// if one of the files is reading from stdin, sum_kmers_ptr is set to 0
// `max_cols_ptr` is used to return the most colours being loaded from a single file
// returns the number of colours being loaded in total
size_t graph_files_open(char **graph_paths,
GraphFileReader *gfiles, size_t num_gfiles,
size_t *max_kmers_ptr, size_t *sum_kmers_ptr)
{
size_t i, ctx_max_kmers = 0, ctx_sum_kmers = 0;
bool ctx_uses_stdin = false;
size_t ncols = 0;
for(i = 0; i < num_gfiles; i++)
{
memset(&gfiles[i], 0, sizeof(GraphFileReader));
graph_file_open2(&gfiles[i], graph_paths[i], "r", ncols);
if(gfiles[0].hdr.kmer_size != gfiles[i].hdr.kmer_size) {
cmd_print_usage("Kmer sizes don't match [%u vs %u]",
gfiles[0].hdr.kmer_size, gfiles[i].hdr.kmer_size);
}
ncols = MAX2(ncols, file_filter_into_ncols(&gfiles[i].fltr));
ctx_max_kmers = MAX2(ctx_max_kmers, graph_file_nkmers(&gfiles[i]));
ctx_sum_kmers += graph_file_nkmers(&gfiles[i]);
ctx_uses_stdin |= file_filter_isstdin(&gfiles[i].fltr);
}
if(ctx_uses_stdin) ctx_sum_kmers = SIZE_MAX;
*max_kmers_ptr = ctx_max_kmers;
*sum_kmers_ptr = ctx_sum_kmers;
return ncols;
}
int ctx_join(int argc, char **argv)
{
struct MemArgs memargs = MEM_ARGS_INIT;
const char *out_path = NULL;
size_t use_ncols = 0;
GraphFileReader tmp_gfile;
GraphFileBuffer isec_gfiles_buf;
gfile_buf_alloc(&isec_gfiles_buf, 8);
// Arg parsing
char cmd[100], shortopts[100];
cmd_long_opts_to_short(longopts, shortopts, sizeof(shortopts));
int c;
while((c = getopt_long_only(argc, argv, shortopts, longopts, NULL)) != -1) {
cmd_get_longopt_str(longopts, c, cmd, sizeof(cmd));
switch(c) {
case 0: /* flag set */ break;
case 'h': cmd_print_usage(NULL); break;
case 'o': cmd_check(!out_path, cmd); out_path = optarg; break;
case 'f': cmd_check(!futil_get_force(), cmd); futil_set_force(true); break;
case 'm': cmd_mem_args_set_memory(&memargs, optarg); break;
case 'n': cmd_mem_args_set_nkmers(&memargs, optarg); break;
case 'N': cmd_check(!use_ncols, cmd); use_ncols = cmd_uint32_nonzero(cmd, optarg); break;
case 'i':
graph_file_reset(&tmp_gfile);
graph_file_open(&tmp_gfile, optarg);
if(file_filter_into_ncols(&tmp_gfile.fltr) > 1)
warn("Flattening intersection graph into colour 0: %s", optarg);
file_filter_flatten(&tmp_gfile.fltr, 0);
gfile_buf_push(&isec_gfiles_buf, &tmp_gfile, 1);
break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
die("`"CMD" join -h` for help. Bad option: %s", argv[optind-1]);
default: abort();
}
}
GraphFileReader *igfiles = isec_gfiles_buf.b;
size_t num_igfiles = isec_gfiles_buf.len;
if(!out_path) cmd_print_usage("--out <out.ctx> required");
if(optind >= argc)
cmd_print_usage("Please specify at least one input graph file");
// optind .. argend-1 are graphs to load
size_t num_gfiles = (size_t)(argc - optind);
char **gfile_paths = argv + optind;
GraphFileReader *gfiles = ctx_calloc(num_gfiles, sizeof(GraphFileReader));
status("Probing %zu graph files and %zu intersect files", num_gfiles, num_igfiles);
// Check all binaries are valid binaries with matching kmer size
size_t i;
size_t ctx_max_cols = 0;
uint64_t min_intersect_num_kmers = 0, ctx_max_kmers = 0, ctx_sum_kmers = 0;
for(i = 0; i < num_gfiles; i++)
{
graph_file_open2(&gfiles[i], gfile_paths[i], "r", true, ctx_max_cols);
if(gfiles[0].hdr.kmer_size != gfiles[i].hdr.kmer_size) {
cmd_print_usage("Kmer sizes don't match [%u vs %u]",
gfiles[0].hdr.kmer_size, gfiles[i].hdr.kmer_size);
}
ctx_max_cols = MAX2(ctx_max_cols, file_filter_into_ncols(&gfiles[i].fltr));
ctx_max_kmers = MAX2(ctx_max_kmers, graph_file_nkmers(&gfiles[i]));
ctx_sum_kmers += graph_file_nkmers(&gfiles[i]);
}
// Probe intersection graph files
for(i = 0; i < num_igfiles; i++)
{
if(gfiles[0].hdr.kmer_size != igfiles[i].hdr.kmer_size) {
cmd_print_usage("Kmer sizes don't match [%u vs %u]",
gfiles[0].hdr.kmer_size, igfiles[i].hdr.kmer_size);
}
uint64_t nkmers = graph_file_nkmers(&igfiles[i]);
if(i == 0) min_intersect_num_kmers = nkmers;
else if(nkmers < min_intersect_num_kmers)
{
// Put smallest intersection binary first
SWAP(igfiles[i], igfiles[0]);
min_intersect_num_kmers = nkmers;
}
}
bool take_intersect = (num_igfiles > 0);
// If we are taking an intersection,
// all kmers intersection kmers will need to be loaded
if(take_intersect)
ctx_max_kmers = ctx_sum_kmers = min_intersect_num_kmers;
