Change meaning of ref and alt fields
Maintainers usually reply within 1 day
Nobody has claimed this yet.
Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 48/100
- Issue type
- Refactor
- Clarity
- Clearly specified
- Activity status
- Stale
- Tech stack
- python
- Domain
- bioinformatics
Research direction
Start by locating the definitions and usages of variant.ref, variant.alt, original_ref, and original_alt, including any related tests. Update the public field names as requested, then verify that callers use the unchanged input values and that the renamed trimmed fields retain their existing meaning.
Written by the indexing model from the issue text.
Description
Currently variant.ref and variant.alt don't contain any shared prefix or suffix. This confuses user since they expect whatever values passed in for these fields to be unchanged.
Breaking change: rename the current ref and alt fields to trimmed_ref and trimmed_alt and get rid of original_ref and original_alt.
- Dominant language
- Python
- Stars
- 88
- Forks
- 28
- Avg merge
- 4h 34m
- Merged PRs (30d)
- 52
Getting set up
- No Dockerfile or Docker Compose file
- No pull request template
- Read the contributing 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.
More from openvax/varcode
-
test_effect_timing's 120 s subprocess timeout is still wall-clock and fails under machine loadPossibly taken A pull request linked to this issue is open or already merged. Open
Difficulty 2/5 1-3 hours Newbie friendliness 69/100
openvax/varcode#702 · 1 comment ·
Maintainers usually reply within 1 day
-
Difficulty 1/5 Under an hour Newbie friendliness 88/100
Maintainers usually reply within 1 day
-
MAF reader: 'Too few columns' error does not name the missing columnsPossibly taken A pull request linked to this issue is open or already merged. Open
Difficulty 2/5 1-3 hours Newbie friendliness 82/100
Maintainers usually reply within 1 day
-
load_maf does not convert UCSC contig names (GDC chr-prefixed MAFs fail annotation)Possibly taken A pull request linked to this issue is open or already merged. Open
Difficulty 2/5 1-3 hours Newbie friendliness 72/100
Maintainers usually reply within 1 day
-
Difficulty 4/5 3-5 days Newbie friendliness 45/100
Maintainers usually reply within 1 day
Similar issues
-
binding:python bug
Difficulty 2/5 1-3 hours Newbie friendliness 82/100
Maintainers usually reply within 1 day
-
The Browser tab fails with a Wayland error when Open Terminal runs from a Wayland desktop sessionOpen
Difficulty 2/5 1-3 hours Newbie friendliness 78/100
open-webui/open-terminal#210 ·
-
triage/confirmed
Difficulty 2/5 1-3 hours Newbie friendliness 78/100
agentscope-ai/agentscope#3807 ·
Maintainers usually reply within 2 days
-
Difficulty 2/5 1-3 hours Newbie friendliness 78/100
NousResearch/hermes-agent#150542 ·
Maintainers usually reply within 1 day
-
Difficulty 1/5 Under an hour Newbie friendliness 91/100
triton-inference-server/server#9069 ·
Maintainers usually reply within 1 day