Ecosyste.ms: Issues

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

GitHub / betteridiot/bamnostic issues and pull requests

#54 - Enable handling of SAM files with `bs.AlignmentFile`

Issue - State: closed - Opened by akikuno about 1 year ago - 2 comments

#53 - Pyscript-Pyodide-PyPI wheel request

Issue - State: closed - Opened by AngelicaLindlof over 1 year ago - 2 comments

#52 - Fix examples in the Quickstart documentation

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

#51 - Issues retrieving alignment sequences from reads

Issue - State: closed - Opened by Jeshuwin over 2 years ago - 1 comment

#50 - reg2bins implementation is incorrect (or inconsistent with the docs)

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

#49 - bam.fetch not working properly

Issue - State: closed - Opened by najoshi almost 3 years ago - 3 comments

#48 - ValueError with example_bam

Issue - State: closed - Opened by Eugene108 about 3 years ago - 2 comments

#47 - an error when read bam

Issue - State: closed - Opened by Frank1219 about 3 years ago - 6 comments

#46 - benchmarking

Issue - State: closed - Opened by ghost over 3 years ago - 6 comments

#45 - report the output of igv

Issue - State: closed - Opened by worker000000 over 3 years ago - 1 comment

#44 - Fix for #41

Pull Request - State: closed - Opened by OliverVoogd over 3 years ago

#43 - Fix parsing for sequences of length 1

Pull Request - State: closed - Opened by giesselmann almost 4 years ago - 1 comment

#42 - Writing out to a new bam file

Issue - State: open - Opened by claudiadast over 4 years ago - 2 comments

#41 - AlignedSegment object has no attribute 'reference_name'

Issue - State: closed - Opened by castrocp over 4 years ago - 1 comment

#40 - Fix typo in `bam.count_coverage`

Pull Request - State: closed - Opened by GeekLogan over 5 years ago - 4 comments

#39 - fetch() no output

Issue - State: closed - Opened by vibhasridavuluri over 5 years ago - 3 comments

#38 - Fixing style errors.

Pull Request - State: closed - Opened by betteridiot over 5 years ago

#37 - Fix nnocoord

Pull Request - State: closed - Opened by betteridiot over 5 years ago

#35 - update versioning

Pull Request - State: closed - Opened by betteridiot over 5 years ago

#34 - core.py has a self.self which should be a self. only

Issue - State: closed - Opened by ThomasH-RGB over 5 years ago - 2 comments

#33 - fixing omitted sequences

Pull Request - State: closed - Opened by betteridiot over 5 years ago

#32 - "IndexError: tuple index out of range"

Issue - State: closed - Opened by Akanksha2511 over 5 years ago - 4 comments

#31 - Adding .stickler.yml configuration file

Pull Request - State: closed - Opened by stickler-ci[bot] over 5 years ago

#30 - Installation bugs

Issue - State: closed - Opened by olgabot over 5 years ago - 2 comments

#29 - Add pip install from pypi after success

Pull Request - State: closed - Opened by olgabot over 5 years ago - 3 comments

#28 - Include version file in manifest

Pull Request - State: closed - Opened by olgabot over 5 years ago - 1 comment

#27 - Cannot load long read BAM files

Issue - State: closed - Opened by betteridiot about 6 years ago

#25 - contig name changed too lower case in bam.py --> contig name not found in header

Issue - State: closed - Opened by envanloo about 6 years ago - 2 comments

#24 - Major fix and feature expansion

Pull Request - State: closed - Opened by betteridiot about 6 years ago

#23 - csi_dev works fine on 10x bam

Issue - State: closed - Opened by olgabot about 6 years ago - 1 comment

#22 - Update quickstart.rst

Pull Request - State: closed - Opened by gmat about 6 years ago - 1 comment

#21 - Fixes #20: Multi-version and runtime compliant LruDict

Pull Request - State: closed - Opened by betteridiot about 6 years ago

#20 - Recursion error when multiprocessing.Pool.map bam file

Issue - State: closed - Opened by olgabot about 6 years ago - 10 comments

#19 - fromstring() --> frombytes() issue

Issue - State: closed - Opened by betteridiot about 6 years ago

#18 - fromstring() --> frombytes()

Pull Request - State: closed - Opened by olgabot about 6 years ago - 3 comments

#17 - ugh yaml

Pull Request - State: closed - Opened by betteridiot about 6 years ago

#16 - Still cannot read 10x bam file

Issue - State: closed - Opened by olgabot about 6 years ago - 6 comments

#15 - Cannot read 10x bam file

Issue - State: closed - Opened by olgabot about 6 years ago - 4 comments

#14 - adding Citation and Contributions to docs

Pull Request - State: closed - Opened by betteridiot over 6 years ago

#13 - Adding contributing

Pull Request - State: closed - Opened by betteridiot over 6 years ago

#12 - JoSS review fixes

Pull Request - State: closed - Opened by betteridiot over 6 years ago

#11 - updated versioning

Pull Request - State: closed - Opened by betteridiot over 6 years ago

#10 - Updating versioning

Pull Request - State: closed - Opened by betteridiot over 6 years ago

#9 - Put bgzf.py under 3-clause BSD

Issue - State: closed - Opened by peterjc over 6 years ago - 1 comment

#8 - Added support for CIGAR strings > 65535

Pull Request - State: closed - Opened by betteridiot over 6 years ago

#7 - added "published" to 2nd paragraph of paper

Pull Request - State: closed - Opened by betteridiot over 6 years ago

#6 - Support CIGARs with >65535 operations in BAM files

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

#5 - BAM output support

Issue - State: open - Opened by peterjc over 6 years ago - 5 comments
Labels: enhancement, in progress

#4 - CRAM support?

Issue - State: closed - Opened by peterjc over 6 years ago - 4 comments
Labels: enhancement

#3 - CSI indexing support as well as BAI indexing

Issue - State: closed - Opened by peterjc over 6 years ago - 1 comment
Labels: enhancement, help wanted

#2 - different bam files

Issue - State: closed - Opened by ghost over 6 years ago

#1 - Create LICENSE

Pull Request - State: closed - Opened by betteridiot over 6 years ago