// Using file so can call fseek and don't need to load whole graph
static size_t inferedges_on_mmap(const dBGraph *db_graph, bool add_all_edges,
GraphFileReader *file)
{
ctx_assert(db_graph->num_of_cols == file->hdr.num_of_cols);
ctx_assert(file_filter_is_direct(&file->fltr));
ctx_assert2(!isatty(fileno(file->fh)), "Use inferedges_on_stream() instead");
ctx_assert(file->num_of_kmers >= 0);
ctx_assert(file->file_size >= 0);
status("[inferedges] Processing mmap file: %s [hdr: %zu bytes file: %zu bytes]",
file_filter_path(&file->fltr),
(size_t)file->hdr_size, (size_t)file->file_size);
if(fseek(file->fh, 0, SEEK_SET) != 0)
die("fseek failed: %s", strerror(errno));
// Open memory mapped file
void *mmap_ptr = mmap(NULL, file->file_size, PROT_WRITE, MAP_SHARED,
fileno(file->fh), 0);
if(mmap_ptr == MAP_FAILED)
die("Cannot memory map file: %s [%s]", file->fltr.path.b, strerror(errno));
const size_t ncols = file->hdr.num_of_cols;
BinaryKmer bkmer;
Edges edges[ncols];
Covg covgs[ncols];
bool updated;
size_t i, num_kmers = file->num_of_kmers, num_kmers_edited = 0;
size_t filekmersize = sizeof(BinaryKmer) + (sizeof(Edges)+sizeof(Covg)) * ncols;
char *ptr = (char*)mmap_ptr + file->hdr_size;
for(i = 0; i < num_kmers; i++, ptr += filekmersize)
{
char *fh_covgs = ptr + sizeof(BinaryKmer);
char *fh_edges = fh_covgs + sizeof(Covg)*ncols;
memcpy(bkmer.b, ptr, sizeof(BinaryKmer));
memcpy(covgs, fh_covgs, ncols * sizeof(Covg));
memcpy(edges, fh_edges, ncols * sizeof(Edges));
updated = (add_all_edges ? infer_all_edges(bkmer, edges, covgs, db_graph)
: infer_pop_edges(bkmer, edges, covgs, db_graph));
if(updated) {
memcpy(fh_covgs, covgs, ncols * sizeof(Covg));
memcpy(fh_edges, edges, ncols * sizeof(Edges));
num_kmers_edited++;
}
}
if(munmap(mmap_ptr, file->file_size) == -1)
die("Cannot release mmap file: %s [%s]", file->fltr.path.b, strerror(errno));
return num_kmers_edited;
}
static inline void infer_edges_node(hkey_t hkey,
bool add_all_edges,
const dBGraph *db_graph,
size_t *num_nodes_modified)
{
BinaryKmer bkmer = db_node_bkmer(db_graph, hkey);
Edges *edges = &db_node_edges(db_graph, hkey, 0);
size_t col;
// Create coverages that are zero or one depending on if node has colour
Covg covgs[db_graph->num_of_cols];
for(col = 0; col < db_graph->num_of_cols; col++)
covgs[col] = db_node_has_col(db_graph, hkey, col);
(*num_nodes_modified)
+= (add_all_edges ? infer_all_edges(bkmer, edges, covgs, db_graph)
: infer_pop_edges(bkmer, edges, covgs, db_graph));
}
// Using file so can call fseek and don't need to load whole graph
static size_t inferedges_on_file(const dBGraph *db_graph, bool add_all_edges,
GraphFileReader *file, FILE *fout)
{
ctx_assert(db_graph->num_of_cols == file->hdr.num_of_cols);
ctx_assert(file_filter_is_direct(&file->fltr));
ctx_assert2(!isatty(fileno(file->fh)), "Use inferedges_on_stream() instead");
ctx_assert(fout != NULL);
ctx_assert(fileno(file->fh) != fileno(fout));
status("[inferedges] Processing file: %s", file_filter_path(&file->fltr));
// Print header
graph_write_header(fout, &file->hdr);
// Read the input file again
if(fseek(file->fh, file->hdr_size, SEEK_SET) != 0)
die("fseek failed: %s", strerror(errno));
const size_t ncols = file->hdr.num_of_cols;
BinaryKmer bkmer;
Edges edges[ncols];
Covg covgs[ncols];
size_t num_kmers_edited = 0;
bool updated;
while(graph_file_read_reset(file, ncols, &bkmer, covgs, edges))
{
updated = (add_all_edges ? infer_all_edges(bkmer, edges, covgs, db_graph)
: infer_pop_edges(bkmer, edges, covgs, db_graph));
graph_write_kmer(fout, file->hdr.num_of_bitfields, file->hdr.num_of_cols,
bkmer, covgs, edges);
num_kmers_edited += updated;
}
return num_kmers_edited;
}
static inline int infer_edges_node(hkey_t hkey,
bool add_all_edges,
Covg *tmp_covgs,
const dBGraph *db_graph,
size_t *num_nodes_modified)
{
BinaryKmer bkmer = db_node_get_bkmer(db_graph, hkey);
Edges *edges = &db_node_edges(db_graph, hkey, 0);
size_t col;
// Create coverages that are zero or one depending on if node has colour
if(db_graph->col_covgs == NULL) {
for(col = 0; col < db_graph->num_of_cols; col++)
tmp_covgs[col] = db_node_has_col(db_graph, hkey, col);
} else {
tmp_covgs = &db_node_covg(db_graph, hkey, 0);
}
(*num_nodes_modified)
+= (add_all_edges ? infer_all_edges(bkmer, edges, tmp_covgs, db_graph)
: infer_pop_edges(bkmer, edges, tmp_covgs, db_graph));
return 0; // => keep iterating
}
