From da445066f3d37f681d25474c6e0fdbbf73dcef95 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Sun, 9 Dec 2018 19:14:51 +0100
Subject: [PATCH] C alignment filter: added a check for sequences not being
 equal when the threshold requires that they are

---
 src/upperband.c | 25 +++++++++++++++++--------
 1 file changed, 17 insertions(+), 8 deletions(-)

diff --git a/src/upperband.c b/src/upperband.c
index 090b417..7833963 100755
--- a/src/upperband.c
+++ b/src/upperband.c
@@ -355,17 +355,26 @@ void align_filters(Kmer_table_p ktable, Obi_blob_p seq1, Obi_blob_p seq2, index_
 
 	*score = -2.0;
 
-	if (can_be_identical && (obi_blob_compare(seq1, seq2) == 0)) // the 2 sequences are identical.
+	if (can_be_identical)
 	{
-		if (similarity_mode && normalize)
-			*score = 1.0;
-		else if (!similarity_mode)
-			*score = 0.0;
-		else
-			*score = l1;
+		if (obi_blob_compare(seq1, seq2) == 0)
+		{
+			if (similarity_mode && normalize)
+				*score = 1.0;
+			else if (!similarity_mode)
+				*score = 0.0;
+			else
+				*score = l1;
+		}
 	}
 
-	else if (threshold != 0)
+	else if ((similarity_mode && normalize && (threshold == 1.0)) ||
+			(!similarity_mode && (threshold == 0.0)))
+	{  // The sequences must be identical but are not
+		return;
+	}
+
+	else if (threshold != 0.0)
 	{
 		l2 = seq2->length_decoded_value;