static void test_walk(GraphWalker *gwlk, RepeatWalker *rptwlk, dBNode node0, dBNodeBuffer *nbuf, const dBGraph *graph, size_t expnkmers, const char *ans) { db_node_buf_reset(nbuf); graph_walker_init(gwlk, graph, 0, 0, node0); do { db_node_buf_add(nbuf, gwlk->node); } while(graph_walker_next(gwlk) && rpt_walker_attempt_traverse(rptwlk, gwlk)); // db_nodes_print(nbuf->data, nbuf->len, graph, stdout); // printf("\n"); // printf("%s\n", graph_step_str[gwlk->last_step.status]); TASSERT2(nbuf->len == expnkmers, "%zu / %zu", nbuf->len, expnkmers); char tmp[nbuf->len+MAX_KMER_SIZE]; db_nodes_to_str(nbuf->data, nbuf->len, graph, tmp); TASSERT2(strcmp(tmp,ans) == 0, "%s vs %s", tmp, ans); graph_walker_finish(gwlk); rpt_walker_fast_clear(rptwlk, nbuf->data, nbuf->len); }
// 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; }
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; }