Пример #1
0
int ctx_correct(int argc, char **argv)
{
  size_t i;
  struct ReadThreadCmdArgs args;
  read_thread_args_alloc(&args);
  read_thread_args_parse(&args, argc, argv, longopts, true);

  GraphFileReader *gfile = &args.gfile;
  GPathFileBuffer *gpfiles = &args.gpfiles;
  CorrectAlnInputBuffer *inputs = &args.inputs;

  // Update colours in graph file - sample in 0, all others in 1
  size_t ncols = gpath_load_sample_pop(gfile, 1, gpfiles->b, gpfiles->len,
                                       args.colour);

  // Check for compatibility between graph files and link files
  graphs_gpaths_compatible(gfile, 1, gpfiles->b, gpfiles->len, 1);

  int64_t ctx_num_kmers = gfile->num_of_kmers;

  //
  // Decide on memory
  //
  size_t bits_per_kmer, kmers_in_hash, graph_mem, path_mem, total_mem;

  // 1 bit needed per kmer if we need to keep track of noreseed
  bits_per_kmer = sizeof(BinaryKmer)*8 + sizeof(Edges)*8 +
                  (gpfiles->len > 0 ? sizeof(GPath*)*8 : 0) +
                  ncols; // in colour

  kmers_in_hash = cmd_get_kmers_in_hash(args.memargs.mem_to_use,
                                        args.memargs.mem_to_use_set,
                                        args.memargs.num_kmers,
                                        args.memargs.num_kmers_set,
                                        bits_per_kmer,
                                        ctx_num_kmers, ctx_num_kmers,
                                        false, &graph_mem);

  // Paths memory
  size_t rem_mem = args.memargs.mem_to_use - MIN2(args.memargs.mem_to_use, graph_mem);
  path_mem = gpath_reader_mem_req(gpfiles->b, gpfiles->len, ncols, rem_mem, false,
                                  kmers_in_hash, false);

  cmd_print_mem(path_mem, "paths");

  // Shift path store memory from graphs->paths
  graph_mem -= sizeof(GPath*)*kmers_in_hash;
  path_mem  += sizeof(GPath*)*kmers_in_hash;

  // Total memory
  total_mem = graph_mem + path_mem;
  cmd_check_mem_limit(args.memargs.mem_to_use, total_mem);

  //
  // Check we can write all output files
  //
  // Open output files
  SeqOutput *outputs = ctx_calloc(inputs->len, sizeof(SeqOutput));
  bool err_occurred = false;

  for(i = 0; i < inputs->len && !err_occurred; i++)
  {
    CorrectAlnInput *input = &inputs->b[i];
    // We loaded target colour into colour zero
    input->crt_params.ctxcol = input->crt_params.ctpcol = 0;
    bool is_pe = asyncio_task_is_pe(&input->files);
    err_occurred = !seqout_open(&outputs[i], input->out_base, args.fmt, is_pe);
    input->output = &outputs[i];
  }

  // Abandon if some of the output files already exist
  if(err_occurred) {
    for(i = 0; i < inputs->len; i++)
      seqout_close(&outputs[i], true);
    die("Error creating output files");
  }

  //
  // Allocate memory
  //

  dBGraph db_graph;
  db_graph_alloc(&db_graph, gfile->hdr.kmer_size, ncols, 1, kmers_in_hash,
                 DBG_ALLOC_EDGES | DBG_ALLOC_NODE_IN_COL);

  // Create a path store that does not tracks path counts
  gpath_reader_alloc_gpstore(gpfiles->b, gpfiles->len, path_mem, false, &db_graph);

  //
  // Load Graph and link files
  //
  GraphLoadingPrefs gprefs = graph_loading_prefs(&db_graph);
  gprefs.empty_colours = true;

  // Load graph, print stats, close file
  graph_load(gfile, gprefs, NULL);
  hash_table_print_stats_brief(&db_graph.ht);
  graph_file_close(gfile);

  // Load link files
  for(i = 0; i < gpfiles->len; i++) {
    gpath_reader_load(&gpfiles->b[i], GPATH_DIE_MISSING_KMERS, &db_graph);
    gpath_reader_close(&gpfiles->b[i]);
  }

  //
  // Run alignment
  //
  correct_reads(inputs->b, inputs->len,
                args.dump_seq_sizes, args.dump_frag_sizes,
                args.fq_zero, args.append_orig_seq,
                args.nthreads, &db_graph);

