minimum_q_delta is taking the difference on a log scale
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- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
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Description
I've been writing up some details of this pipeline for a review paper that Chanson and I are revising for a journal, and I just realized that when sam2aln.pyis resolving discordant bases while merging reads, it is taking the arithmetic differences of their respective quality scores. However, quality scores are a log-transformation of estimated error probabilities, which means that a difference of Q1-Q2=5 means something completely different for Q1=15, Q2=10 (-0.068) than it does for Q1=40, Q2=35 (-0.00022).
I don't think this is going to make a big difference, but I just thought I'd say something :)
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Research direction
Start by reading sam2aln.py and locate how minimum_q_delta is applied while resolving discordant bases during read merging. Confirm how quality scores are compared and determine the intended behavior from their error-probability interpretation. Done should mean the comparison is consistent with the documented quality-score semantics, with relevant behavior verified by the available tests.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100