Wrap a couple more calloc, malloc and realloc calls

Needed when using add_sat, prod_sat functions.  A couple
can also be converted to the _pse variants.

Author: daviesrob

cram/cram_encode.c

@@ -2107,7 +2107,7 @@ int cram_encode_container(cram_fd *fd, cram_container *c) {
         // slice can start aggregating them from the start again.
         if (c->tags_used->n_occupied) {
             int ntags = c->tags_used->n_occupied;
-            s->aux_block = calloc(hts_prod_sat2(ntags, 2), sizeof(*s->aux_block));
+            s->aux_block = hts_calloc(hts_prod_sat2(ntags, 2), sizeof(*s->aux_block));
             if (!s->aux_block)
                 return -1;
 

faidx.c

@@ -744,7 +744,7 @@ static char *fai_retrieve(const faidx_t *fai, const faidx1_t *val,
     }
 
     // Over-allocate so there is extra space for one end-of-line sequence
-    buffer = malloc(hts_add_sat3(end - beg, val->line_len - val->line_blen, 1));
+    buffer = hts_malloc(hts_add_sat3(end - beg, val->line_len - val->line_blen, 1));
     if (!buffer) {
         *len = -1;
         return NULL;

realn.c

@@ -220,7 +220,7 @@ int sam_prob_realn(bam1_t *b, const char *ref, hts_pos_t ref_len, int flag) {
         }
 
         assert(bq == NULL); // bq was used above, but should now be NULL
-        bq = malloc(hts_add_sat2(hts_prod_sat2(align_lqseq, 3), lref));
+        bq = hts_malloc_pse(3, align_lqseq, 0, lref);
         if (!bq) goto fail;
         q = bq + align_lqseq;
         tseq = q + align_lqseq;

sam.c

@@ -3410,7 +3410,7 @@ static void *sam_dispatcher_read(void *vp) {
             // entire buffer is part of a single line
             if (cp == l->data) {
                 line_frag = l->data_size;
-                char *rp = realloc(l->data, hts_add_sat2(hts_prod_sat2(l->alloc, 2), 8));
+                char *rp = hts_realloc_pse(l->data, 2, l->alloc, 0, 8);
                 if (!rp)
                     goto err;
                 l->alloc *= 2;