// Traverse from node0 -> node1
static void traverse_5pflank(BreakpointCaller *caller, GraphCrawler *crawler,
dBNode node0, dBNode node1)
{
const dBGraph *db_graph = crawler->cache.db_graph;
dBNode next_nodes[4];
Nucleotide next_nucs[4];
size_t i, num_next;
BinaryKmer bkmer0 = db_node_get_bkmer(db_graph, node0.key);
num_next = db_graph_next_nodes(db_graph, bkmer0, node0.orient,
db_node_edges(db_graph, node0.key, 0),
next_nodes, next_nucs);
// Find index of previous node
for(i = 0; i < num_next && !db_nodes_are_equal(next_nodes[i],node1); i++) {}
ctx_assert(i < num_next && db_nodes_are_equal(next_nodes[i],node1));
kmer_run_buf_reset(&caller->koruns_5p);
kmer_run_buf_reset(&caller->koruns_5p_ended);
kmer_run_buf_reset(&caller->flank5p_run_buf);
// Go backwards to get 5p flank
// NULL means loop from 0..(ncols-1)
graph_crawler_fetch(crawler, node0,
next_nodes, next_nucs, i, num_next,
NULL, db_graph->num_of_cols,
gcrawler_flank5p_stop_at_ref_covg,
gcrawler_flank5p_finish_ref_covg,
caller);
}
static inline void infer_edges_node(hkey_t hkey,
bool add_all_edges,
const dBGraph *db_graph,
size_t *num_nodes_modified)
{
BinaryKmer bkmer = db_node_bkmer(db_graph, hkey);
Edges *edges = &db_node_edges(db_graph, hkey, 0);
size_t col;
// Create coverages that are zero or one depending on if node has colour
Covg covgs[db_graph->num_of_cols];
for(col = 0; col < db_graph->num_of_cols; col++)
covgs[col] = db_node_has_col(db_graph, hkey, col);
(*num_nodes_modified)
+= (add_all_edges ? infer_all_edges(bkmer, edges, covgs, db_graph)
: infer_pop_edges(bkmer, edges, covgs, db_graph));
}
static inline int infer_edges_node(hkey_t hkey,
bool add_all_edges,
Covg *tmp_covgs,
const dBGraph *db_graph,
size_t *num_nodes_modified)
{
BinaryKmer bkmer = db_node_get_bkmer(db_graph, hkey);
Edges *edges = &db_node_edges(db_graph, hkey, 0);
size_t col;
// Create coverages that are zero or one depending on if node has colour
if(db_graph->col_covgs == NULL) {
for(col = 0; col < db_graph->num_of_cols; col++)
tmp_covgs[col] = db_node_has_col(db_graph, hkey, col);
} else {
tmp_covgs = &db_node_covg(db_graph, hkey, 0);
}
(*num_nodes_modified)
+= (add_all_edges ? infer_all_edges(bkmer, edges, tmp_covgs, db_graph)
: infer_pop_edges(bkmer, edges, tmp_covgs, db_graph));
return 0; // => keep iterating
}
// `fork_node` is a node with outdegree > 1
void find_bubbles(BubbleCaller *caller, dBNode fork_node)
{
graph_cache_reset(&caller->cache);
const dBGraph *db_graph = caller->db_graph;
GraphCache *cache = &caller->cache;
GraphWalker *wlk = &caller->wlk;
RepeatWalker *rptwlk = &caller->rptwlk;
// char tmpstr[MAX_KMER_SIZE+3];
// db_node_to_str(db_graph, fork_node, tmpstr);
// status("Calling from %s", tmpstr);
dBNode nodes[4];
Nucleotide bases[4];
size_t i, num_next, num_edges_in_col;
BinaryKmer fork_bkmer = db_node_get_bkmer(db_graph, fork_node.key);
num_next = db_graph_next_nodes(db_graph, fork_bkmer, fork_node.orient,
db_node_edges(db_graph, fork_node.key, 0),
nodes, bases);
// loop over alleles, then colours
Colour colour, colours_loaded = db_graph->num_of_cols;
bool node_has_col[4];
uint32_t pathid;
for(colour = 0; colour < colours_loaded; colour++)
{
if(!db_node_has_col(db_graph, fork_node.key, colour)) continue;
// Determine if this fork is a fork in the current colour
num_edges_in_col = 0;
for(i = 0; i < num_next; i++) {
node_has_col[i] = (db_node_has_col(db_graph, nodes[i].key, colour) > 0);
num_edges_in_col += node_has_col[i];
}
graph_walker_setup(wlk, true, colour, colour, db_graph);
for(i = 0; i < num_next; i++)
{
if(node_has_col[i])
{
graph_walker_start(wlk, fork_node);
graph_walker_force(wlk, nodes[i], num_edges_in_col > 1);
pathid = graph_crawler_load_path_limit(cache, nodes[i], wlk, rptwlk,
caller->prefs.max_allele_len);
graph_walker_finish(wlk);
graph_crawler_reset_rpt_walker(rptwlk, cache, pathid);
}
}
}
// Set up 5p flank
caller->flank5p.b[0] = db_node_reverse(fork_node);
caller->flank5p.len = 0; // set to one to signify we haven't fetched flank yet
}