int ctx_clean(int argc, char **argv) { size_t nthreads = 0, use_ncols = 0; struct MemArgs memargs = MEM_ARGS_INIT; const char *out_ctx_path = NULL; bool tip_cleaning = false, supernode_cleaning = false; size_t min_keep_tip = 0; Covg threshold = 0, fallback_thresh = 0; const char *len_before_path = NULL, *len_after_path = NULL; const char *covg_before_path = NULL, *covg_after_path = NULL; // Arg parsing char cmd[100]; char shortopts[300]; cmd_long_opts_to_short(longopts, shortopts, sizeof(shortopts)); int c; // silence error messages from getopt_long // opterr = 0; while((c = getopt_long(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 'f': cmd_check(!futil_get_force(), cmd); futil_set_force(true); break; case 'o': if(out_ctx_path != NULL) cmd_print_usage(NULL); out_ctx_path = optarg; break; case 'm': cmd_mem_args_set_memory(&memargs, optarg); break; case 'n': cmd_mem_args_set_nkmers(&memargs, optarg); break; case 'N': use_ncols = cmd_uint32_nonzero(cmd, optarg); break; case 't': cmd_check(!nthreads, cmd); nthreads = cmd_uint32_nonzero(cmd, optarg); break; case 'T': cmd_check(!tip_cleaning, cmd); min_keep_tip = cmd_uint32_nonzero(cmd, optarg); tip_cleaning = true; break; case 'S': cmd_check(!supernode_cleaning, cmd); if(optarg != NULL) threshold = cmd_uint32_nonzero(cmd, optarg); supernode_cleaning = true; break; case 'B': cmd_check(!fallback_thresh, cmd); fallback_thresh = cmd_uint32_nonzero(cmd, optarg); break; case 'l': cmd_check(!len_before_path, cmd); len_before_path = optarg; break; case 'L': cmd_check(!len_after_path, cmd); len_after_path = optarg; break; case 'c': cmd_check(!covg_before_path, cmd); covg_before_path = optarg; break; case 'C': cmd_check(!covg_after_path, cmd); covg_after_path = optarg; break; case ':': /* BADARG */ case '?': /* BADCH getopt_long has already printed error */ // cmd_print_usage(NULL); die("`"CMD" clean -h` for help. Bad option: %s", argv[optind-1]); default: abort(); } } if(nthreads == 0) nthreads = DEFAULT_NTHREADS; if(optind >= argc) cmd_print_usage("Please give input graph files"); // Default behaviour if(!tip_cleaning && !supernode_cleaning) { if(out_ctx_path != NULL) supernode_cleaning = tip_cleaning = true; // do both else warn("No cleaning being done: you did not specify --out <out.ctx>"); } bool doing_cleaning = (supernode_cleaning || tip_cleaning); if(doing_cleaning && out_ctx_path == NULL) { cmd_print_usage("Please specify --out <out.ctx> for cleaned graph"); } if(!doing_cleaning && (covg_after_path || len_after_path)) { cmd_print_usage("You gave --len-after <out> / --covg-after <out> without " "any cleaning (set -s, --supernodes or -t, --tips)"); } if(doing_cleaning && strcmp(out_ctx_path,"-") != 0 && !futil_get_force() && futil_file_exists(out_ctx_path)) { cmd_print_usage("Output file already exists: %s", out_ctx_path); } if(fallback_thresh && !supernode_cleaning) cmd_print_usage("-B, --fallback <T> without --supernodes"); // Use remaining args as graph files char **gfile_paths = argv + optind; size_t i, j, num_gfiles = (size_t)(argc - optind); // Open graph files GraphFileReader *gfiles = ctx_calloc(num_gfiles, sizeof(GraphFileReader)); size_t ncols, ctx_max_kmers = 0, ctx_sum_kmers = 0; ncols = graph_files_open(gfile_paths, gfiles, num_gfiles, &ctx_max_kmers, &ctx_sum_kmers); size_t kmer_size = gfiles[0].hdr.kmer_size; // default to one colour for now if(use_ncols == 0) use_ncols = 1; // Flatten if we don't have to remember colours / output a graph if(!doing_cleaning) { ncols = use_ncols = 1; for(i = 0; i < num_gfiles; i++) file_filter_flatten(&gfiles[i].fltr, 0); } if(ncols < use_ncols) { warn("I only need %zu colour%s ('--ncols %zu' ignored)", ncols, util_plural_str(ncols), use_ncols); use_ncols = ncols; } char max_kmers_str[100]; ulong_to_str(ctx_max_kmers, max_kmers_str); status("%zu input graph%s, max kmers: %s, using %zu colours", num_gfiles, util_plural_str(num_gfiles), max_kmers_str, use_ncols); // If no arguments given we default to removing tips < 2*kmer_size if(tip_cleaning && min_keep_tip == 0) min_keep_tip = 2 * kmer_size; // Warn if any graph files already cleaned size_t fromcol, intocol; ErrorCleaning *cleaning; for(i = 0; i < num_gfiles; i++) { for(j = 0; j < file_filter_num(&gfiles[i].fltr); j++) { fromcol = file_filter_fromcol(&gfiles[i].fltr, j); cleaning = &gfiles[i].hdr.ginfo[fromcol].cleaning; if(cleaning->cleaned_snodes && supernode_cleaning) { warn("%s:%zu already has supernode cleaning with threshold: <%zu", file_filter_path(&gfiles[i].fltr), fromcol, (size_t)cleaning->clean_snodes_thresh); } if(cleaning->cleaned_tips && tip_cleaning) { warn("%s:%zu already has had tip cleaned", file_filter_path(&gfiles[i].fltr), fromcol); } } } // Print steps size_t step = 0; status("Actions:\n"); if(covg_before_path != NULL) status("%zu. Saving kmer coverage distribution to: %s", step++, covg_before_path); if(len_before_path != NULL) status("%zu. Saving supernode length distribution to: %s", step++, len_before_path); if(tip_cleaning) status("%zu. Cleaning tips shorter than %zu nodes", step++, min_keep_tip); if(supernode_cleaning && threshold > 0) status("%zu. Cleaning supernodes with coverage < %u", step++, threshold); if(supernode_cleaning && threshold <= 0) status("%zu. Cleaning supernodes with auto-detected threshold", step++); if(covg_after_path != NULL) status("%zu. Saving kmer coverage distribution to: %s", step++, covg_after_path); if(len_after_path != NULL) status("%zu. Saving supernode length distribution to: %s", step++, len_after_path); // // Decide memory usage // bool all_colours_loaded = (ncols <= use_ncols); bool use_mem_limit = (memargs.mem_to_use_set && num_gfiles > 1) || !ctx_max_kmers; size_t kmers_in_hash, bits_per_kmer, graph_mem; size_t per_kmer_per_col_bits = (sizeof(BinaryKmer)+sizeof(Covg)+sizeof(Edges)) * 8; size_t pop_edges_per_kmer_bits = (all_colours_loaded ? 0 : sizeof(Edges) * 8); bits_per_kmer = per_kmer_per_col_bits * use_ncols + pop_edges_per_kmer_bits; 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, use_mem_limit, &graph_mem); // Maximise the number of colours we load to fill the mem size_t max_usencols = (memargs.mem_to_use*8 - pop_edges_per_kmer_bits * kmers_in_hash) / (per_kmer_per_col_bits * kmers_in_hash); use_ncols = MIN2(max_usencols, ncols); cmd_check_mem_limit(memargs.mem_to_use, graph_mem); // // Check output files are writable // futil_create_output(out_ctx_path); // Does nothing if arg is NULL futil_create_output(covg_before_path); futil_create_output(covg_after_path); futil_create_output(len_before_path); futil_create_output(len_after_path); // Create db_graph // Load as many colours as possible // Use an extra set of edge to take intersections dBGraph db_graph; db_graph_alloc(&db_graph, gfiles[0].hdr.kmer_size, use_ncols, use_ncols, kmers_in_hash, DBG_ALLOC_COVGS); // Edges is a special case size_t num_edges = db_graph.ht.capacity * (use_ncols + !all_colours_loaded); db_graph.col_edges = ctx_calloc(num_edges, sizeof(Edges)); // Load graph into a single colour LoadingStats stats = LOAD_STATS_INIT_MACRO; GraphLoadingPrefs gprefs = {.db_graph = &db_graph, .boolean_covgs = false, .must_exist_in_graph = false, .must_exist_in_edges = NULL, .empty_colours = false}; // Construct cleaned graph header