request - State: closed - Opened by rhpvorderman over 2 years ago - 3 comments

#73 - Fix typo in tutorial

Pull Request - State: closed - Opened by luchaoqi over 2 years ago - 1 comment

#72 - Add a little tutorial

Pull Request - State: closed - Opened by marcelm over 2 years ago - 2 comments

#71 - Use Black for formatting

Pull Request - State: closed - Opened by marcelm over 2 years ago - 2 comments

#70 - API review: an alternative namo for `dnaio.open`?

Issue - State: closed - Opened by marcelm over 2 years ago - 2 comments

#69 - Avoid some "unclosed file" ResourceWarnings

Pull Request - State: closed - Opened by marcelm over 2 years ago - 1 comment

#68 - Branchless checking for ASCII

Pull Request - State: closed - Opened by rhpvorderman over 2 years ago - 1 comment

#67 - Remove BytesSequenceRecord

Pull Request - State: closed - Opened by rhpvorderman over 2 years ago - 1 comment

#66 - Remove BytesSequenceRecord

Issue - State: closed - Opened by rhpvorderman over 2 years ago - 2 comments

#65 - Implement reverse complement.

Pull Request - State: closed - Opened by rhpvorderman over 2 years ago - 7 comments

#64 - reverse complement

Issue - State: closed - Opened by jazberna1 over 2 years ago - 6 comments

#63 - Drop Python 3.6 support

Pull Request - State: closed - Opened by marcelm over 2 years ago - 5 comments

#62 - Move dnaio to its own organization

Issue - State: closed - Opened by marcelm over 2 years ago - 2 comments

#61 - ascii_check.h should be in its own repo

Issue - State: closed - Opened by rhpvorderman over 2 years ago - 6 comments

#60 - Move string_is_ascii to _update_buffer

Pull Request - State: closed - Opened by rhpvorderman over 2 years ago - 2 comments

#59 - ASCII check should be moved to update buffer.

Issue - State: closed - Opened by rhpvorderman over 2 years ago

#58 - Use Py_SIZE instead of PyBytes_GET_SIZE

Pull Request - State: closed - Opened by rhpvorderman over 2 years ago - 3 comments

#57 - Deprecate record_names_match()

Pull Request - State: closed - Opened by marcelm over 2 years ago

#56 - API review

Issue - State: closed - Opened by marcelm over 2 years ago - 4 comments

#55 - Remove unused imports. Make checks more consistent.

Pull Request - State: closed - Opened by rhpvorderman over 2 years ago - 1 comment

#54 - Bytes object touchups: no None, docstrings.

Pull Request - State: closed - Opened by rhpvorderman over 2 years ago

#53 - Rename (Bytes-)Sequence to (Bytes-)SequenceRecord

Pull Request - State: closed - Opened by marcelm over 2 years ago - 3 comments

#52 - MANIFEST.in is not needed

Pull Request - State: closed - Opened by marcelm over 2 years ago - 1 comment

#51 - Do not ship C file in source distribution

Pull Request - State: closed - Opened by rhpvorderman over 2 years ago - 2 comments

#50 - Stop shipping Cython-generated .c files

Issue - State: closed - Opened by marcelm over 2 years ago

#49 - Implement buffer protocol and use memchr for paired fastq heads

Pull Request - State: closed - Opened by rhpvorderman over 2 years ago - 4 comments

#48 - Add stringent ASCII-checks to Sequence object

Pull Request - State: closed - Opened by rhpvorderman almost 3 years ago - 11 comments

#47 - Refactor _read_into_buffer

Pull Request - State: closed - Opened by rhpvorderman almost 3 years ago - 1 comment

#46 - Refactor two header determination

Pull Request - State: closed - Opened by rhpvorderman almost 3 years ago - 1 comment