Ecosyste.ms: Issues

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GitHub / dnanexus/IndexTools issues and pull requests

#38 - Make it clear that `contig_sizes` can have more than two columns (e.g…

Pull Request - State: open - Opened by jdidion over 2 years ago - 1 comment

#37 - Make it clear that `contig_sizes` can be a file with more than two co…

Pull Request - State: open - Opened by jdidion over 2 years ago - 1 comment

#36 - Add option to partition to specify problematic regions

Issue - State: open - Opened by jdidion over 5 years ago

#35 - Aggregate data across multiple samples

Issue - State: open - Opened by jdidion over 5 years ago

#34 - Enhancements to Docker image and makefile

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

#33 - Add LPT grouping

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

#32 - IndexTools broken on python 3.7

Issue - State: closed - Opened by jdidion over 5 years ago - 2 comments
Labels: bug

#31 - Add option for using LPT algorithm to compute interval groups

Issue - State: closed - Opened by jdidion over 5 years ago
Labels: enhancement

#30 - Build Docker image that contains IndexTools

Issue - State: closed - Opened by jdidion over 5 years ago
Labels: enhancement

#29 - Feat/28 support faidx

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

#28 - Support using .faidx files for chromosome sizes

Issue - State: closed - Opened by jdidion over 5 years ago
Labels: enhancement

#27 - Add code coverage checking

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

#26 - Merge multiple test_data.json files in directory hierarchy

Issue - State: closed - Opened by jdidion over 5 years ago

#25 - Add unit tests for index.py

Issue - State: open - Opened by Damien-Black over 5 years ago
Labels: good first issue

#24 - Replace InterLap with cgranges

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

#23 - Set up travis CI

Issue - State: open - Opened by jdidion over 5 years ago

#22 - Cleanup formatting and type hints

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

#21 - Add basic dev process docu

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

#20 - Add unit tests for regions.py

Issue - State: open - Opened by xquek over 5 years ago

#19 - Replace pysam with a pure-python library

Issue - State: open - Opened by jdidion over 5 years ago - 1 comment
Labels: enhancement, good first issue

#18 - Use RefGet to fetch contig information

Issue - State: closed - Opened by jdidion over 5 years ago
Labels: duplicate

#17 - Wrap datadir fixture

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

#16 - InterLap and Quicksect give different results for find nearest operation

Issue - State: closed - Opened by jdidion over 5 years ago - 1 comment

#15 - Integration test partition only index

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

#14 - Update toml to use autoclick 0.6.0

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

#13 - Update the links on Readme.md

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

#12 - adding small.bam for testing purposes

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

#11 - update git ignore for python, Mac, poetry

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

#10 - Add unit tests for bed.py

Issue - State: open - Opened by jdidion over 5 years ago
Labels: help wanted, good first issue

#9 - Add unit tests for utils.py

Issue - State: open - Opened by jdidion over 5 years ago
Labels: help wanted, good first issue

#8 - Add integration tests for partition command

Issue - State: closed - Opened by jdidion over 5 years ago
Labels: help wanted

#7 - Replace InterLap with a library

Issue - State: closed - Opened by jdidion over 5 years ago - 6 comments

#6 - Add a development Dockerfile

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

#5 - Switch to using scm-based plugin for version management

Issue - State: open - Opened by jdidion over 5 years ago

#4 - Add invert option to partition

Issue - State: open - Opened by jdidion over 5 years ago

#3 - Add ability to partition around N's

Issue - State: open - Opened by jdidion over 5 years ago

#2 - Support RefGet

Issue - State: open - Opened by jdidion over 5 years ago

#1 - Add support for Augmented Interval Lists

Issue - State: open - Opened by jdidion over 5 years ago