  // Close and free output files
  for(i = 0; i < inputs->len; i++)
    seqout_close(&outputs[i], false);
  ctx_free(outputs);

  // Closes input files
  read_thread_args_dealloc(&args);
  db_graph_dealloc(&db_graph);

  return EXIT_SUCCESS;
}
Пример #2
0
int ctx_thread(int argc, char **argv)
{
  struct ReadThreadCmdArgs args;
  read_thread_args_alloc(&args);
  read_thread_args_parse(&args, argc, argv, longopts, false);

  GraphFileReader *gfile = &args.gfile;
  GPathFileBuffer *gpfiles = &args.gpfiles;
  CorrectAlnInputBuffer *inputs = &args.inputs;
  size_t i;

  if(args.zero_link_counts && gpfiles->len == 0)
    cmd_print_usage("-0,--zero-paths without -p,--paths <in.ctp> has no meaning");

  // Check each path file only loads one colour
  gpaths_only_for_colour(gpfiles->b, gpfiles->len, 0);

  //
  // Decide on memory
  //
  size_t bits_per_kmer, kmers_in_hash, graph_mem, total_mem;
  size_t path_hash_mem, path_store_mem, path_mem;
  bool sep_path_list = (!args.use_new_paths && gpfiles->len > 0);

  bits_per_kmer = sizeof(BinaryKmer)*8 + sizeof(Edges)*8 + sizeof(GPath*)*8 +
                  2 * args.nthreads; // Have traversed

  // false -> don't use mem_to_use to decide how many kmers to store in hash
  // since we need some of that memory for storing paths
  kmers_in_hash = cmd_get_kmers_in_hash(args.memargs.mem_to_use,
                                        args.memargs.mem_to_use_set,
                                        args.memargs.num_kmers,
                                        args.memargs.num_kmers_set,
                                        bits_per_kmer,
                                        gfile->num_of_kmers,
                                        gfile->num_of_kmers,
                                        false, &graph_mem);

  // Paths memory
  size_t min_path_mem = 0;
  gpath_reader_sum_mem(gpfiles->b, gpfiles->len, 1, true, true, &min_path_mem);

  if(graph_mem + min_path_mem > args.memargs.mem_to_use) {
    char buf[50];
    die("Require at least %s memory", bytes_to_str(graph_mem+min_path_mem, 1, buf));
  }

  path_mem = args.memargs.mem_to_use - graph_mem;
  size_t pentry_hash_mem = sizeof(GPEntry)/0.7;
  size_t pentry_store_mem = sizeof(GPath) + 8 + // struct + sequence
                            1 + // in colour
                            sizeof(uint8_t) + // counts
                            sizeof(uint32_t); // kmer length

  size_t max_paths = path_mem / (pentry_store_mem + pentry_hash_mem);
  path_store_mem = max_paths * pentry_store_mem;
  path_hash_mem = max_paths * pentry_hash_mem;
  cmd_print_mem(path_hash_mem, "paths hash");
  cmd_print_mem(path_store_mem, "paths store");

  total_mem = graph_mem + path_mem;
  cmd_check_mem_limit(args.memargs.mem_to_use, total_mem);

  //
  // Open output file
  //
  gzFile gzout = futil_gzopen_create(args.out_ctp_path, "w");

  status("Creating paths file: %s", futil_outpath_str(args.out_ctp_path));

  //
  // Allocate memory
  //
  dBGraph db_graph;
  size_t kmer_size = gfile->hdr.kmer_size;
  db_graph_alloc(&db_graph, kmer_size, 1, 1, kmers_in_hash,
                 DBG_ALLOC_EDGES | DBG_ALLOC_NODE_IN_COL);

  // Split path memory 2:1 between store and hash
  // Create a path store that tracks path counts
  gpath_store_alloc(&db_graph.gpstore,
                    db_graph.num_of_cols, db_graph.ht.capacity,
                    0, path_store_mem, true, sep_path_list);

  // Create path hash table for fast lookup
  gpath_hash_alloc(&db_graph.gphash, &db_graph.gpstore, path_hash_mem);

  if(args.use_new_paths) {
    status("Using paths as they are added (risky)");
  } else {
    status("Not using new paths as they are added (safe)");
  }

