// If `pickup_new_runs` is true we pick up runs starting at this supernode
static inline bool gcrawler_stop_at_ref_covg(const GraphCache *cache,
const GCacheStep *step,
BreakpointCaller *caller,
KOccurRunBuffer *koruns,
KOccurRunBuffer *koruns_ended,
bool pickup_new_runs)
{
GCacheSnode *snode = graph_cache_snode(cache, step->supernode);
GCachePath *path = graph_cache_path(cache, step->pathid);
const dBNode *nodes = graph_cache_first_node(cache, snode);
bool forward = (step->orient == FORWARD);
// Use index of last step as qoffset
size_t qoffset = path->num_steps-1;
// Kmer occurance runs are added to koruns_3p_ended only if they end and are
// longer than the mininum length in kmers (caller->min_ref_nkmers)
kograph_filter_extend(caller->kograph,
nodes, snode->num_nodes, forward,
caller->min_ref_nkmers, qoffset,
koruns, koruns_ended,
pickup_new_runs);
size_t i, min_run_qoffset = SIZE_MAX, min_ended_run_qoffset = SIZE_MAX;
for(i = 0; i < koruns->len; i++)
min_run_qoffset = MIN2(min_run_qoffset, koruns->data[i].qoffset);
// Stop if all our earliest runs have finished
for(i = 0; i < koruns_ended->len; i++) {
min_ended_run_qoffset = MIN2(min_ended_run_qoffset, koruns_ended->data[i].qoffset);
}
// Continue if...
return min_run_qoffset <= min_ended_run_qoffset;
}
static inline void walk_supernode_end(const GraphCache *cache,
const GCacheSnode *snode,
Orientation snorient,
GraphWalker *wlk)
{
// Only need to traverse the first and last nodes of a supernode
const dBNode *first = graph_cache_first_node(cache, snode);
const dBNode *last = graph_cache_last_node(cache, snode);
dBNode lastnode;
size_t num_nodes = last - first + 1;
if(num_nodes > 1) {
lastnode = (snorient == FORWARD ? *last : db_node_reverse(*first));
graph_walker_jump_along_snode(wlk, lastnode, num_nodes);
}
}
void graph_crawler_reset_rpt_walker(RepeatWalker *rptwlk,
const GraphCache *cache, uint32_t pathid)
{
rpt_walker_fast_clear(rptwlk, NULL, 0);
const GCachePath *path = graph_cache_path(cache, pathid);
const GCacheStep *step = graph_cache_step(cache, path->first_step), *endstep;
const GCacheSnode *snode;
const dBNode *node0, *node1;
// Loop over supernodes in the path
for(endstep = step + path->num_steps; step < endstep; step++)
{
// We don't care about orientation here
snode = graph_cache_snode(cache, step->supernode);
node0 = graph_cache_first_node(cache, snode);
node1 = graph_cache_last_node(cache, snode);
rpt_walker_fast_clear_single_node(rptwlk, *node0);
rpt_walker_fast_clear_single_node(rptwlk, *node1);
}
}