GraphFileHeader outhdr; memset(&outhdr, 0, sizeof(GraphFileHeader)); outhdr.version = CTX_GRAPH_FILEFORMAT; outhdr.kmer_size = db_graph.kmer_size; outhdr.num_of_cols = ncols; outhdr.num_of_bitfields = (db_graph.kmer_size*2+63)/64; graph_header_alloc(&outhdr, ncols); // Merge info into header size_t gcol = 0; for(i = 0; i < num_gfiles; i++) { for(j = 0; j < file_filter_num(&gfiles[i].fltr); j++, gcol++) { fromcol = file_filter_fromcol(&gfiles[i].fltr, j); intocol = file_filter_intocol(&gfiles[i].fltr, j); graph_info_merge(&outhdr.ginfo[intocol], &gfiles[i].hdr.ginfo[fromcol]); } } if(ncols > use_ncols) { graph_files_load_flat(gfiles, num_gfiles, gprefs, &stats); } else { for(i = 0; i < num_gfiles; i++) graph_load(&gfiles[i], gprefs, &stats); } char num_kmers_str[100]; ulong_to_str(db_graph.ht.num_kmers, num_kmers_str); status("Total kmers loaded: %s\n", num_kmers_str); size_t initial_nkmers = db_graph.ht.num_kmers; hash_table_print_stats(&db_graph.ht); uint8_t *visited = ctx_calloc(roundup_bits2bytes(db_graph.ht.capacity), 1); uint8_t *keep = ctx_calloc(roundup_bits2bytes(db_graph.ht.capacity), 1); if((supernode_cleaning && threshold <= 0) || covg_before_path || len_before_path) { // Get coverage distribution and estimate cleaning threshold int est_threshold = cleaning_get_threshold(nthreads, covg_before_path, len_before_path, visited, &db_graph); if(est_threshold < 0) status("Cannot find recommended cleaning threshold"); else status("Recommended cleaning threshold is: %i", est_threshold); // Use estimated threshold if threshold not set if(threshold <= 0) { if(fallback_thresh > 0 && est_threshold < (int)fallback_thresh) { status("Using fallback threshold: %i", fallback_thresh); threshold = fallback_thresh; } else if(est_threshold >= 0) threshold = est_threshold; } } // Die if we failed to find suitable cleaning threshold if(supernode_cleaning && threshold <= 0) die("Need cleaning threshold (--supernodes=<D> or --fallback <D>)"); if(doing_cleaning) { // Clean graph of tips (if min_keep_tip > 0) and supernodes (if threshold > 0) clean_graph(nthreads, threshold, min_keep_tip, covg_after_path, len_after_path, visited, keep, &db_graph); } ctx_free(visited); ctx_free(keep); if(doing_cleaning) { // Output graph file Edges *intersect_edges = NULL; bool kmers_loaded = true; size_t col, thresh; // Set output header ginfo cleaned for(col = 0; col < ncols; col++) { cleaning = &outhdr.ginfo[col].cleaning; cleaning->cleaned_snodes |= supernode_cleaning; cleaning->cleaned_tips |= tip_cleaning; // if(tip_cleaning) { // strbuf_append_str(&outhdr.ginfo[col].sample_name, ".tipclean"); // } if(supernode_cleaning) { thresh = cleaning->clean_snodes_thresh; thresh = cleaning->cleaned_snodes ? MAX2(thresh, (uint32_t)threshold) : (uint32_t)threshold; cleaning->clean_snodes_thresh = thresh; // char name_append[200]; // sprintf(name_append, ".supclean%zu", thresh); // strbuf_append_str(&outhdr.ginfo[col].sample_name, name_append); } } if(!all_colours_loaded) { // We haven't loaded all the colours // intersect_edges are edges to mask with // resets graph edges intersect_edges = db_graph.col_edges; db_graph.col_edges += db_graph.ht.capacity; } // Print stats on removed kmers size_t removed_nkmers = initial_nkmers - db_graph.ht.num_kmers; double removed_pct = (100.0 * removed_nkmers) / initial_nkmers; char removed_str[100], init_str[100]; ulong_to_str(removed_nkmers, removed_str); ulong_to_str(initial_nkmers, init_str); status("Removed %s of %s (%.2f%%) kmers", removed_str, init_str, removed_pct); graph_files_merge(out_ctx_path, gfiles, num_gfiles, kmers_loaded, all_colours_loaded, intersect_edges, &outhdr, &db_graph); // Swap back if(!all_colours_loaded) db_graph.col_edges = intersect_edges; } ctx_check(db_graph.ht.num_kmers == hash_table_count_kmers(&db_graph.ht)); graph_header_dealloc(&outhdr); for(i = 0; i < num_gfiles; i++) graph_file_close(&gfiles[i]); ctx_free(gfiles); db_graph_dealloc(&db_graph); return EXIT_SUCCESS; }
