// 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; }
int ctx_view(int argc, char **argv) { // Arg parsing char cmd[100]; char shortopts[300]; cmd_long_opts_to_short(longopts, shortopts, sizeof(shortopts)); int c; // TODO: // print_action actions[argc]; // bool read_kmers = false; // silence error messages from getopt_long // opterr = 0; 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 ':': /* BADARG */ case '?': /* BADCH getopt_long has already printed error */ // cmd_print_usage(NULL); cmd_print_usage("`"CMD" "SUBCMD" -h` for help. Bad option: %s", argv[optind-1]); default: cmd_print_usage("Programmer fail. Tell Isaac."); } } if(print_kmers) parse_kmers = 1; bool no_flags = (!print_info && !parse_kmers && !print_kmers); if(no_flags) { print_info = parse_kmers = 1; } if(optind+1 != argc) cmd_print_usage("Require one input graph file (.ctx)"); char *path = argv[optind]; size_t num_errors = 0, num_warnings = 0; GraphFileReader gfile; memset(&gfile, 0, sizeof(gfile)); int ret = graph_file_open(&gfile, path); if(ret == 0) die("Cannot open file: %s", path); if(print_info) { char fsize_str[50]; bytes_to_str((size_t)gfile.file_size, 0, fsize_str); printf("Loading file: %s\n", file_filter_path(&gfile.fltr)); printf("File size: %s\n", fsize_str); printf("----\n"); } size_t i, col, ncols = file_filter_into_ncols(&gfile.fltr); size_t kmer_size = gfile.hdr.kmer_size; ctx_assert(ncols > 0); GraphFileHeader hdr; memset(&hdr, 0, sizeof(hdr)); graph_file_merge_header(&hdr, &gfile); uint64_t nkmers_read = 0, nkmers_loaded = 0; uint64_t num_all_zero_kmers = 0, num_zero_covg_kmers = 0; uint64_t *col_nkmers, *col_sum_covgs; col_nkmers = ctx_calloc(ncols, sizeof(col_nkmers[0])); col_sum_covgs = ctx_calloc(ncols, sizeof(col_sum_covgs[0])); // Print header if(print_info) print_header(&hdr, gfile.num_of_kmers); BinaryKmer bkmer; Covg covgs[ncols], keep_kmer; Edges edges[ncols]; bool direct_read = file_filter_is_direct(&gfile.fltr); if(parse_kmers || print_kmers) { if(print_info && print_kmers) printf("----\n"); for(; graph_file_read_reset(&gfile, &bkmer, covgs, edges); nkmers_read++) { // If kmer has no covg in any samples -> don't load keep_kmer = 0; for(col = 0; col < ncols; col++) { col_nkmers[col] += (covgs[col] > 0); col_sum_covgs[col] += covgs[col]; keep_kmer |= covgs[col]; } if(!direct_read && !keep_kmer) continue; nkmers_loaded++; /* Kmer Checks */ // graph_file_read_reset() already checks for: // 1. oversized kmers // 2. kmers with covg 0 in all colours // 3. edges without coverage in a colour // Check for all-zeros (i.e. all As kmer: AAAAAA) uint64_t kmer_words_or = 0; for(i = 0; i < hdr.num_of_bitfields; i++) kmer_words_or |= bkmer.b[i]; if(kmer_words_or == 0) { if(num_all_zero_kmers == 1) { loading_error("more than one all 'A's kmers seen [index: %"PRIu64"]\n", nkmers_read); } num_all_zero_kmers++; } // Check covg is 0 for all colours for(i = 0; i < ncols && covgs[i] == 0; i++); num_zero_covg_kmers += (i == ncols); // Print if(print_kmers) db_graph_print_kmer2(bkmer, covgs, edges, ncols, kmer_size, stdout); } } // check for various reading errors // if(errno != 0) // loading_error("errno set [%i]: %s\n", (int)errno, strerror(errno)); int err = ferror(gfile.fh); if(err != 0) loading_error("occurred after file reading [%i]\n", err); char nstr[50]; if(print_kmers || parse_kmers) { // file_size is set to -1 if we are reading from a stream, // therefore won't be able to check number of kmers read if(gfile.file_size != -1 && nkmers_read != (uint64_t)gfile.num_of_kmers) { loading_warning("Expected %zu kmers, read %zu\n", (size_t)gfile.num_of_kmers, (size_t)nkmers_read); } if(num_all_zero_kmers > 1) { loading_error("%s all-zero-kmers seen\n", ulong_to_str(num_all_zero_kmers, nstr)); } if(num_zero_covg_kmers > 0) { loading_warning("%s kmers have no coverage in any colour\n", ulong_to_str(num_zero_covg_kmers, nstr)); } } // Count warnings printed by graph_file_reader.c num_warnings += gfile.error_zero_covg; num_warnings += gfile.error_missing_covg; // Can only print these stats if we're read in the kmers if((print_kmers || parse_kmers) && print_info) { // print kmer coverage per sample printf("\n---- Per colour stats\n"); printf("num. kmers:"); for(col = 0; col < ncols; col++) printf("\t%s", ulong_to_str(col_nkmers[col], nstr)); printf("\n"); printf("sum coverage:"); for(col = 0; col < ncols; col++) printf("\t%s", ulong_to_str(col_sum_covgs[col], nstr)); printf("\n"); printf("kmer coverage:"); for(col = 0; col < ncols; col++) printf("\t%.2f", safe_frac(col_sum_covgs[col], col_nkmers[col])); printf("\n"); // Overall stats uint64_t sum_covgs = 0; double mean_kmer_covg = 0.0; for(col = 0; col < ncols; col++) sum_covgs += col_sum_covgs[col]; mean_kmer_covg = nkmers_loaded ? (double)sum_covgs / nkmers_loaded : 0.0; printf("\n---- Overall stats\n"); printf("Total kmers: %s\n", ulong_to_str(nkmers_loaded, nstr)); printf("Total coverage: %s\n", ulong_to_str(sum_covgs, nstr)); printf("Mean coverage: %s\n", double_to_str(mean_kmer_covg, 2, nstr)); } if(print_info) { // Print memory stats uint64_t mem, capacity, num_buckets, req_capacity; uint8_t bucket_size; req_capacity = (size_t)(gfile.num_of_kmers / IDEAL_OCCUPANCY); capacity = hash_table_cap(req_capacity, &num_buckets, &bucket_size); mem = ht_mem(bucket_size, num_buckets, sizeof(BinaryKmer)*8 + ncols*(sizeof(Covg)+sizeof(Edges))*8); char memstr[100], capacitystr[100], bucket_size_str[100], num_buckets_str[100]; bytes_to_str(mem, 1, memstr); ulong_to_str(capacity, capacitystr); ulong_to_str(bucket_size, bucket_size_str); ulong_to_str(num_buckets, num_buckets_str); size_t mem_height = (size_t)__builtin_ctzl(num_buckets); printf("\n---- Memory\n"); printf("memory required: %s [capacity: %s]\n", memstr, capacitystr); printf(" bucket size: %s; number of buckets: %s\n", bucket_size_str, num_buckets_str); printf(" --kmer_size %zu --mem_height %zu --mem_width %i\n", kmer_size, mem_height, bucket_size); } if((print_kmers || parse_kmers) && print_info) { printf("\n----\n"); if(num_warnings > 0 || num_errors > 0) { printf("Warnings: %zu; Errors: %zu\n", (size_t)num_warnings, (size_t)num_errors); } if(num_errors == 0) printf(num_warnings ? "Graph may be ok\n" : "Graph is valid\n"); } ctx_free(col_nkmers); ctx_free(col_sum_covgs); // Close file (which zeros it) graph_file_close(&gfile); graph_header_dealloc(&hdr); return num_errors ? EXIT_FAILURE : EXIT_SUCCESS; }