Switch to interbase coordinates
Open
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 87
- Forks
- 28
- Avg merge
- 3h 27m
- Merged PRs (30d)
- 27
Description
Currently have a lot of special case logic for insertions (e.g. if len(ref) == 0), can use unified logic if the start/end coordinates are between bases.
See: http://alternateallele.blogspot.de/2012/03/genome-coordinate-conventions.html
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the insertion handling and the start/end coordinate logic in the Python code, then read the linked genome coordinate conventions article. Done means insertions use unified coordinates between bases without special cases such as if len(ref) == 0; the issue names no specific files or tests.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Refactor
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100