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Realloc zero, fixes undefined behaviour #119

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Realloc zero, fixes undefined behaviour #119

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d4e3d76
fix error report if /dev/stdin could not be opened
berthubert Aug 6, 2025
4e3b87b
when resizing the nodes array, the newly allocated space was not zero…
berthubert Aug 6, 2025
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17 changes: 13 additions & 4 deletions main.c
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,7 @@ int main(int argc, char *argv[]) {
struct stat fbuf;
pid_t pid;
struct _node *nodes;
size_t nodesize;
struct _gene *genes;
struct _training tinf;
struct _metagenomic_bin meta[NUM_META];
Expand All @@ -64,7 +65,9 @@ int main(int argc, char *argv[]) {
seq = (unsigned char *)malloc(MAX_SEQ/4*sizeof(unsigned char));
rseq = (unsigned char *)malloc(MAX_SEQ/4*sizeof(unsigned char));
useq = (unsigned char *)malloc(MAX_SEQ/8*sizeof(unsigned char));
nodes = (struct _node *)malloc(STT_NOD*sizeof(struct _node));
nodesize = STT_NOD*sizeof(struct _node);
nodes = (struct _node *)malloc(nodesize);

genes = (struct _gene *)malloc(MAX_GENES*sizeof(struct _gene));
if(seq == NULL || rseq == NULL || nodes == NULL || genes == NULL) {
fprintf(stderr, "\nError: Malloc failed on sequence/orfs\n\n"); exit(1);
Expand Down Expand Up @@ -262,7 +265,7 @@ int main(int argc, char *argv[]) {
if(input_ptr == NULL) {
input_ptr = INPUT_OPEN("/dev/stdin", "r");
if(input_ptr == NULL) {
fprintf(stderr, "\nError: can't open input file %s.\n\n", input_file);
fprintf(stderr, "\nError: can't open input file stdin.\n\n");
exit(5);
}
}
Expand Down Expand Up @@ -340,11 +343,14 @@ int main(int argc, char *argv[]) {
fprintf(stderr, "Locating all potential starts and stops...");
}
if(slen > max_slen && slen > STT_NOD*8) {
nodes = (struct _node *)realloc(nodes, (int)(slen/8)*sizeof(struct _node));
size_t newnodesize = (int)(slen/8)*sizeof(struct _node);
nodes = (struct _node *)realloc(nodes, newnodesize);
if(nodes == NULL) {
fprintf(stderr, "Realloc failed on nodes\n\n");
exit(11);
}
memset( ((char*) &nodes[0]) + nodesize, 0, newnodesize-nodesize);
nodesize = newnodesize;
max_slen = slen;
}
nn = add_nodes(seq, rseq, slen, nodes, closed, mlist, nmask, &tinf);
Expand Down Expand Up @@ -485,11 +491,14 @@ int main(int argc, char *argv[]) {

/* Reallocate memory if this is the biggest sequence we've seen */
if(slen > max_slen && slen > STT_NOD*8) {
nodes = (struct _node *)realloc(nodes, (int)(slen/8)*sizeof(struct _node));
size_t newnodesize = (int)(slen/8)*sizeof(struct _node);
nodes = (struct _node *)realloc(nodes, newnodesize);
if(nodes == NULL) {
fprintf(stderr, "Realloc failed on nodes\n\n");
exit(11);
}
memset( ((char*) &nodes[0]) + nodesize, 0, newnodesize-nodesize);
nodesize = newnodesize;
max_slen = slen;
}

Expand Down