Matiq
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  • Joined on 2026-03-13
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Matiq pushed to main at Matiq/ffpe_damage 2026-09-09 00:29:37 +03:00
ffaa3c5cdd progress for 141/84: annotate 10/84, oncokb 1/84 every 10, GTF indexed
Matiq pushed to main at Matiq/ffpe_damage 2026-09-08 23:31:29 +03:00
baa87ea048 fix OncoKB endpoint byHgvsVariant->byGenomicChange (GRCh38)
Matiq pushed to main at Matiq/ffpe_damage 2026-09-08 23:08:09 +03:00
1f28f60bc0 fix ClinVar header #AlleleID + GRCh38 filter (was UnboundLocalError)
Matiq pushed to main at Matiq/ffpe_damage 2026-09-07 01:24:23 +03:00
c20f61240f ClinVar P/L + VAF>20% default for online
Matiq pushed to main at Matiq/ffpe_damage 2026-09-07 01:06:00 +03:00
fb99880b80 README: threads, VCF filtering, annotation (GENCODE/OncoKB), VAF filter
Matiq pushed to main at Matiq/ffpe_damage 2026-09-07 01:01:11 +03:00
8f8d728edd pick best transcript per variant (1:1) default, --all-transcripts for expansion
Matiq pushed to main at Matiq/ffpe_damage 2026-09-07 00:48:03 +03:00
9f4312ba3a offline all-transcripts via GENCODE GTF + VAF>10% filter
Matiq pushed to main at Matiq/ffpe_damage 2026-09-07 00:34:38 +03:00
b33f8c28a2 fix hang: offline mode, short timeouts, progress for large clean sets
Matiq pushed to main at Matiq/ffpe_damage 2026-09-06 20:21:00 +03:00
ea8f531211 all transcripts via Ensembl REST (expand per variant, pan-cancer)
Matiq pushed to main at Matiq/ffpe_damage 2026-09-06 19:19:31 +03:00
a3589279b9 annotate clean variants: Gen/HGVS/Effect + ACMG + AMP/Onco pan-cancer -> Excel
Matiq pushed to main at Matiq/ffpe_damage 2026-09-06 18:47:14 +03:00
4e19fbdb8a replace TSV with CSV for variant outputs
Matiq pushed to main at Matiq/ffpe_damage 2026-09-06 18:28:06 +03:00
0f40945d58 parallel: auto threads (n-1, capped at 8)
Matiq pushed to main at Matiq/ffpe_damage 2026-09-06 18:18:43 +03:00
5385f76447 filter damaged variants: clean output + VCF filtering
Matiq pushed to main at Matiq/soothe2-re 2026-09-03 14:11:22 +03:00
627c35dd53 AGENTS.md: document new env flags (RT_CASC/IIR4/KMAP/DELTA), chain wired status, capture proof
Matiq pushed to main at Matiq/soothe2-re 2026-09-03 00:21:35 +03:00
3fe44255fa Δ-rule: distance-aware gain wired (default flat), ph*.npz capture proof
Matiq pushed to main at Matiq/soothe2-re 2026-09-03 00:04:26 +03:00
a96e46bb69 NOTES_LEVEL: ph*.npz capture proof — rendersnap2 works, mask chain runs in render window
Matiq pushed to main at Matiq/soothe2-re 2026-09-02 23:51:06 +03:00
a562f6f56a NOTES_LEVEL 25b: Δ-rule wired, calibration blocked on ph*.npz
Matiq pushed to main at Matiq/soothe2-re 2026-09-02 23:50:27 +03:00
c85b888745 Δ-rule: wire distance-aware template-local gain (calibration blocked on ph*.npz)
Matiq pushed to main at Matiq/soothe2-re 2026-09-02 23:20:29 +03:00
a881ee280a AGENTS.md: add vlaw_check to test target list
Matiq pushed to main at Matiq/soothe2-re 2026-09-02 23:19:48 +03:00
2f854cd1da spectral: vectors instead of new[]; vlaw: extract law + vlaw_check target