Prevent out of bounds memory usage

dpryan79 · May 23, 2020 · dfa5206 · dfa5206
1 parent ba5eb8e
commit dfa5206
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/MBias.c b/MBias.c
@@ -58,7 +58,7 @@ void *extractMBias(void *foo) {
     Config *config = (Config*) foo;
     bam_hdr_t *hdr;
     bam_mplp_t iter;
-    int ret, tid, pos, i, seqlen, rv, o = 0;
+    int ret, tid, pos = 0, i, seqlen, rv, o = 0;
     int32_t bedIdx = 0;
     int strand;
     int n_plp; //This will need to be modified for multiple input files

diff --git a/common.c b/common.c
@@ -47,6 +47,7 @@ void print_version() {
 }
 
 inline int isCpG(char *seq, int pos, int seqlen) {
+    if(pos >= seqlen) return 0;
     if(*(seq+pos) == 'C' || *(seq+pos) == 'c') {
         if(pos+1 == seqlen) return 0;
         if(*(seq+pos+1) == 'G' || *(seq+pos+1) == 'g') return 1;
@@ -60,6 +61,7 @@ inline int isCpG(char *seq, int pos, int seqlen) {
 }
 
 inline int isCHG(char *seq, int pos, int seqlen) {
+    if(pos >= seqlen) return 0;
     if(*(seq+pos) == 'C' || *(seq+pos) == 'c') {
         if(pos+2 >= seqlen) return 0;
         if(*(seq+pos+2) == 'G' || *(seq+pos+2) == 'g') return 1;
@@ -73,6 +75,7 @@ inline int isCHG(char *seq, int pos, int seqlen) {
 }
 
 inline int isCHH(char *seq, int pos, int seqlen) {
+    if(pos >= seqlen) return 0;
     if(*(seq+pos) == 'C' || *(seq+pos) == 'c') return 1;
     else if(*(seq+pos) == 'G' || *(seq+pos) == 'g') return -1;
     return 0;