From e5bf0dcee20981b0eebaf3b25802670d70b540b7 Mon Sep 17 00:00:00 2001
From: Kemal Yaylali <kemal.yaylali@gmail.com>
Date: Tue, 29 Sep 2026 00:29:25 +0100
Subject: [PATCH] sesame oracle: compare without bead-count masking on both
 sides

---
 scripts/v2/methyl_oracle_compare.py | 3 ++-
 scripts/v2/sesame_oracle.R          | 4 +++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/scripts/v2/methyl_oracle_compare.py b/scripts/v2/methyl_oracle_compare.py
index f9bdddb..28d616d 100644
--- a/scripts/v2/methyl_oracle_compare.py
+++ b/scripts/v2/methyl_oracle_compare.py
@@ -36,7 +36,8 @@ def main() -> int:
     pos = {p: i for i, p in enumerate(man.probe_ids)}
     res = {}
     for prefix in a.prefixes:
-        s = sig.assemble(read_idat(prefix + "_Grn.idat"), read_idat(prefix + "_Red.idat"), man)
+        # min_beads=0: the oracle runs without bead-count masking (see sesame_oracle.R)
+        s = sig.assemble(read_idat(prefix + "_Grn.idat"), read_idat(prefix + "_Red.idat"), man, min_beads=0)
         p = sig.detection_p(s)
         n, fg, fr = sig.noob(s)
         b = sig.beta_values(n)
diff --git a/scripts/v2/sesame_oracle.R b/scripts/v2/sesame_oracle.R
index 7b998a7..daec1af 100644
--- a/scripts/v2/sesame_oracle.R
+++ b/scripts/v2/sesame_oracle.R
@@ -24,7 +24,9 @@ inband <- function(s) {
   list(m = m, u = u)
 }
 for (prefix in args[-(1:3)]) {
-  read <- function() readIDATpair(prefix, platform = "EPIC", manifest = mft, controls = controls, min_beads = 3)
+  # no bead-count masking here (sesame's min_beads also masks every Infinium II probe, whose M address is NA);
+  # the comparison script runs simurg with the same setting
+  read <- function() readIDATpair(prefix, platform = "EPIC", manifest = mft, controls = controls)
   sdf <- tryCatch(read(), error = function(e) {
     message("first read failed (", conditionMessage(e), "); caching idatSignature and retrying")
     sesameDataCache("idatSignature")