//
// Integrity checks
//
// Check an array of nodes denote a contigous path
bool db_node_check_nodes(const dBNode *nodes, size_t num,
const dBGraph *db_graph)
{
if(num == 0) return true;
const size_t kmer_size = db_graph->kmer_size;
BinaryKmer bkmer0, bkmer1, tmp;
Nucleotide nuc;
size_t i;
bkmer0 = db_node_oriented_bkmer(db_graph, nodes[0]);
for(i = 0; i+1 < num; i++)
{
bkmer1 = db_node_oriented_bkmer(db_graph, nodes[i+1]);
nuc = binary_kmer_last_nuc(bkmer1);
tmp = binary_kmer_left_shift_add(bkmer0, kmer_size, nuc);
ctx_assert_ret(binary_kmers_are_equal(tmp, bkmer1));
bkmer0 = bkmer1;
}
return true;
}
// Print:
// 0: AAACCCAAATGCAAACCCAAATGCAAACCCA:1 TGGGTTTGCATTTGGGTTTGCATTTGGGTTT
// 1: CAAACCCAAATGCAAACCCAAATGCAAACCC:1 GGGTTTGCATTTGGGTTTGCATTTGGGTTTG
// ...
void db_nodes_print_verbose(const dBNode *nodes, size_t num,
const dBGraph *db_graph, FILE *out)
{
if(num == 0) return;
const size_t kmer_size = db_graph->kmer_size;
size_t i;
BinaryKmer bkmer, bkey;
char kmerstr[MAX_KMER_SIZE+1], keystr[MAX_KMER_SIZE+1];
bkmer = db_node_get_bkmer(db_graph, nodes[0].key);
bkey = db_node_oriented_bkmer(db_graph, nodes[0]);
binary_kmer_to_str(bkmer, kmer_size, kmerstr);
binary_kmer_to_str(bkey, kmer_size, keystr);
fprintf(out, "%3zu: %s:%i %s\n", (size_t)0, kmerstr, (int)nodes[0].orient, keystr);
for(i = 1; i < num; i++) {
bkmer = db_node_get_bkmer(db_graph, nodes[i].key);
bkey = db_node_oriented_bkmer(db_graph, nodes[i]);
binary_kmer_to_str(bkmer, kmer_size, kmerstr);
binary_kmer_to_str(bkey, kmer_size, keystr);
fprintf(out, "%3zu: %s:%i %s\n", i, kmerstr, (int)nodes[i].orient, keystr);
}
}
void db_nodes_gzprint(const dBNode *nodes, size_t num,
const dBGraph *db_graph, gzFile out)
{
size_t i, kmer_size = db_graph->kmer_size;
Nucleotide nuc;
BinaryKmer bkmer;
char tmp[MAX_KMER_SIZE+1];
bkmer = db_node_oriented_bkmer(db_graph, nodes[0]);
binary_kmer_to_str(bkmer, kmer_size, tmp);
gzputs(out, tmp);
for(i = 1; i < num; i++) {
nuc = db_node_get_last_nuc(nodes[i], db_graph);
gzputc(out, dna_nuc_to_char(nuc));
}
}
void db_nodes_print(const dBNode *nodes, size_t num,
const dBGraph *db_graph, FILE *out)
{
const size_t kmer_size = db_graph->kmer_size;
size_t i;
Nucleotide nuc;
BinaryKmer bkmer;
char tmp[MAX_KMER_SIZE+1];
bkmer = db_node_oriented_bkmer(db_graph, nodes[0]);
binary_kmer_to_str(bkmer, kmer_size, tmp);
fputs(tmp, out);
for(i = 1; i < num; i++) {
nuc = db_node_get_last_nuc(nodes[i], db_graph);
fputc(dna_nuc_to_char(nuc), out);
}
}
// Extend a supernode, nlist[offset] must already be set
// Walk along nodes starting from node/or, storing the supernode in nlist
// Returns the number of nodes added, adds no more than `limit`
// return false if out of space and limit > 0
bool supernode_extend(dBNodeBuffer *nbuf, size_t limit,
const dBGraph *db_graph)
{
ctx_assert(nbuf->len > 0);
const size_t kmer_size = db_graph->kmer_size;
dBNode node0 = nbuf->data[0], node1 = nbuf->data[nbuf->len-1], node = node1;
BinaryKmer bkmer = db_node_oriented_bkmer(db_graph, node);
Edges edges = db_node_get_edges_union(db_graph, node.key);
Nucleotide nuc;
while(edges_has_precisely_one_edge(edges, node.orient, &nuc))
{
bkmer = binary_kmer_left_shift_add(bkmer, kmer_size, nuc);
node = db_graph_find(db_graph, bkmer);
edges = db_node_get_edges_union(db_graph, node.key);
ctx_assert(node.key != HASH_NOT_FOUND);
if(edges_has_precisely_one_edge(edges, rev_orient(node.orient), &nuc))
{
if(node.key == node0.key || node.key == nbuf->data[nbuf->len-1].key) {
// don't create a loop A->B->A or a->b->B->A
break;
}
if(limit && nbuf->len >= limit) return false;
db_node_buf_add(nbuf, node);
}
else break;
}
return true;
}
static void branch_to_str(const dBNode *nodes, size_t len, bool print_first_kmer,
StrBuf *sbuf, const dBGraph *db_graph)
{
size_t i = print_first_kmer, kmer_size = db_graph->kmer_size;
Nucleotide nuc;
BinaryKmer bkmer;
if(print_first_kmer) {
strbuf_ensure_capacity(sbuf, sbuf->end + kmer_size);
bkmer = db_node_oriented_bkmer(db_graph, nodes[0]);
binary_kmer_to_str(bkmer, kmer_size, sbuf->b+sbuf->end);
sbuf->end += kmer_size;
}
// i == 1 if print_first_kmer, otherwise 0
strbuf_ensure_capacity(sbuf, sbuf->end + len + 1); // +1 for '\n'
for(; i < len; i++) {
nuc = db_node_get_last_nuc(nodes[i], db_graph);
sbuf->b[sbuf->end++] = dna_nuc_to_char(nuc);
}
sbuf->b[sbuf->end++] = '\n';
sbuf->b[sbuf->end] = '\0';
}
