// Returns 1 if a read is a substring of ANY read in the list or a complete
// match with a read before it in the list. Returns <= 0 otherwise.
// 1 => is substr
// 0 => not substr
// -1 => not enough bases of ACGT
static int _is_substr(const ReadBuffer *rbuf, size_t idx,
const KOGraph *kograph, const dBGraph *db_graph)
{
const size_t kmer_size = db_graph->kmer_size;
const read_t *r = &rbuf->b[idx], *r2;
size_t contig_start;
contig_start = seq_contig_start(r, 0, kmer_size, 0, 0);
if(contig_start >= r->seq.end) return -1; // No kmers in this sequence
dBNode node = db_graph_find_str(db_graph, r->seq.b+contig_start);
ctx_assert(node.key != HASH_NOT_FOUND);
// expect at least one hit (for this read!)
ctx_assert(kograph_occurs(kograph, node.key));
KOccur *hit;
for(hit = kograph_get(kograph, node.key); 1; hit++)
{
if(hit->chrom != idx)
{
r2 = &rbuf->b[hit->chrom];
// A read is a duplicate (i.e. return 1) if it is a substring of ANY
// read in the list or a complete match with a read before it in the list.
// That is why we have: (hit->chrom < idx || r->seq.end < r2->seq.end)
// since identical strings have equal length
if(hit->chrom < idx || r->seq.end < r2->seq.end) {
if(hit->orient == node.orient) {
// potential FORWARD match
if(hit->offset >= contig_start &&
hit->offset + r->seq.end <= r2->seq.end &&
strncasecmp(r->seq.b, r2->seq.b+hit->offset-contig_start, r->seq.end) == 0)
{
return 1;
}
}
else {
// potential REVERSE match
// if read is '<NNNN>[kmer]<rem>' rX_rem is the number of chars after
// the first valid kmer
size_t r1_rem = r->seq.end - (contig_start + kmer_size);
size_t r2_rem = r2->seq.end - (hit->offset + kmer_size);
if(r1_rem <= hit->offset && r2_rem >= contig_start &&
dna_revncasecmp(r->seq.b, r2->seq.b+hit->offset-r1_rem, r->seq.end) == 0)
{
return 1;
}
}
}
}
if(!hit->next) break;
}
return 0;
}
static bool read_touches_graph(const read_t *r, const dBGraph *db_graph,
LoadingStats *stats)
{
bool found = false;
BinaryKmer bkmer; Nucleotide nuc; dBNode node;
const size_t kmer_size = db_graph->kmer_size;
size_t i, num_contigs = 0, num_kmers_loaded = 0;
size_t search_pos = 0, start, end = 0, contig_len;
if(r->seq.end >= kmer_size)
{
while((start = seq_contig_start(r, search_pos, kmer_size, 0,0)) < r->seq.end &&
!found)
{
end = seq_contig_end(r, start, kmer_size, 0, 0, &search_pos);
contig_len = end - start;
__sync_fetch_and_add((volatile size_t*)&stats->total_bases_loaded, contig_len);
num_contigs++;
bkmer = binary_kmer_from_str(r->seq.b + start, kmer_size);
num_kmers_loaded++;
node = db_graph_find(db_graph, bkmer);
if(node.key != HASH_NOT_FOUND) { found = true; break; }
for(i = start+kmer_size; i < end; i++)
{
nuc = dna_char_to_nuc(r->seq.b[i]);
bkmer = binary_kmer_left_shift_add(bkmer, kmer_size, nuc);
num_kmers_loaded++;
node = db_graph_find(db_graph, bkmer);
if(node.key != HASH_NOT_FOUND) { found = true; break; }
}
}
}
// Update stats
__sync_fetch_and_add((volatile size_t*)&stats->total_bases_read, r->seq.end);
__sync_fetch_and_add((volatile size_t*)&stats->num_kmers_loaded, num_kmers_loaded);
__sync_fetch_and_add((volatile size_t*)&stats->num_kmers_novel, num_kmers_loaded - found);
__sync_fetch_and_add((volatile size_t*)&stats->num_good_reads, num_contigs > 0);
__sync_fetch_and_add((volatile size_t*)&stats->num_bad_reads, num_contigs == 0);
return found;
}
// if colour is -1 aligns to all colours, otherwise aligns to given colour only
// Returns number of kmers lost from the end
static size_t db_alignment_from_read(dBAlignment *aln, const read_t *r,
uint8_t qcutoff, uint8_t hp_cutoff,
const dBGraph *db_graph, int colour)
{
size_t contig_start, contig_end = 0, search_start = 0;
const size_t kmer_size = db_graph->kmer_size;
BinaryKmer bkmer, tmp_key;
Nucleotide nuc;
hkey_t node;
size_t i, offset, nxtbse;
dBNodeBuffer *nodes = &aln->nodes;
Int32Buffer *rpos = &aln->rpos;
ctx_assert(nodes->len == rpos->len);
size_t n = nodes->len, init_len = n;
db_node_buf_capacity(nodes, n + r->seq.end);
int32_buf_capacity(rpos, n + r->seq.end);
while((contig_start = seq_contig_start(r, search_start, kmer_size,
qcutoff, hp_cutoff)) < r->seq.end)
{
contig_end = seq_contig_end(r, contig_start, kmer_size,
qcutoff, hp_cutoff, &search_start);
const char *contig = r->seq.b + contig_start;
size_t contig_len = contig_end - contig_start;
bkmer = binary_kmer_from_str(contig, kmer_size);
bkmer = binary_kmer_right_shift_one_base(bkmer);
for(offset=contig_start, nxtbse=kmer_size-1; nxtbse < contig_len; nxtbse++,offset++)
{
nuc = dna_char_to_nuc(contig[nxtbse]);
bkmer = binary_kmer_left_shift_add(bkmer, kmer_size, nuc);
tmp_key = binary_kmer_get_key(bkmer, kmer_size);
node = hash_table_find(&db_graph->ht, tmp_key);
if(node != HASH_NOT_FOUND &&
(colour == -1 || db_node_has_col(db_graph, node, colour)))
{
nodes->b[n].key = node;
nodes->b[n].orient = bkmer_get_orientation(bkmer, tmp_key);
rpos->b[n] = offset;
n++;
}
}
}
// Return number of bases from the last kmer found until read end
size_t ret = (n == init_len ? r->seq.end /* No kmers found */
: r->seq.end - (rpos->b[n-1] + kmer_size));
nodes->len = rpos->len = n;
// Check for sequence gaps
for(i = init_len; i+1 < nodes->len; i++) {
if(rpos->b[i]+1 < rpos->b[i+1]) {
aln->seq_gaps = true;
break;
}
}
return ret;
}