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vepyr corrupts CSQ on raw multi-allelic input (per-(allele×transcript) emission missing)

bugSomething isn't workingSomething isn't working

Status: Open.

#35 In biodatageeks/vepyr;

· sitekwb opened on Jul 22, 2026

Tracking / SSOT: wynik walidacji VEP 116 — status fixów vepyr (#29/#30/#31/#32), co NIE jest bugiem, tor pluginów

Status: Open.

#34 In biodatageeks/vepyr;

· sitekwb opened on Jul 22, 2026

HGVS 3'-shift silently skipped when transcript has bam_edit_status='failed' (wrong HGVSc, empty HGVS_OFFSET, no error)

bugSomething isn't workingSomething isn't working

Status: Open.

#32 In biodatageeks/vepyr;

· sitekwb opened on Jul 13, 2026

CDS-terminus edge cases: Protein_position range truncated, insertion after last CDS base placed inside the CDS, spurious stop_retained_variant

bugSomething isn't workingSomething isn't working

Status: Open.

#31 In biodatageeks/vepyr;

· sitekwb opened on Jul 13, 2026

MotifFeature: Feature ID and MOTIF_NAME always empty, and overlapping motifs collapsed into one entry (accounts for 100% of the VEP-116 coverage gap)

bugSomething isn't workingSomething isn't working

Status: Open.

#30 In biodatageeks/vepyr;

· sitekwb opened on Jul 13, 2026

pick_order: a list is silently accepted and IGNORED (falls back to default order → 14.7% wrong --pick_allele output, no error)

bugSomething isn't workingSomething isn't working

Status: Open.

#29 In biodatageeks/vepyr;

· sitekwb opened on Jul 12, 2026

compare_vcfs: CSQ-entry-count accounting omits empty-CSQ variants (match + mismatch ≠ variants_compared)

Status: Open.

#19 In biodatageeks/vepyr;

· mwiewior opened on Jul 3, 2026

Defer HGVSc + output materialization until after pick (engine computes them for all overlapping transcripts pre-pick)

Status: Open.

#18 In biodatageeks/vepyr;

· mwiewior opened on Jun 15, 2026

Integrate RefSeq and merged VEP cache flags

Status: Open.

#10 In biodatageeks/vepyr;

· mwiewior opened on Apr 10, 2026

Cap tokio blocking thread pool with max_blocking_threads(partitions)

Status: Open.

#7 In biodatageeks/vepyr;

· mwiewior opened on Apr 1, 2026