bool use_ncols_set = (use_ncols > 0);
bool output_to_stdout = (strcmp(out_path,"-") == 0);
// if(use_ncols == 0) use_ncols = 1;
if(use_ncols_set) {
if(use_ncols < ctx_max_cols && output_to_stdout)
die("I need %zu colours if outputting to STDOUT (--ncols)", ctx_max_cols);
if(use_ncols > ctx_max_cols) {
warn("I only need %zu colour%s ('--ncols %zu' ignored)",
ctx_max_cols, util_plural_str(ctx_max_cols), use_ncols);
use_ncols = ctx_max_cols;
}
}
else {
use_ncols = output_to_stdout ? ctx_max_cols : 1;
}
// Check out_path is writable
futil_create_output(out_path);
status("Output %zu cols; from %zu files; intersecting %zu graphs; ",
ctx_max_cols, num_gfiles, num_igfiles);
if(num_gfiles == 1 && num_igfiles == 0)
{
// Loading only one file with no intersection files
// Don't need to store a graph in memory, can filter as stream
// Don't actually store anything in the de Bruijn graph, but we need to
// pass it, so mock one up
dBGraph db_graph;
db_graph_alloc(&db_graph, gfiles[0].hdr.kmer_size,
file_filter_into_ncols(&gfiles[0].fltr), 0, 1024, 0);
graph_writer_stream_mkhdr(out_path, &gfiles[0], &db_graph, NULL, NULL);
graph_file_close(&gfiles[0]);
gfile_buf_dealloc(&isec_gfiles_buf);
ctx_free(gfiles);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}
//
// Decide on memory
//
size_t bits_per_kmer, kmers_in_hash, graph_mem;
bits_per_kmer = sizeof(BinaryKmer)*8 +
(sizeof(Covg) + sizeof(Edges)) * 8 * use_ncols;
kmers_in_hash = cmd_get_kmers_in_hash(memargs.mem_to_use,
memargs.mem_to_use_set,
memargs.num_kmers,
memargs.num_kmers_set,
bits_per_kmer,
ctx_max_kmers, ctx_sum_kmers,
true, &graph_mem);
if(!use_ncols_set)
{
// Maximise use_ncols
size_t max_usencols = (memargs.mem_to_use*8) / bits_per_kmer;
use_ncols = MIN2(max_usencols, ctx_max_cols);
bits_per_kmer = sizeof(BinaryKmer)*8 +
(sizeof(Covg) + sizeof(Edges)) * 8 * use_ncols;
// Re-check memory used
kmers_in_hash = cmd_get_kmers_in_hash(memargs.mem_to_use,
memargs.mem_to_use_set,
memargs.num_kmers,
memargs.num_kmers_set,
bits_per_kmer,
ctx_max_kmers, ctx_sum_kmers,
true, &graph_mem);
}
status("Using %zu colour%s in memory", use_ncols, util_plural_str(use_ncols));
cmd_check_mem_limit(memargs.mem_to_use, graph_mem);
// Create db_graph
dBGraph db_graph;
Edges *intersect_edges = NULL;
size_t edge_cols = (use_ncols + take_intersect);
db_graph_alloc(&db_graph, gfiles[0].hdr.kmer_size, use_ncols, use_ncols,
kmers_in_hash, DBG_ALLOC_COVGS);
// We allocate edges ourself since it's a special case
db_graph.col_edges = ctx_calloc(db_graph.ht.capacity*edge_cols, sizeof(Edges));
// Load intersection binaries
char *intsct_gname_ptr = NULL;
StrBuf intersect_gname;
strbuf_alloc(&intersect_gname, 1024);
if(take_intersect)
{
GraphLoadingPrefs gprefs = graph_loading_prefs(&db_graph);
gprefs.boolean_covgs = true; // covg++ only
for(i = 0; i < num_igfiles; i++)
{
graph_load(&igfiles[i], gprefs, NULL);
// Update intersect header
// note: intersection graphs all load exactly one colour into colour 0
graph_info_make_intersect(&igfiles[i].hdr.ginfo[0], &intersect_gname);
gprefs.must_exist_in_graph = true;
gprefs.must_exist_in_edges = db_graph.col_edges;
}
if(num_igfiles > 1)
{
// Remove nodes where covg != num_igfiles
HASH_ITERATE_SAFE(&db_graph.ht, remove_non_intersect_nodes,
db_graph.col_covgs, (Covg)num_igfiles, &db_graph.ht);
}
status("Loaded intersection set\n");
intsct_gname_ptr = intersect_gname.b;
for(i = 0; i < num_igfiles; i++) graph_file_close(&igfiles[i]);
// Reset graph info
for(i = 0; i < db_graph.num_of_cols; i++)
graph_info_init(&db_graph.ginfo[i]);
// Zero covgs
memset(db_graph.col_covgs, 0, db_graph.ht.capacity * sizeof(Covg));
// Use union edges we loaded to intersect new edges
intersect_edges = db_graph.col_edges;
db_graph.col_edges += db_graph.ht.capacity;
}
bool kmers_loaded = take_intersect, colours_loaded = false;
graph_writer_merge_mkhdr(out_path, gfiles, num_gfiles,
kmers_loaded, colours_loaded, intersect_edges,
intsct_gname_ptr, &db_graph);
if(take_intersect)
db_graph.col_edges -= db_graph.ht.capacity;
for(i = 0; i < num_gfiles; i++) graph_file_close(&gfiles[i]);
strbuf_dealloc(&intersect_gname);
gfile_buf_dealloc(&isec_gfiles_buf);
ctx_free(gfiles);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}
