// `node1` should be the first node of a supernode
// `node0` should be the previous node
// `next_base` is the last base of `node1`
// `jmpfunc` is called with each supernode traversed and if it returns true
// we continue crawling, otherwise we stop
// `endfunc` is a function called at the end of traversal
void graph_crawler_fetch(GraphCrawler *crawler, dBNode node0,
dBNode next_nodes[4],
size_t take_idx, size_t num_next,
uint32_t *cols, size_t ncols,
bool (*jmpfunc)(GraphCache *_cache, GCacheStep *_step, void *_arg),
void (*endfunc)(GraphCache *_cache, uint32_t _pathid, void *_arg),
void *arg)
{
const dBGraph *db_graph = crawler->cache.db_graph;
GraphCache *cache = &crawler->cache;
GraphWalker *wlk = &crawler->wlk;
RepeatWalker *rptwlk = &crawler->rptwlk;
GCUniColPath *unipaths = crawler->unicol_paths;
ctx_assert(take_idx < num_next);
ctx_assert(!db_nodes_are_equal(node0, next_nodes[take_idx]));
// Fetch all paths in all colours
dBNode node1 = next_nodes[take_idx];
bool is_fork;
size_t i, c, col, nedges_cols, num_unicol_paths = 0;
int pathid;
for(c = 0; c < ncols; c++)
{
col = (cols != NULL ? cols[c] : c);
if(db_node_has_col(db_graph, node0.key, col) &&
db_node_has_col(db_graph, node1.key, col))
{
// Determine if this fork is a fork in the current colour
for(nedges_cols = 0, i = 0; i < num_next && nedges_cols <= 1; i++)
nedges_cols += db_node_has_col(db_graph, next_nodes[i].key, col);
is_fork = (nedges_cols > 1);
graph_walker_setup(wlk, true, col, col, db_graph);
graph_walker_start(wlk, node0);
graph_walker_force(wlk, node1, is_fork);
pathid = graph_crawler_load_path(cache, node1, wlk, rptwlk, jmpfunc, arg);
if(endfunc != NULL) endfunc(cache, pathid, arg);
graph_walker_finish(wlk);
graph_crawler_reset_rpt_walker(rptwlk, cache, pathid);
unipaths[num_unicol_paths++] = (GCUniColPath){.colour = col,
.pathid = pathid};
}
else
pathid = -1;
crawler->col_paths[col] = pathid;
}
// Check we can walk along a set of nodes through the graph
// If @allow_extend is true, traverse past the end of the buffer and add nodes
static inline int confirm_seq(size_t startidx, bool allow_extend,
GraphWalker *wlk, RepeatWalker *rpt,
dBNodeBuffer *nbuf, size_t colour,
const dBGraph *db_graph)
{
ctx_assert(startidx < nbuf->len);
size_t i, init_len = nbuf->len;
graph_walker_setup(wlk, true, colour, colour, db_graph);
graph_walker_start(wlk, nbuf->b[startidx]);
for(i = startidx+1; graph_walker_next(wlk); i++) {
if(!rpt_walker_attempt_traverse(rpt, wlk)) {
reset(wlk,rpt,nbuf);
return CONFIRM_REPEAT;
}
if(i < init_len) {
if(!db_nodes_are_equal(nbuf->b[i], wlk->node)) {
reset(wlk,rpt,nbuf);
return CONFIRM_WRONG;
}
}
else {
db_node_buf_add(nbuf, wlk->node);
if(!allow_extend) {
reset(wlk,rpt,nbuf);
nbuf->len--; // Remove node we added
return CONFIRM_OVERSHOT;
}
}
}
// printf("stopped %zu / %zu %zu\n", i, init_len, nbuf->len);
reset(wlk,rpt,nbuf);
return i < init_len ? CONFIRM_SHORT : CONFIRM_SUCCESS;
}
// `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
}
static inline
int test_statement_node(dBNode node, ExpABCWorker *wrkr)
{
const dBGraph *db_graph = wrkr->db_graph;
dBNodeBuffer *nbuf = &wrkr->nbuf;
GraphWalker *wlk = &wrkr->gwlk;
RepeatWalker *rpt = &wrkr->rptwlk;
size_t b_idx, col = wrkr->colour;
// rpt_walker_clear(rpt);
db_node_buf_reset(nbuf);
db_node_buf_add(nbuf, node);
// size_t AB_limit = wrkr->prime_AB ? SIZE_MAX : wrkr->max_AB_dist;
size_t walk_limit = wrkr->max_AB_dist;
// status("walk_limit: %zu", walk_limit);
// Walk from B to find A
graph_walker_setup(wlk, true, col, col, db_graph);
graph_walker_start(wlk, nbuf->b[0]);
while(graph_walker_next(wlk) && nbuf->len < walk_limit) {
if(!rpt_walker_attempt_traverse(rpt, wlk)) {
reset(wlk,rpt,nbuf); return RES_LOST_IN_RPT;
}
db_node_buf_add(nbuf, wlk->node);
}
reset(wlk,rpt,nbuf);
if(nbuf->len == 1) return RES_NO_TRAVERSAL;
// Traverse A->B
db_nodes_reverse_complement(nbuf->b, nbuf->len);
b_idx = nbuf->len - 1;
if(wrkr->prime_AB)
{
// Prime A->B without attempting to cross
graph_walker_prime(wlk, nbuf->b, nbuf->len, nbuf->len, true);
while(graph_walker_next(wlk)) {
if(!rpt_walker_attempt_traverse(rpt, wlk)) {
reset(wlk,rpt,nbuf); return RES_LOST_IN_RPT;
}
db_node_buf_add(nbuf, wlk->node);
}
}
else
{
// Attempt to traverse A->B then extend past B
int r = confirm_seq(0, true, wlk, rpt, nbuf, col, db_graph);
switch(r) {
case CONFIRM_REPEAT: return RES_LOST_IN_RPT;
case CONFIRM_OVERSHOT: ctx_assert2(0,"Can't 'overshoot' when extending");
case CONFIRM_WRONG: return RES_AB_WRONG;
case CONFIRM_SHORT:
if(wrkr->print_failed_contigs)
print_failed(node, nbuf, db_graph, true, wrkr->prime_AB);
wrkr->ab_fail_state[wlk->last_step.status]++;
return RES_AB_FAILED;
}
}
reset(wlk,rpt,nbuf);
if(nbuf->len == b_idx+1) return RES_NO_TRAVERSAL; // Couldn't get past B
// Last node is now C
// Walk from B... record whether or not we reach C
ctx_assert(db_nodes_are_equal(nbuf->b[b_idx], db_node_reverse(node)));
int r = confirm_seq(b_idx, false, wlk, rpt, nbuf, col, db_graph);
switch(r) {
case CONFIRM_REPEAT: return RES_LOST_IN_RPT;
case CONFIRM_OVERSHOT: return RES_BC_OVERSHOT;
case CONFIRM_WRONG: return RES_BC_WRONG;
case CONFIRM_SHORT:
if(wrkr->print_failed_contigs)
print_failed(node, nbuf, db_graph, false, wrkr->prime_AB);
wrkr->bc_fail_state[wlk->last_step.status]++;
return RES_BC_FAILED;
case CONFIRM_SUCCESS: return RES_ABC_SUCCESS;
}
die("Shouldn't reach here: r=%i", r);
return -1;
}