biocore / biocore/zebra_filter
More precise handling of CIGAR scores
- Dominant language
- Python
- Stars
- 7
- Forks
- 6
- PR merge metrics
- No merged PRs in 30d
Description
https://github.com/biocore/zebra_filter/blob/6b11797e81e3b184dae540c069f6871f929e0222/calculate_coverages.py#L66
Calculation of start and end coordinates is not precise. Ideally, zebra would use the procedure implemented in [woltka's coverages method](https://github.com/qiyunzhu/woltka/blob/51f3100b60a5ecfec9ea3ded6aab8313454a9bf3/woltka/align.py#L460).
Contributor guide
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Research direction
Start in calculate_coverages.py around line 66, then compare its start and end coordinate calculation with woltka's coverage method in woltka/align.py around line 460. Update the handling so CIGAR scores produce precise coordinates, and verify that zebra's coverage results match the intended procedure.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100