// 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 void test_kmer_occur_filter() { // Construct 1 colour graph with kmer-size=11 dBGraph graph; const size_t kmer_size = 11, ncols = 3; size_t i; // Create graph db_graph_alloc(&graph, kmer_size, ncols, 1, 2000, DBG_ALLOC_EDGES | DBG_ALLOC_NODE_IN_COL | DBG_ALLOC_BKTLOCKS); // xyz------->>> y > < X // TTCGACCCGACAGGGCAACGTAGTCCGACAGGGCACAGCCCTGTCGGGGGGTGCA #define NUM_NODES 3 #define NUM_READS 3 const char *tmp[NUM_READS] = { "AACA", "TTCGACCCGACAGGGCAACGTAGTCCGACAGGGCACAGCCCTGTCGGGGGGTGCA", "TCTAGCATGTGTGTT"}; read_t reads[NUM_READS]; for(i = 0; i < NUM_READS; i++) { seq_read_alloc(&reads[i]); seq_read_set(&reads[i], tmp[i]); } KOGraph kograph = kograph_create(reads, NUM_READS, true, 0, 1, &graph); TASSERT(kograph.nchroms == NUM_READS); TASSERT(kograph.koccurs != NULL); KOccurRunBuffer koruns, koruns_tmp, koruns_ended; korun_buf_alloc(&koruns, 16); korun_buf_alloc(&koruns_tmp, 16); korun_buf_alloc(&koruns_ended, 16); // Check CCCGACAGGGCAA starts at CCCGACAGGGC // x=CCCGACAGGGC, y=CCGACAGGGCA, z=CGACAGGGCAA // X=GCCCTGTCGGG, Y=TGCCCTGTCGG, Z=TTGCCCTGTCG dBNode nodes[NUM_NODES]; for(i = 0; i < NUM_NODES; i++) nodes[i] = db_graph_find_str(&graph, &"CCCGACAGGGCAA"[i]); korun_buf_reset(&koruns); korun_buf_reset(&koruns_ended); kograph_filter_extend(&kograph, nodes, NUM_NODES, true, 0, 0, &koruns, &koruns_tmp, &koruns_ended); // Checks TASSERT2(koruns.len == 1, "koruns.len: %zu", koruns.len); TASSERT(koruns.b[0].strand == STRAND_PLUS); // left-to-right with ref TASSERT2(koruns.b[0].chrom == 1, "chrom: %zu", (size_t)koruns.b[0].chrom); TASSERT2(koruns.b[0].first == 5, "offset: %zu", (size_t)koruns.b[0].first); TASSERT2(koruns.b[0].last == 7, "last: %zu", (size_t)koruns.b[0].last); // Test reverse db_nodes_reverse_complement(nodes, NUM_NODES); korun_buf_reset(&koruns); korun_buf_reset(&koruns_ended); kograph_filter_extend(&kograph, nodes, 1, true, 0, 0, &koruns, &koruns_tmp, &koruns_ended); kograph_filter_extend(&kograph, nodes+1, 1, true, 0, 1, &koruns, &koruns_tmp, &koruns_ended); kograph_filter_extend(&kograph, nodes+2, 1, true, 0, 2, &koruns, &koruns_tmp, &koruns_ended); // Print out for debugging // printf("koruns: "); // koruns_print(koruns.b, koruns.len, kmer_size, stdout); // printf("\nkoruns_ended: "); // koruns_print(koruns_ended.b, koruns_ended.len, kmer_size, stdout); // printf("\n"); // Check results match: // koruns: chromid:1:17-5:-, chromid:1:37-47:+ // koruns_ended: chromid:1:34-24:- TASSERT2(koruns.len == 2, "koruns.len: %zu", koruns.len); TASSERT2(koruns_ended.len == 1, "koruns_ended.len: %zu", koruns_ended.len); TASSERT(koruns.b[0].strand == STRAND_MINUS); // reverse complement of ref TASSERT2(koruns.b[0].chrom == 1, "chrom: %zu", (size_t)koruns.b[0].chrom); TASSERT2(koruns.b[0].first == 7, "offset: %zu", (size_t)koruns.b[0].first); TASSERT2(koruns.b[0].last == 5, "last: %zu", (size_t)koruns.b[0].last); korun_buf_dealloc(&koruns); korun_buf_dealloc(&koruns_tmp); korun_buf_dealloc(&koruns_ended); for(i = 0; i < NUM_READS; i++) seq_read_dealloc(&reads[i]); kograph_dealloc(&kograph); db_graph_dealloc(&graph); }