// Return 1 if changed; 0 otherwise
bool infer_pop_edges(const BinaryKmer node_bkey, Edges *edges,
const Covg *covgs, const dBGraph *db_graph)
{
Edges uedges = 0, iedges = 0xf, add_edges, edge;
size_t orient, nuc, col, kmer_size = db_graph->kmer_size;
const size_t ncols = db_graph->num_of_cols;
BinaryKmer bkey, bkmer;
hkey_t next;
Edges newedges[ncols];
// char tmp[MAX_KMER_SIZE+1];
// binary_kmer_to_str(node_bkey, db_graph->kmer_size, tmp);
// status("Inferring %s", tmp);
for(col = 0; col < ncols; col++) {
uedges |= edges[col]; // union of edges
iedges &= edges[col]; // intersection of edges
newedges[col] = edges[col];
}
add_edges = uedges & ~iedges;
if(!add_edges) return 0;
for(orient = 0; orient < 2; orient++)
{
bkmer = (orient == FORWARD ? binary_kmer_left_shift_one_base(node_bkey, kmer_size)
: binary_kmer_right_shift_one_base(node_bkey));
for(nuc = 0; nuc < 4; nuc++)
{
edge = nuc_orient_to_edge(nuc, orient);
if(add_edges & edge)
{
// get next bkmer, look up in graph
if(orient == FORWARD) binary_kmer_set_last_nuc(&bkmer, nuc);
else binary_kmer_set_first_nuc(&bkmer, dna_nuc_complement(nuc), kmer_size);
bkey = bkmer_get_key(bkmer, kmer_size);
next = hash_table_find(&db_graph->ht, bkey);
ctx_assert(next != HASH_NOT_FOUND);
for(col = 0; col < ncols; col++)
if(covgs[col] > 0 && db_node_has_col(db_graph, next, col))
newedges[col] |= edge;
}
}
}
int cmp = memcmp(edges, newedges, sizeof(Edges)*ncols);
memcpy(edges, newedges, sizeof(Edges)*ncols);
return (cmp != 0);
}
// Return 1 if changed; 0 otherwise
bool infer_all_edges(const BinaryKmer node_bkey, Edges *edges,
const Covg *covgs, const dBGraph *db_graph)
{
Edges iedges = 0xff, edge;
size_t orient, nuc, col, kmer_size = db_graph->kmer_size;
const size_t ncols = db_graph->num_of_cols;
BinaryKmer bkey, bkmer;
hkey_t next;
Edges newedges[ncols];
memcpy(newedges, edges, ncols * sizeof(Edges));
// intersection of edges
for(col = 0; col < ncols; col++) iedges &= edges[col];
for(orient = 0; orient < 2; orient++)
{
bkmer = (orient == FORWARD ? binary_kmer_left_shift_one_base(node_bkey, kmer_size)
: binary_kmer_right_shift_one_base(node_bkey));
for(nuc = 0; nuc < 4; nuc++)
{
edge = nuc_orient_to_edge(nuc, orient);
if(!(iedges & edge))
{
// edges are missing from some samples
if(orient == FORWARD) binary_kmer_set_last_nuc(&bkmer, nuc);
else binary_kmer_set_first_nuc(&bkmer, dna_nuc_complement(nuc), kmer_size);
bkey = bkmer_get_key(bkmer, kmer_size);
next = hash_table_find(&db_graph->ht, bkey);
if(next != HASH_NOT_FOUND) {
for(col = 0; col < ncols; col++) {
if(covgs[col] > 0 && db_node_has_col(db_graph, next, col)) {
newedges[col] |= edge;
}
}
}
}
}
}
// Check if we changed the edges
int cmp = memcmp(edges, newedges, sizeof(Edges)*ncols);
memcpy(edges, newedges, sizeof(Edges)*ncols);
return (cmp != 0);
}
static char* binary_kmer_to_seq(uint64_t* bkmer, char * seq,
int kmer_size, int num_of_bitfields)
{
uint64_t local_bkmer[num_of_bitfields];
int i;
// Copy over a word at a time
for(i = 0; i < num_of_bitfields; i++)
{
local_bkmer[i] = bkmer[i];
}
// Loop backwards over bases
for(i = kmer_size-1; i >= 0; i--)
{
seq[i] = binary_nucleotide_to_char(local_bkmer[num_of_bitfields-1] & 0x3);
binary_kmer_right_shift_one_base(local_bkmer, num_of_bitfields);
}
seq[kmer_size] = '\0';
return seq;
}
// 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;
}
