From e07500c38252feadeeb223a65e9c65bb0723f28b Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Tue, 26 May 2026 16:11:55 -0400
Subject: [PATCH] fix(anomaly scores): Standardize column names for the Run
 name

---
 .Rbuildignore           | 2 ++
 .gitignore              | 3 ++-
 R/utils_anomaly_score.R | 1 +
 3 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index fa5533c3..613e0b64 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -6,3 +6,5 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^\.positai$
+^\.claude$
diff --git a/.gitignore b/.gitignore
index 9d0335a5..6d24a0fd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,4 +10,5 @@ inst/doc
 *.so
 *.dll
 .lintr
-.vscode
\ No newline at end of file
+.vscode
+.positai
diff --git a/R/utils_anomaly_score.R b/R/utils_anomaly_score.R
index d5981732..a5a7225d 100644
--- a/R/utils_anomaly_score.R
+++ b/R/utils_anomaly_score.R
@@ -32,6 +32,7 @@
     input = input[feature_counts, on = .(ProteinName, Fragment)]
     
     # Model at PSM level
+    run_order$Run = .standardizeColnames(run_order$Run)
     input = merge(input, run_order, by="Run", 
                   all.x=TRUE, all.y=FALSE)
     cols=c("ProteinName", "PSM", "Run", "Order", quality_metrics)