// For a given kmer, get the BinaryKmer 'key':
// the lower of the kmer vs reverse complement of itself
// kmer and kmer_key must NOT point to overlapping memory
BinaryKmer bkmer_get_key(const BinaryKmer bkmer, size_t kmer_size)
{
BinaryKmer bkey;
// Get first and last nucleotides
Nucleotide first = binary_kmer_first_nuc(bkmer, kmer_size);
Nucleotide last = binary_kmer_last_nuc(bkmer);
Nucleotide rev_last = dna_nuc_complement(last);
if(first < rev_last) return bkmer;
// Don't know which is going to be correct -- this will happen 1 in 4 times
bkey = binary_kmer_reverse_complement(bkmer, kmer_size);
return (binary_kmer_less_than(bkmer, bkey) ? bkmer : bkey);
}
Key element_get_key(BinaryKmer * kmer, short kmer_size, Key preallocated_key)
{
BinaryKmer local_rev_kmer;
binary_kmer_initialise_to_zero(&local_rev_kmer);
binary_kmer_reverse_complement(kmer, kmer_size, &local_rev_kmer);
if (binary_kmer_less_than(local_rev_kmer, *kmer, kmer_size)) {
binary_kmer_assignment_operator(*((BinaryKmer *)
preallocated_key),
local_rev_kmer);
} else {
binary_kmer_assignment_operator(*((BinaryKmer *)
preallocated_key), *kmer);
}
return preallocated_key;
}
dBNode * db_graph_get_next_node(dBNode * current_node, Orientation current_orientation,
Orientation * next_orientation,
Nucleotide edge, Nucleotide * reverse_edge,dBGraph * db_graph){
BinaryKmer local_copy_of_kmer;
binary_kmer_assignment_operator(local_copy_of_kmer, current_node->kmer);
BinaryKmer tmp_kmer;
dBNode * next_node=NULL;
// after the following line tmp_kmer and rev_kmer are pointing to the same B Kmer
BinaryKmer* rev_kmer = binary_kmer_reverse_complement(&local_copy_of_kmer,db_graph->kmer_size, &tmp_kmer);
if (current_orientation == reverse){
*reverse_edge = binary_kmer_get_last_nucleotide(&local_copy_of_kmer);
binary_kmer_assignment_operator(local_copy_of_kmer,*rev_kmer);
}
else{
*reverse_edge = binary_kmer_get_last_nucleotide(rev_kmer);
}
binary_kmer_left_shift_one_base_and_insert_new_base_at_right_end(&local_copy_of_kmer, edge, db_graph->kmer_size);
//get node from table
next_node = hash_table_find(element_get_key(&local_copy_of_kmer,db_graph->kmer_size, &tmp_kmer),db_graph);
if (next_node != NULL){
*next_orientation = db_node_get_orientation(&local_copy_of_kmer,next_node,db_graph->kmer_size);
}
else
{
// debug
char tmpzamseq[db_graph->kmer_size+1];
warn("Cannot find %s so get a NULL node\n", binary_kmer_to_seq(&tmp_kmer, db_graph->kmer_size, tmpzamseq));
}
return next_node;
}
static bool supernode_is_closed_cycle(const dBNode *nlist, size_t len,
BinaryKmer bkmer0, BinaryKmer bkmer1,
const dBGraph *db_graph)
{
Edges edges0, edges1;
BinaryKmer shiftkmer;
Nucleotide nuc;
const size_t kmer_size = db_graph->kmer_size;
edges0 = db_node_get_edges_union(db_graph, nlist[0].key);
if(edges_get_indegree(edges0, nlist[0].orient) != 1) return false;
edges1 = db_node_get_edges_union(db_graph, nlist[len-1].key);
if(edges_get_outdegree(edges1, nlist[len-1].orient) != 1) return false;
nuc = bkmer_get_last_nuc(bkmer0, nlist[0].orient, kmer_size);
shiftkmer = bkmer_shift_add_last_nuc(bkmer1, nlist[len-1].orient, kmer_size, nuc);
if(binary_kmers_are_equal(bkmer0, shiftkmer)) return true;
shiftkmer = binary_kmer_reverse_complement(shiftkmer, kmer_size);
return binary_kmers_are_equal(bkmer0, shiftkmer);
}
Orientation db_node_get_orientation(BinaryKmer * k, Element * e, short kmer_size)
{
if (binary_kmer_comparison_operator(e->kmer, *k) == true) {
return forward;
}
BinaryKmer tmp_kmer;
if (binary_kmer_comparison_operator(e->kmer,
*(binary_kmer_reverse_complement
(k, kmer_size,
&tmp_kmer))) == true) {
return reverse;
}
printf("programming error - you have called db_node_get_orientation with a kmer that is neither equal to the kmer in this node, nor its rev comp\n");
char tmpseq1[kmer_size];
char tmpseq2[kmer_size];
printf("Arg 1 Kmer is %s and Arg 2 node kmer is %s\n",
binary_kmer_to_seq(k, kmer_size, tmpseq1),
binary_kmer_to_seq(&(e->kmer), kmer_size, tmpseq2));
exit(1);
}