static pathStep *get_next_step(pathStep * current_step, pathStep * next_step, pathStep * reverse_step, dBGraph * db_graph)
{
pathStep *step = db_graph_get_next_step(current_step, next_step, reverse_step, db_graph);
assert(step != NULL);
step->label = Undefined;
Nucleotide n;
// TODO: If this works, then there's possibly a bug to fix for the multi-colour situation
if (next_step->node == NULL) {
next_step->label = Undefined;
return next_step;
}
if (db_node_has_precisely_one_edge_all_colours(next_step->node, next_step->orientation, &n)) {
next_step->label = n;
}
if (!db_node_has_precisely_one_edge_all_colours(next_step->node, opposite_orientation(next_step->orientation), &n)) {
next_step->label = Undefined;
}
return next_step;
}
/*----------------------------------------------------------------------*
* Function: *
* Purpose: *
* Params: *
* Returns: *
*----------------------------------------------------------------------*/
Nucleotide coverage_walk_get_best_label(dBNode* node, Orientation orientation, dBGraph* db_graph)
{
Nucleotide label = Undefined;
int highest_coverage = 0;
//void check_edge(Nucleotide nucleotide) {
Nucleotide nucleotide;
for (nucleotide = Adenine; nucleotide < Undefined; nucleotide++) {
//if (debugme) log_printf(" Trying nucleotide %c\n", binary_nucleotide_to_char(nucleotide));
if (db_node_edge_exist_any_colour(node, nucleotide, orientation)) {
pathStep step, reverse_step, next_step;
int coverage;
step.node = node;
step.label = nucleotide;
step.orientation = orientation;
db_graph_get_next_step(&step, &next_step, &reverse_step, db_graph);
coverage = element_get_coverage_all_colours(next_step.node);
//if (debugme) log_printf(" Coverage %i\n", coverage);
if (coverage > highest_coverage) {
label = nucleotide;
highest_coverage = coverage;
}
}
}
// nucleotide_iterator(&check_edge);
return label;
}
/*----------------------------------------------------------------------*
* Function: *
* Purpose: *
* Params: *
* Returns: *
*----------------------------------------------------------------------*/
static pathStep *coverage_walk_get_next_step(pathStep * current_step, pathStep * next_step, pathStep * reverse_step, dBGraph * db_graph)
{
db_graph_get_next_step(current_step, next_step, reverse_step, db_graph);
assert(next_step != NULL);
next_step->label = Undefined;
if (db_node_edges_count_all_colours(next_step->node, next_step->orientation) >= 1) {
next_step->label = coverage_walk_get_best_label(next_step->node, next_step->orientation, db_graph);
} else {
//char seq[1024];
//binary_kmer_to_seq(&(next_step->node->kmer), db_graph->kmer_size, seq);
//log_printf(" No edge at %s orientation %s\n", seq, next_step->orientation == forward ? "Fwd":"Rev");
}
return next_step;
}
static pathStep *get_next_step(pathStep * current_step, pathStep * next_step,
pathStep * reverse_step, dBGraph * db_graph)
{
pathStep *step = db_graph_get_next_step(current_step, next_step, reverse_step, db_graph);
assert(step != NULL);
if (step->node != NULL) {
step->label = Undefined;
Nucleotide n;
if (db_node_has_precisely_one_edge_all_colours
(next_step->node, next_step->orientation, &n)) {
next_step->label = n;
}else{
next_step->label = path_step_get_unvisited_edge_all_colours(next_step);
}
}
return next_step;
}
