From 82fdfdc6b9249d005b9dd5e146dd842261787822 Mon Sep 17 00:00:00 2001
From: coolneng <akasroua@gmail.com>
Date: Thu, 8 Apr 2021 18:31:50 +0200
Subject: [PATCH] Exchange pattern and subject in the alignment

---
 src/alignment.r | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/alignment.r b/src/alignment.r
index f4bbee4..25facbb 100644
--- a/src/alignment.r
+++ b/src/alignment.r
@@ -35,8 +35,8 @@ construct_full_sequences <- function(vdj_segments, metadata) {
 
 align_sequence <- function(sequence, vdj_segment) {
   return(Biostrings::pairwiseAlignment(
-    pattern = sequence,
-    subject = vdj_segment,
+    subject = sequence,
+    pattern = vdj_segment,
     type = "global-local",
     gapOpening = 1,
   ))