kemal/SimurgArray
1
0 Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

CN: noise-corrected BAF split and complete-loss MF (CYTO-041); Pi tuning harness
ci / test (3.12) (push) Failing after 10s
Details
ci / test (3.13) (push) Failing after 12s
Details

Browse Source 
Mosaic fraction from the BAF split now subtracts the heterozygous BAF noise (median |BAF-0.5| of unsplit
hets = 0.6745 sigma_b), and a mosaic loss lacking its expected heterozygotes gets MF 1 and is promoted to a
constitutional DEL (CYTO-020). Adds scripts/v2/cn_tune.sh + cn_tune_report.py (GSE165845 rounds on the Pi).

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
This commit is contained in:
kemalandClaude Opus 5.5 committed 2026-09-29 10:30:12 +01:00
1 parent 8ab8e632b9
commit 19bc6ca986
6 files changed
+140 -8
Download Patch File Download Diff File Expand all files Collapse all files

No files matched your search

src/simurg/pipeline/cn.py
+1 -1
View File
@@ -392,7 +392,7 @@ def call_sample(si: SampleInput, ctx: dict[str, Any], opts: CnCallOptions) -> di
post = hmm.forward_backward(e, sw, prior)
evs = extract(chrom, path, states, p)
for ev in evs:
annotate_stats(ev, p, x_raw, b, gt, post, states, m_sp, ctx["gamma"], haploid)
annotate_stats(ev, p, x_raw, b, gt, post, states, m_sp, ctx["gamma"], haploid, baf_sd, pfb[idx])
evs = post_filter(evs, [x_raw[ev.i0 : ev.i1] for ev in evs], th, counts)
for s_, e_ in _runs(path):
st = states[int(path[s_])]