From da8d017b925b7affa5f5d075c146f57c6b981131 Mon Sep 17 00:00:00 2001
From: Qile0317 <qile0317@gmail.com>
Date: Wed, 4 Feb 2026 10:34:47 -0800
Subject: [PATCH] fix expanded sequence check

---
 R/Ibex_matrix.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/Ibex_matrix.R b/R/Ibex_matrix.R
index 3b23b7d..3e4922e 100644
--- a/R/Ibex_matrix.R
+++ b/R/Ibex_matrix.R
@@ -102,9 +102,9 @@ Ibex_matrix <- function(input.data,
   # Determine dictionary for sequence encoding
   if (expanded.sequences) {
     #Quick Check to see if there are - corresponding to CDR1-CDR2-CDR3
-    if (all(grepl("-", BCR[,"cdr3_aa"]))) {
+    if (!all(grepl("-", BCR[,"cdr3_aa"]))) {
       stop("Expanded sequences are not properly formated, please use 
-           combineExpandedBCR().")
+           combineExpandedBCR() or ensure each element is CDRs 1, 2, and 3 joined by `-`")
     }
     BCR[,"cdr3_aa"] <- gsub("-", "_", BCR[,"cdr3_aa"])
     dictionary <- c(amino.acids, "_")