Switch to interbase coordinates

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Refactor
Clarity
Mostly clear
Activity status
Stale
Tech stack
python
Domain
bioinformatics

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.

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

Dominant language
Python
Stars
88
Forks
28
Avg merge
2h 11m
Merged PRs (30d)
45

Getting set up

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

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