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Task
Implement prioritize_variant() and prioritize_collection() in src/clarvar/prioritizer.py.
prioritize_variant() computes:
score = (consequence_weight × _score_consequence())
+ (clinvar_weight ...
good first issue
prioritizer
NosakhareOsaro
Goal
The gate experiment for the theory upgrade. Before investing in the full directed/noisy reframe (JS-divergence
γ-resolving sets, hardness proofs, ILP solvers), validate that the richer observation ...
priority-high
theory
track-b-paper
aryan5v
Task
Implement the three scoring methods and populate the scoring tables in src/clarvar/prioritizer.py.
Step 1 — fill in the scoring dicts:
CONSEQUENCE_SCORES = {
Consequence.FRAMESHIFT: 100,
...
good first issue
prioritizer
Task
Implement annotate_collection() in src/clarvar/annotator.py.
This is the main public annotation method. Steps:
1. Build a lookup dict: {vep_region_string: Variant} using _to_vep_region()
2. Send ...
annotator
intermediate
Description
The current test suite for Quadratic-Solver covers:
- Distinct real roots
- Repeated real roots
- Complex roots
- Invalid coefficient (a = 0)
- Several interactive CLI flows
However, ...
type:bug
jyotish6699
Task
Implement _post_vep_batch() in src/clarvar/annotator.py.
Build a JSON payload and POST to the VEP endpoint:
{
variants : [ 1 100 100 A/T 1 , ...],
CADD : 1,
gnomAD : 1,
ClinVar ...
annotator
intermediate
Task
Implement _apply_vep_result() in src/clarvar/annotator.py.
This ties together the helper functions from issues #1–#4 and writes all annotation fields onto a Variant object
in-place.
From the most ...
annotator
intermediate
@ Analysis of shots.db (2026-06-09, n=269 shots on gp/trajectory_* predictors) to explain the low and inconsistent make
rate.
Findings
1. Aim is fine; mislaunches are the problem. Misses are bimodal: ...
minigame:hoops
jandersson
Task
Implement _pick_most_severe_transcript() in src/clarvar/annotator.py.
VEP returns a list of transcript_consequences, each with a consequence_terms list. Use the CONSEQUENCE_SEVERITY dict
(already ...
annotator
good first issue
Task
Implement _extract_clinvar() in src/clarvar/annotator.py.
ClinVar data lives in:
hit[ colocated_variants ][i][ clin_sig ] # list of strings
hit[ colocated_variants ][i][ ...
annotator
good first issue
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Learn how you can use GitHub Issues to plan and track your work.
Save views for sprints, backlogs, teams, or releases. Rank, sort, and filter issues to suit the occasion. The possibilities are endless.Learn more about GitHub IssuesProTip! Restrict your search to the title by using the in:title qualifier.