  //
  // Start up workers to add paths to the graph
  //
  GenPathWorker *workers;
  workers = gen_paths_workers_alloc(args.nthreads, &db_graph);

  // Setup for loading graphs graph
  LoadingStats gstats;
  loading_stats_init(&gstats);

  // Path statistics
  LoadingStats *load_stats = gen_paths_get_stats(workers);
  CorrectAlnStats *aln_stats = gen_paths_get_aln_stats(workers);

  // Load contig hist distribution
  for(i = 0; i < gpfiles->len; i++) {
    gpath_reader_load_contig_hist(gpfiles->b[i].json,
                                  gpfiles->b[i].fltr.path.b,
                                  file_filter_fromcol(&gpfiles->b[i].fltr, 0),
                                  &aln_stats->contig_histgrm);
  }

  GraphLoadingPrefs gprefs = {.db_graph = &db_graph,
                              .boolean_covgs = false,
                              .must_exist_in_graph = false,
                              .must_exist_in_edges = NULL,
                              .empty_colours = false}; // already loaded paths

  // Load graph, print stats, close file
  graph_load(gfile, gprefs, &gstats);
  hash_table_print_stats_brief(&db_graph.ht);
  graph_file_close(gfile);

  // Load existing paths
  for(i = 0; i < gpfiles->len; i++)
    gpath_reader_load(&gpfiles->b[i], GPATH_DIE_MISSING_KMERS, &db_graph);

  // zero link counts of already loaded links
  if(args.zero_link_counts) {
    status("Zeroing link counts for loaded links");
    gpath_set_zero_nseen(&db_graph.gpstore.gpset);
  }

  if(!args.use_new_paths)
    gpath_store_split_read_write(&db_graph.gpstore);

  // Deal with a set of files at once
  // Can have different numbers of inputs vs threads
  size_t start, end;
  for(start = 0; start < inputs->len; start += MAX_IO_THREADS)
  {
    end = MIN2(inputs->len, start+MAX_IO_THREADS);
    generate_paths(inputs->b+start, end-start, workers, args.nthreads);
  }

  // Print memory statistics
  gpath_hash_print_stats(&db_graph.gphash);
  gpath_store_print_stats(&db_graph.gpstore);

  correct_aln_dump_stats(aln_stats, load_stats,
                         args.dump_seq_sizes,
                         args.dump_frag_sizes,
                         db_graph.ht.num_kmers);

  // Don't need GPathHash anymore
  gpath_hash_dealloc(&db_graph.gphash);

  cJSON **hdrs = ctx_malloc(gpfiles->len * sizeof(cJSON*));
  for(i = 0; i < gpfiles->len; i++) hdrs[i] = gpfiles->b[i].json;

  size_t output_threads = MIN2(args.nthreads, MAX_IO_THREADS);

  // Generate a cJSON header for all inputs
  cJSON *thread_hdr = cJSON_CreateObject();
  cJSON *inputs_hdr = cJSON_CreateArray();
  cJSON_AddItemToObject(thread_hdr, "inputs", inputs_hdr);
  for(i = 0; i < inputs->len; i++)
    cJSON_AddItemToArray(inputs_hdr, correct_aln_input_json_hdr(&inputs->b[i]));

  // Write output file
  gpath_save(gzout, args.out_ctp_path, output_threads, true,
             "thread", thread_hdr, hdrs, gpfiles->len,
             &aln_stats->contig_histgrm, 1,
             &db_graph);

  gzclose(gzout);
  ctx_free(hdrs);

  // Optionally run path checks for debugging
  // gpath_checks_all_paths(&db_graph, args.nthreads);

  // ins_gap, err_gap no longer allocated after this line
  gen_paths_workers_dealloc(workers, args.nthreads);

  // Close and free input files etc.
  read_thread_args_dealloc(&args);
  db_graph_dealloc(&db_graph);

  return EXIT_SUCCESS;
}
Пример #3
0
int ctx_correct(int argc, char **argv)
{
  size_t i, j;
  struct ReadThreadCmdArgs args = READ_THREAD_CMD_ARGS_INIT;
  read_thread_args_alloc(&args);
  read_thread_args_parse(&args, argc, argv, longopts, true);

