// Reverse ordering and orientations
void db_nodes_reverse_complement(dBNode *nlist, size_t len)
{
if(len == 0) return;
size_t i, j;
dBNode tmp;
for(i = 0, j = len-1; i+1 < j; i++, j--) {
tmp = nlist[i];
nlist[i] = db_node_reverse(nlist[j]);
nlist[j] = db_node_reverse(tmp);
}
tmp = nlist[i];
nlist[i] = db_node_reverse(nlist[j]);
nlist[j] = db_node_reverse(tmp);
}
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);
}
}
// `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
}
// Walk the graph remembering the last time we met the ref
// When traversal fails, dump sequence up to last meeting with the ref
static void follow_break(BreakpointCaller *caller, dBNode node)
{
size_t i, j, k, num_next;
dBNode next_nodes[4];
Nucleotide next_nucs[4];
size_t nonref_idx[4], num_nonref_next = 0;
const dBGraph *db_graph = caller->db_graph;
BinaryKmer bkey = db_node_get_bkmer(db_graph, node.key);
Edges edges = db_node_get_edges(db_graph, node.key, 0);
num_next = db_graph_next_nodes(db_graph, bkey, node.orient, edges,
next_nodes, next_nucs);
// Filter out next nodes in the reference
for(i = 0; i < num_next; i++) {
if(kograph_num(caller->kograph, next_nodes[i].key) == 0) {
nonref_idx[num_nonref_next] = i;
num_nonref_next++;
}
}
// Abandon if all options are in ref or none are
if(num_nonref_next == num_next || num_nonref_next == 0) return;
// Follow all paths not in ref, in all colours
GraphCrawler *fw_crawler = &caller->crawlers[node.orient];
GraphCrawler *rv_crawler = &caller->crawlers[!node.orient];
dBNodeBuffer *allelebuf = &caller->allelebuf, *flank5pbuf = &caller->flank5pbuf;
GCMultiColPath *flank5p_multicolpath, *allele_multicolpath;
KOccurRun *flank5p_runs, *flank3p_runs;
size_t flank5p_pathid, allele_pathid;
size_t num_flank5p_runs, num_flank3p_runs;
// We fetch 5' flanks in all colours then merge matching paths
// we stop fetching a single path if it stops tracking the reference
// Alternatively, we could fetch the 5' flank in everyone and stop after a
// given distance, then check for that set of paths how much it tracks the
// reference. This has the advantage of scaling much better with number of
// samples, but not so well as min_ref_nkmers increases (since we fetch
// many flanks that can't be used) - I think this is less of a worry.
// Loop over possible next nodes at this junction
for(i = 0; i < num_nonref_next; i++)
{
size_t next_idx = nonref_idx[i];
// Go backwards to get 5p flank
traverse_5pflank(caller, rv_crawler, db_node_reverse(next_nodes[next_idx]),
db_node_reverse(node));
// Loop over the flanks we got
for(j = 0; j < rv_crawler->num_paths; j++)
{
// Get 5p flank
db_node_buf_reset(flank5pbuf);
graph_crawler_get_path_nodes(rv_crawler, j, flank5pbuf);
flank5p_multicolpath = &rv_crawler->multicol_paths[j];
flank5p_pathid = flank5p_multicolpath->pathid;
// Fetch 3pflank ref position
num_flank5p_runs = caller->flank5p_refs[flank5p_pathid].num_runs;
flank5p_runs = fetch_ref_contact(&rv_crawler->cache, flank5p_pathid,
caller->flank5p_refs,
&caller->flank5p_run_buf);
koruns_reverse(flank5p_runs, num_flank5p_runs, flank5pbuf->len);
koruns_sort_by_qoffset(flank5p_runs, num_flank5p_runs);
db_nodes_reverse_complement(flank5pbuf->data, flank5pbuf->len);
if(num_flank5p_runs > 0)
{
// Reset caller
kmer_run_buf_reset(&caller->koruns_3p);
kmer_run_buf_reset(&caller->koruns_3p_ended);
kmer_run_buf_reset(&caller->allele_run_buf);
// functions gcrawler_path_stop_at_ref_covg(),
// gcrawler_path_finish_ref_covg()
// both fill koruns_3p, koruns_3p_ended and allele_run_buf
// Only traverse in the colours we have a flank for
graph_crawler_fetch(fw_crawler, node,
next_nodes, next_nucs, next_idx, num_next,
flank5p_multicolpath->cols,
flank5p_multicolpath->num_cols,
gcrawler_path_stop_at_ref_covg,
gcrawler_path_finish_ref_covg,
caller);
// Assemble contigs - fetch forwards for each path for given 5p flank
for(k = 0; k < fw_crawler->num_paths; k++)
{
// Fetch nodes
db_node_buf_reset(allelebuf);
graph_crawler_get_path_nodes(fw_crawler, k, allelebuf);
ctx_assert(allelebuf->len > 0);
allele_multicolpath = &fw_crawler->multicol_paths[k];
allele_pathid = allele_multicolpath->pathid;
// Fetch 3pflank ref position
num_flank3p_runs = caller->allele_refs[allele_pathid].num_runs;
flank3p_runs = fetch_ref_contact(&fw_crawler->cache, allele_pathid,
caller->allele_refs,
&caller->allele_run_buf);
process_contig(caller,
allele_multicolpath->cols,
allele_multicolpath->num_cols,
flank5pbuf, allelebuf,
flank5p_runs, num_flank5p_runs,
flank3p_runs, num_flank3p_runs);
}
}
}
}
}
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;
}
