// Returns sorted array of hkey_t from the hash table
hkey_t* hash_table_sorted(const HashTable *htable)
{
ctx_assert(sizeof(hkey_t) == sizeof(BinaryKmer*));
ctx_assert(sizeof(hkey_t) == sizeof(BkmerPtrHkeyUnion));
BkmerPtrHkeyUnion *kmers, *nxt, *end;
nxt = kmers = ctx_malloc(sizeof(BkmerPtrHkeyUnion) * htable->num_kmers);
end = kmers + htable->num_kmers;
HASH_ITERATE(htable, _fetch_kmer_union, htable, &nxt);
// Can sort ignoring that the top flag bit is set on all kmers
qsort(kmers, htable->num_kmers, sizeof(BinaryKmer*), binary_kmers_qcmp_ptrs);
for(nxt = kmers; nxt < end; nxt++) nxt->h = nxt->bptr - htable->table;
return (hkey_t*)kmers;
}
static void pull_out_supernodes(const char **seq, const char **ans, size_t n,
const dBGraph *graph)
{
dBNodeBuffer nbuf;
db_node_buf_alloc(&nbuf, 1024);
// 1. Check pulling out supernodes works for iterating over the graph
uint64_t *visited;
visited = ctx_calloc(roundup_bits2words64(graph->ht.capacity), 8);
HASH_ITERATE(&graph->ht, supernode_from_kmer,
&nbuf, visited, graph, ans, n);
ctx_free(visited);
// 2. Check pulling out supernodes works when we iterate over inputs
size_t i, j, len;
dBNode node;
char tmpstr[SNODEBUF];
for(i = 0; i < n; i++) {
len = strlen(seq[i]);
for(j = 0; j+graph->kmer_size <= len; j++)
{
// Find node
node = db_graph_find_str(graph, seq[i]+j);
TASSERT(node.key != HASH_NOT_FOUND);
// Fetch supernode
db_node_buf_reset(&nbuf);
supernode_find(node.key, &nbuf, graph);
supernode_normalise(nbuf.b, nbuf.len, graph);
// Compare
TASSERT(nbuf.len < SNODEBUF);
db_nodes_to_str(nbuf.b, nbuf.len, graph, tmpstr);
if(strcmp(tmpstr, ans[i]) != 0) {
test_status("Got: %s from ans[i]:%s\n", tmpstr, ans[i]);
}
TASSERT(strcmp(tmpstr, ans[i]) == 0);
}
}
db_node_buf_dealloc(&nbuf);
}
uint64_t hash_table_count_kmers(const HashTable *const ht)
{
uint64_t count = 0;
HASH_ITERATE(ht, increment_count, &count);
return count;
}