int ctx_clean(int argc, char **argv) { size_t nthreads = 0, use_ncols = 0; struct MemArgs memargs = MEM_ARGS_INIT; const char *out_ctx_path = NULL; int min_keep_tip = -1, unitig_min = -1; // <0 => default, 0 => noclean uint32_t fallback_thresh = 0; const char *len_before_path = NULL, *len_after_path = NULL; const char *covg_before_path = NULL, *covg_after_path = NULL; // Arg parsing char cmd[100]; char shortopts[300]; cmd_long_opts_to_short(longopts, shortopts, sizeof(shortopts)); int c; // silence error messages from getopt_long // opterr = 0; while((c = getopt_long(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 'f': cmd_check(!futil_get_force(), cmd); futil_set_force(true); break; case 'o': if(out_ctx_path != NULL) cmd_print_usage(NULL); out_ctx_path = optarg; break; case 'm': cmd_mem_args_set_memory(&memargs, optarg); break; case 'n': cmd_mem_args_set_nkmers(&memargs, optarg); break; case 'N': use_ncols = cmd_uint32_nonzero(cmd, optarg); break; case 't': cmd_check(!nthreads, cmd); nthreads = cmd_uint32_nonzero(cmd, optarg); break; case 'T': cmd_check(min_keep_tip<0, cmd); min_keep_tip = (optarg != NULL ? (int)cmd_uint32(cmd, optarg) : -1); break; case 'S': case 'U': cmd_check(unitig_min<0, cmd); unitig_min = (optarg != NULL ? cmd_uint32(cmd, optarg) : -1); break; case 'B': cmd_check(!fallback_thresh, cmd); fallback_thresh = cmd_uint32_nonzero(cmd, optarg); break; case 'l': cmd_check(!len_before_path, cmd); len_before_path = optarg; break; case 'L': cmd_check(!len_after_path, cmd); len_after_path = optarg; break; case 'c': cmd_check(!covg_before_path, cmd); covg_before_path = optarg; break; case 'C': cmd_check(!covg_after_path, cmd); covg_after_path = optarg; break; case ':': /* BADARG */ case '?': /* BADCH getopt_long has already printed error */ // cmd_print_usage(NULL); die("`"CMD" clean -h` for help. Bad option: %s", argv[optind-1]); default: abort(); } } if(nthreads == 0) nthreads = DEFAULT_NTHREADS; if(optind >= argc) cmd_print_usage("Please give input graph files"); bool unitig_cleaning = (unitig_min != 0); bool tip_cleaning = (min_keep_tip != 0); bool doing_cleaning = (unitig_cleaning || tip_cleaning); // If you ever want to estimate cleaning threshold without outputting // a graph, change this to a warning if(doing_cleaning && out_ctx_path == NULL) { cmd_print_usage("Please specify --out <out.ctx> for cleaned graph"); // warn("No cleaning being done: you did not specify --out <out.ctx>"); } if(!doing_cleaning && (covg_after_path || len_after_path)) { warn("You gave --len-after <out> / --covg-after <out> without " "any cleaning (set -U, --unitigs or -t, --tips)"); } if(doing_cleaning && strcmp(out_ctx_path,"-") != 0 && !futil_get_force() && futil_file_exists(out_ctx_path)) { cmd_print_usage("Output file already exists: %s", out_ctx_path); } if(fallback_thresh && !unitig_cleaning) warn("-B, --fallback <T> without --unitigs"); // Use remaining args as graph files char **gfile_paths = argv + optind; size_t i, j, num_gfiles = (size_t)(argc - optind); // Open graph files GraphFileReader *gfiles = ctx_calloc(num_gfiles, sizeof(GraphFileReader)); size_t col, ncols, ctx_max_kmers = 0, ctx_sum_kmers = 0; ncols = graph_files_open(gfile_paths, gfiles, num_gfiles, &ctx_max_kmers, &ctx_sum_kmers); size_t kmer_size = gfiles[0].hdr.kmer_size; // default to one colour for now if(use_ncols == 0) use_ncols = 1; // Flatten if we don't have to remember colours / output a graph if(out_ctx_path == NULL) { ncols = use_ncols = 1; for(i = 0; i < num_gfiles; i++) file_filter_flatten(&gfiles[i].fltr, 0); } if(ncols < use_ncols) { warn("I only need %zu colour%s ('--ncols %zu' ignored)", ncols, util_plural_str(ncols), use_ncols); use_ncols = ncols; } char max_kmers_str[100]; ulong_to_str(ctx_max_kmers, max_kmers_str); status("%zu input graph%s, max kmers: %s, using %zu colours", num_gfiles, util_plural_str(num_gfiles), max_kmers_str, use_ncols); // If no arguments given we default to removing tips < 2*kmer_size if(min_keep_tip < 0) min_keep_tip = 2 * kmer_size; // Warn if any graph files already cleaned size_t fromcol; ErrorCleaning *cleaning; for(i = 0; i < num_gfiles; i++) { for(j = 0; j < file_filter_num(&gfiles[i].fltr); j++) { fromcol = file_filter_fromcol(&gfiles[i].fltr, j); cleaning = &gfiles[i].hdr.ginfo[fromcol].cleaning; if(cleaning->cleaned_snodes && unitig_cleaning) { warn("%s:%zu already has unitig cleaning with threshold: <%zu", file_filter_path(&gfiles[i].fltr), fromcol, (size_t)cleaning->clean_snodes_thresh); } if(cleaning->cleaned_tips && tip_cleaning) { warn("%s:%zu already has had tip cleaned", file_filter_path(&gfiles[i].fltr), fromcol); } } } // Print steps size_t step = 0; status("Actions:\n"); if(covg_before_path != NULL) status("%zu. Saving kmer coverage distribution to: %s", step++, covg_before_path); if(len_before_path != NULL) status("%zu. Saving unitig length distribution to: %s", step++, len_before_path); if(min_keep_tip > 0) status("%zu. Cleaning tips shorter than %i nodes", step++, min_keep_tip); if(unitig_min > 0) status("%zu. Cleaning unitigs with coverage < %i", step++, unitig_min); if(unitig_min < 0) status("%zu. Cleaning unitigs with auto-detected threshold", step++); if(covg_after_path != NULL) status("%zu. Saving kmer coverage distribution to: %s", step++, covg_after_path); if(len_after_path != NULL) status("%zu. Saving unitig length distribution to: %s", step++, len_after_path); // // Decide memory usage // bool all_colours_loaded = (ncols <= use_ncols); bool use_mem_limit = (memargs.mem_to_use_set && num_gfiles > 1) || !ctx_max_kmers; size_t kmers_in_hash, bits_per_kmer, graph_mem; size_t per_col_bits = (sizeof(Covg)+sizeof(Edges)) * 8; size_t extra_edge_bits = (all_colours_loaded ? 0 : sizeof(Edges) * 8); bits_per_kmer = sizeof(BinaryKmer)*8 + per_col_bits * use_ncols + extra_edge_bits; 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, use_mem_limit, &graph_mem); // Maximise the number of colours we load to fill the mem size_t max_usencols = (memargs.mem_to_use*8 - sizeof(BinaryKmer)*8*kmers_in_hash + extra_edge_bits*kmers_in_hash) / (per_col_bits*kmers_in_hash); use_ncols = MIN2(max_usencols, ncols); cmd_check_mem_limit(memargs.mem_to_use, graph_mem); // // Check output files are writable // futil_create_output(out_ctx_path); // Does nothing if arg is NULL futil_create_output(covg_before_path); futil_create_output(covg_after_path); futil_create_output(len_before_path); futil_create_output(len_after_path); // Create db_graph // Load as many colours as possible // Use an extra set of edge to take intersections dBGraph db_graph; db_graph_alloc(&db_graph, gfiles[0].hdr.kmer_size, use_ncols, use_ncols, kmers_in_hash, DBG_ALLOC_EDGES | DBG_ALLOC_COVGS); // Extra edges required to hold union of kept edges Edges *edges_union = NULL; if(use_ncols < ncols) edges_union = ctx_calloc(db_graph.ht.capacity, sizeof(Edges)); // Load graph into a single colour GraphLoadingPrefs