From b84698058f08759ca33f56edad08a2ffdc2f3cff Mon Sep 17 00:00:00 2001
From: Hasindu Gamaarachchi <hasindu2008@gmail.com>
Date: Tue, 4 Jun 2024 16:43:55 +1000
Subject: [PATCH] fix bug assert(outIndex < (int)(n_events * 2))

---
 src/align.c | 2 +-
 src/f5c.c   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/align.c b/src/align.c
index b58b823e..78c8f750 100644
--- a/src/align.c
+++ b/src/align.c
@@ -454,7 +454,7 @@ int32_t align(AlignedPair* out_2, char* sequence, int32_t sequence_len,
     while (curr_kmer_idx >= 0 && curr_event_idx >= 0) {
         // emit alignment
         //>>>>>>>New Repalcement begin
-        assert(outIndex < (int)(n_events * 2));
+        assert(outIndex < (int)(n_events + sequence_len));
         out_2[outIndex].ref_pos = curr_kmer_idx;
         out_2[outIndex].read_pos = curr_event_idx;
         outIndex++;
diff --git a/src/f5c.c b/src/f5c.c
index 319ca4c8..3ced84ee 100644
--- a/src/f5c.c
+++ b/src/f5c.c
@@ -722,7 +722,7 @@ void event_single(core_t* core,db_t* db, int32_t i) {
 
         //allocate memory for the next alignment step
         db->event_align_pairs[i] = (AlignedPair*)malloc(
-                    sizeof(AlignedPair) * db->et[i].n * 2); //todo : find a good heuristic to save memory
+                    sizeof(AlignedPair) * (db->et[i].n + db->read_len[i]));
         MALLOC_CHK(db->event_align_pairs[i]);
     }
     else{