  GraphFileReader *gfile = &args.gfile;
  PathFileBuffer *pfiles = &args.pfiles;
  CorrectAlnInputBuffer *inputs = &args.inputs;
  size_t ctx_total_cols = gfile->hdr.num_of_cols;
  size_t ctx_num_kmers = gfile->num_of_kmers;

  if(args.colour > ctx_total_cols)
    cmd_print_usage("-c %zu is too big [> %zu]", args.colour, ctx_total_cols);

  size_t ctp_usedcols = 0;
  for(i = 0; i < pfiles->len; i++) {
    if(!file_filter_iscolloaded(&pfiles->data[i].fltr, args.colour)) {
      cmd_print_usage("Path file doesn't load into colour %zu: %s",
                      args.colour, pfiles->data[i].fltr.orig_path.buff);
    }
    ctp_usedcols = MAX2(ctp_usedcols, path_file_usedcols(&pfiles->data[i]));
  }

  //
  // Decide on memory
  //
  size_t bits_per_kmer, kmers_in_hash, graph_mem, path_mem, total_mem;

  // 1 bit needed per kmer if we need to keep track of noreseed
  bits_per_kmer = sizeof(Edges)*8 + ctx_num_kmers + sizeof(uint64_t)*8;
  kmers_in_hash = cmd_get_kmers_in_hash2(args.memargs.mem_to_use,
                                         args.memargs.mem_to_use_set,
                                         args.memargs.num_kmers,
                                         args.memargs.num_kmers_set,
                                         bits_per_kmer,
                                         ctx_num_kmers, ctx_num_kmers,
                                         false, &graph_mem);

  // Paths memory
  path_mem = path_files_mem_required(pfiles->data, pfiles->len, false, false,
                                     ctp_usedcols, 0);
  cmd_print_mem(path_mem, "paths");

  // Total memory
  total_mem = graph_mem + path_mem;
  cmd_check_mem_limit(args.memargs.mem_to_use, total_mem);

  //
  // Check we can read all output files
  //
  // Open output files
  SeqOutput *outputs = ctx_calloc(inputs->len, sizeof(SeqOutput));
  bool output_files_exist = false;

  for(i = 0; i < inputs->len; i++)
  {
    CorrectAlnInput *input = &inputs->data[i];
    input->crt_params.ctxcol = input->crt_params.ctpcol = args.colour;
    SeqOutput *output = &outputs[i];
    seq_output_alloc(output);
    seq_output_set_paths(output, input->out_base,
                         async_task_pe_output(&input->files));
    input->output = output;
    // output check prints warnings and returns true if errors
    output_files_exist |= seq_output_files_exist_check(output);
  }

  // Abandon if some of the output files already exist
  if(output_files_exist) die("Output files already exist");

  // Attempt to open all files
  for(i = 0; i < inputs->len && seq_output_open(&outputs[i]); i++) {}

  // Check if something went wrong - if so remove all output files
  if(i < inputs->len) {
    for(j = 0; j < i; j++) seq_output_delete(&outputs[i]);
    die("Couldn't open output files");
  }

  //
  // Allocate memory
  //

  dBGraph db_graph;
  db_graph_alloc(&db_graph, gfile->hdr.kmer_size, ctx_total_cols, 1, kmers_in_hash);

  size_t bytes_per_col = roundup_bits2bytes(db_graph.ht.capacity);

  db_graph.col_edges = ctx_calloc(db_graph.ht.capacity, sizeof(Edges));
  db_graph.node_in_cols = ctx_calloc(bytes_per_col * ctx_total_cols, 1);

  // Paths
  path_store_alloc(&db_graph.pstore, path_mem, false,
                   db_graph.ht.capacity, ctp_usedcols);

  //
  // Load Graph and Path files
  //
  LoadingStats gstats = 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 = true};

  // Load graph, print stats, close file
  graph_load(gfile, gprefs, &gstats);
  hash_table_print_stats_brief(&db_graph.ht);
  graph_file_close(gfile);

  // Load path files (does nothing if num_fpiles == 0)
  paths_format_merge(pfiles->data, pfiles->len, false, false,
                     args.num_of_threads, &db_graph);

  //
  // Run alignment
  //
  correct_reads(args.num_of_threads, MAX_IO_THREADS,
                inputs->data, inputs->len,
                &db_graph);

  // Close and free output files
  for(i = 0; i < inputs->len; i++) seq_output_dealloc(&outputs[i]);
  ctx_free(outputs);

  read_thread_args_dealloc(&args);

  db_graph_dealloc(&db_graph);

  return EXIT_SUCCESS;
}