From 6e83b04e289dc1f5a1457d2e3125dd7acbf2fbe8 Mon Sep 17 00:00:00 2001
From: Hasindu Gamaarachchi <hasindu2008@gmail.com>
Date: Tue, 5 Mar 2024 18:36:27 +0530
Subject: [PATCH] fix potential bug

---
 src/genread.c | 50 ++++++++++++++++++++++++++------------------------
 1 file changed, 26 insertions(+), 24 deletions(-)

diff --git a/src/genread.c b/src/genread.c
index 8781a04..df204b4 100644
--- a/src/genread.c
+++ b/src/genread.c
@@ -205,32 +205,34 @@ static inline int get_rlen(core_t *core, int tid){
 }
 
 static void methylate_dna(core_t *core, int32_t ref_len, int32_t ref_pos, int32_t rlen, char c, char *seq, int seq_i, int tid){
-    for(int i=0; i<rlen; i++){
-        int rpos = ref_pos+i;
-        if(rpos+1 < ref_len && i+1<rlen){
-            if(core->ref->ref_seq[seq_i][ref_pos+i] == 'C' &&
-                        core->ref->ref_seq[seq_i][ref_pos+i+1] == 'G'){
-                int methr = rng(&core->rand_meth[tid]) * 254;
-                if( methr <= core->ref->ref_meth[seq_i][ref_pos+i]){
-
-                    int p = i;
-                    if(c == '-'){
-                        //fprintf(stderr,"here\n");
-                        p = rlen - i - 2;
-                    }
-                    if(!(p>=0 && p<rlen)){
-                        fprintf(stderr,"p: %d, i: %d, rlen: %d, c: %c, ref_pos: %d, ref_len: %d\n",p,i,rlen,c,ref_pos,ref_len);
+    if(core->ref->ref_meth[seq_i]){
+        for(int i=0; i<rlen; i++){
+            int rpos = ref_pos+i;
+            if(rpos+1 < ref_len && i+1<rlen){
+                if(core->ref->ref_seq[seq_i][ref_pos+i] == 'C' &&
+                            core->ref->ref_seq[seq_i][ref_pos+i+1] == 'G'){
+                    int methr = rng(&core->rand_meth[tid]) * 254;
+                    if( methr <= core->ref->ref_meth[seq_i][ref_pos+i]){
+
+                        int p = i;
+                        if(c == '-'){
+                            //fprintf(stderr,"here\n");
+                            p = rlen - i - 2;
+                        }
+                        if(!(p>=0 && p<rlen)){
+                            fprintf(stderr,"p: %d, i: %d, rlen: %d, c: %c, ref_pos: %d, ref_len: %d\n",p,i,rlen,c,ref_pos,ref_len);
+
+                            assert(0);
+                        }
+                        assert(seq[p] == 'C' || seq[p] == 'c');
+                        if(!(seq[p+1] == 'G' || seq[p+1] == 'g')){
+                            fprintf(stderr,"p: %d, i: %d, rlen: %d, c: %c, ref_pos: %d, ref_len: %d\n",p,i,rlen,c,ref_pos,ref_len);
+                            fprintf(stderr,"seq: %c%c%c%c%c%c%c%c%c%c\n",seq[p],seq[p+1],seq[p+2],seq[p+3],seq[p+4],seq[p+5],seq[p+6],seq[p+7],seq[p+8],seq[p+9]);
+                            assert(0);
+                        }
+                        seq[p] = 'M';
 
-                        assert(0);
-                    }
-                    assert(seq[p] == 'C' || seq[p] == 'c');
-                    if(!(seq[p+1] == 'G' || seq[p+1] == 'g')){
-                        fprintf(stderr,"p: %d, i: %d, rlen: %d, c: %c, ref_pos: %d, ref_len: %d\n",p,i,rlen,c,ref_pos,ref_len);
-                        fprintf(stderr,"seq: %c%c%c%c%c%c%c%c%c%c\n",seq[p],seq[p+1],seq[p+2],seq[p+3],seq[p+4],seq[p+5],seq[p+6],seq[p+7],seq[p+8],seq[p+9]);
-                        assert(0);
                     }
-                    seq[p] = 'M';
-
                 }
             }
         }