// 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);
}
