Mainly the pull request 'Fix unhandled errors of malloc' by Thomas1664

src/amplicontm.c

@@ -159,6 +159,11 @@ amplicon_result amplicontm(const  char *inseq,
     int orilen = strlen(inseq);
     int gc_count = 0;
     ret.seq = (char *) malloc(sizeof(char) * (orilen + 1));
+    if ((ret.seq == NULL)) {
+        ret.error = 1;
+        amp_free_all(alloc_box, alloc_count);
+        return ret;
+    }
     for (i = 0 ; i < orilen ; i++) {
         ret.seq[ret.seq_len]=toupper(inseq[i]);
         switch(ret.seq[ret.seq_len]) {

src/libprimer3.cc

@@ -1167,29 +1167,32 @@ create_seq_arg()
 
 /* Free a seq_arg data structure */
 void
-destroy_seq_args(seq_args *sa) 
+destroy_seq_args(seq_args *sa)
 {
   if (NULL == sa) return;
-  free(sa->internal_input);
-  free(sa->left_input);
-  free(sa->right_input);
-  free(sa->sequence);
+
   free(sa->quality);
+  free(sa->sequence);
+  free(sa->sequence_name);
   free(sa->trimmed_seq);
 
-  free(sa->overhang_left);
-  free(sa->overhang_right);
-  free(sa->overhang_right_rv);
-
   /* edited by T. Koressaar for lowercase masking */
   free(sa->trimmed_orig_seq);
-
-  free(sa->trimmed_masked_seq_r);
+
   free(sa->trimmed_masked_seq);
-
+  free(sa->trimmed_masked_seq_r);
+
   free(sa->upcased_seq);
   free(sa->upcased_seq_r);
-  free(sa->sequence_name);
+
+  free(sa->left_input);
+  free(sa->right_input);
+  free(sa->internal_input);
+
+  free(sa->overhang_left);
+  free(sa->overhang_right);
+  free(sa->overhang_right_rv);
+
   free(sa);
 }
 
@@ -6404,7 +6407,7 @@ destroy_pr_append_str(pr_append_str *str)
 int
 pr_append_external(pr_append_str *x,  const char *s) 
 {
-  int xlen, slen;
+  size_t xlen, slen;
 
   PR_ASSERT(NULL != s);
   PR_ASSERT(NULL != x);
@@ -10014,7 +10017,6 @@ p3_print_args(const p3_global_settings *p, seq_args *s)
     printf("quality_storage_size %i\n", s->quality_storage_size) ;
     printf("*sequence %s\n", s->sequence) ;
     printf("*sequence_name %s\n", s->sequence_name) ;
-    printf("*sequence_file %s\n", s->sequence_file) ;
     printf("*trimmed_seq %s\n", s->trimmed_seq) ;
     printf("*trimmed_orig_seq %s\n", s->trimmed_orig_seq) ;
     printf("*trimmed_masked_seq %s\n", s->trimmed_masked_seq) ;

src/libprimer3.h

@@ -110,7 +110,7 @@ typedef enum p3_output_type {
 
 /* pr_append_str is an append-only string ADT. */
 typedef struct pr_append_str {
-  int storage_size;
+  size_t storage_size;
   char *data;
 } pr_append_str;
 
@@ -867,7 +867,6 @@ typedef struct seq_args {
   char *sequence;         /* The template sequence itself as input, 
                              not trimmed, not up-cased. */
   char *sequence_name;    /* An identifier for the sequence. */
-  char *sequence_file;    /* Another identifier for the sequence. */
   char *trimmed_seq;      /* The included region only, _UPCASED_. */
 
   /* Element add by T. Koressaar support lowercase masking: */