gprefs = graph_loading_prefs(&db_graph); // Construct cleaned graph header GraphFileHeader outhdr; memset(&outhdr, 0, sizeof(GraphFileHeader)); for(i = 0; i < num_gfiles; i++) graph_file_merge_header(&outhdr, &gfiles[i]); if(ncols > use_ncols) { db_graph.num_of_cols = db_graph.num_edge_cols = 1; SWAP(edges_union, db_graph.col_edges); graphs_load_files_flat(gfiles, num_gfiles, gprefs, NULL); SWAP(edges_union, db_graph.col_edges); db_graph.num_of_cols = db_graph.num_edge_cols = use_ncols; } else { for(i = 0; i < num_gfiles; i++) graph_load(&gfiles[i], gprefs, NULL); } char num_kmers_str[100]; ulong_to_str(db_graph.ht.num_kmers, num_kmers_str); status("Total kmers loaded: %s\n", num_kmers_str); size_t initial_nkmers = db_graph.ht.num_kmers; hash_table_print_stats(&db_graph.ht); uint8_t *visited = ctx_calloc(roundup_bits2bytes(db_graph.ht.capacity), 1); uint8_t *keep = ctx_calloc(roundup_bits2bytes(db_graph.ht.capacity), 1); // Always estimate cleaning threshold // if(unitig_min <= 0 || covg_before_path || len_before_path) // { // Get coverage distribution and estimate cleaning threshold int est_min_covg = cleaning_get_threshold(nthreads, covg_before_path, len_before_path, visited, &db_graph); if(est_min_covg < 0) status("Cannot find recommended cleaning threshold"); else status("Recommended cleaning threshold is: %i", est_min_covg); // Use estimated threshold if threshold not set if(unitig_min < 0) { if(fallback_thresh > 0 && est_min_covg < (int)fallback_thresh) { status("Using fallback threshold: %i", fallback_thresh); unitig_min = fallback_thresh; } else if(est_min_covg >= 0) unitig_min = est_min_covg; } // } // Die if we failed to find suitable cleaning threshold if(unitig_min < 0) die("Need cleaning threshold (--unitigs=<D> or --fallback <D>)"); // Cleaning parameters should now be set (>0) or turned off (==0) ctx_assert(unitig_min >= 0); ctx_assert(min_keep_tip >= 0); if(unitig_min || min_keep_tip) { // Clean graph of tips (if min_keep_tip > 0) and unitigs (if threshold > 0) clean_graph(nthreads, unitig_min, min_keep_tip, covg_after_path, len_after_path, visited, keep, &db_graph); } ctx_free(visited); ctx_free(keep); if(out_ctx_path != NULL) { // Set output header ginfo cleaned for(col = 0; col < ncols; col++) { cleaning = &outhdr.ginfo[col].cleaning; cleaning->cleaned_snodes |= unitig_cleaning; cleaning->cleaned_tips |= tip_cleaning; // if(tip_cleaning) { // strbuf_append_str(&outhdr.ginfo[col].sample_name, ".tipclean"); // } if(unitig_cleaning) { size_t thresh = cleaning->clean_snodes_thresh; thresh = cleaning->cleaned_snodes ? MAX2(thresh, (uint32_t)unitig_min) : (uint32_t)unitig_min; cleaning->clean_snodes_thresh = thresh; // char name_append[200]; // sprintf(name_append, ".supclean%zu", thresh); // strbuf_append_str(&outhdr.ginfo[col].sample_name, name_append); } } // Print stats on removed kmers size_t removed_nkmers = initial_nkmers - db_graph.ht.num_kmers; double removed_pct = (100.0 * removed_nkmers) / initial_nkmers; char removed_str[100], init_str[100]; ulong_to_str(removed_nkmers, removed_str); ulong_to_str(initial_nkmers, init_str); status("Removed %s of %s (%.2f%%) kmers", removed_str, init_str, removed_pct); // kmers_loaded=true graph_writer_merge(out_ctx_path, gfiles, num_gfiles, true, all_colours_loaded, edges_union, &outhdr, &db_graph); } ctx_check(db_graph.ht.num_kmers == hash_table_count_kmers(&db_graph.ht)); // TODO: report kmer coverage for each sample graph_header_dealloc(&outhdr); for(i = 0; i < num_gfiles; i++) graph_file_close(&gfiles[i]); ctx_free(gfiles); ctx_free(edges_union); db_graph_dealloc(&db_graph); return EXIT_SUCCESS; }