C++ (Cpp) covg_buf_dealloc Examples

Example #1

File: clean_graph.c Project: ambarrio/mccortex

static void supernode_cleaner_alloc(SupernodeCleaner *cl, size_t nthreads,
                                    size_t covg_threshold, size_t min_keep_tip,
                                    uint8_t *keep_flags,
                                    const dBGraph *db_graph)
{
  size_t i;
  CovgBuffer *cbufs = ctx_calloc(nthreads, sizeof(CovgBuffer));
  for(i = 0; i < nthreads; i++)
    covg_buf_alloc(&cbufs[i], 1024);

  uint64_t *covg_hist_init, *covg_hist_cleaned;
  uint64_t *mean_covg_hist_init, *mean_covg_hist_cleaned;
  uint64_t *len_hist_init, *len_hist_cleaned;

  covg_hist_init          = ctx_calloc(DUMP_COVG_ARRSIZE, sizeof(uint64_t));
  covg_hist_cleaned       = ctx_calloc(DUMP_COVG_ARRSIZE, sizeof(uint64_t));
  mean_covg_hist_init     = ctx_calloc(DUMP_MEAN_COVG_ARRSIZE, sizeof(uint64_t));
  mean_covg_hist_cleaned  = ctx_calloc(DUMP_MEAN_COVG_ARRSIZE, sizeof(uint64_t));
  len_hist_init           = ctx_calloc(DUMP_LEN_ARRSIZE,  sizeof(uint64_t));
  len_hist_cleaned        = ctx_calloc(DUMP_LEN_ARRSIZE,  sizeof(uint64_t));

  SupernodeCleaner tmp = {.nthreads = nthreads,
                          .covg_threshold = covg_threshold,
                          .min_keep_tip = min_keep_tip,
                          .cbufs = cbufs,
                          .covg_hist_init    = covg_hist_init,
                          .covg_hist_cleaned = covg_hist_cleaned,
                          .covg_arrsize = DUMP_COVG_ARRSIZE,
                          .mean_covg_hist_init = mean_covg_hist_init,
                          .mean_covg_hist_cleaned = mean_covg_hist_cleaned,
                          .mean_covg_arrsize = DUMP_MEAN_COVG_ARRSIZE,
                          .len_hist_init     = len_hist_init,
                          .len_hist_cleaned  = len_hist_cleaned,
                          .len_arrsize = DUMP_LEN_ARRSIZE,
                          .keep_flags = keep_flags,
                          .num_tips = 0,
                          .num_low_covg_snodes = 0,
                          .num_tip_and_low_snodes = 0,
                          .num_tip_kmers = 0,
                          .num_low_covg_snode_kmers = 0,
                          .num_tip_and_low_snode_kmers = 0,
                          .db_graph = db_graph};

  memcpy(cl, &tmp, sizeof(SupernodeCleaner));
}

static void supernode_cleaner_dealloc(SupernodeCleaner *cl)
{
  size_t i;
  for(i = 0; i < cl->nthreads; i++)
    covg_buf_dealloc(&cl->cbufs[i]);
  ctx_free(cl->cbufs);
  ctx_free(cl->covg_hist_init);
  ctx_free(cl->covg_hist_cleaned);
  ctx_free(cl->mean_covg_hist_init);
  ctx_free(cl->mean_covg_hist_cleaned);
  ctx_free(cl->len_hist_init);
  ctx_free(cl->len_hist_cleaned);
  memset(cl, 0, sizeof(SupernodeCleaner));
}

Example #2

File: clean_graph.c Project: Phelimb/mccortex

static void unitig_cleaner_alloc(UnitigCleaner *cl, size_t nthreads,
                                 size_t covg_threshold, size_t min_keep_tip,
                                 uint8_t *keep_flags,
                                 const dBGraph *db_graph)
{
  size_t i;
  CovgBuffer *cbufs = ctx_calloc(nthreads, sizeof(CovgBuffer));
  for(i = 0; i < nthreads; i++)
    covg_buf_alloc(&cbufs[i], 1024);

  uint64_t *kmer_covgs_init, *kmer_covgs_clean;
  uint64_t *unitig_covgs_init, *unitig_covg_clean;
  uint64_t *len_hist_init, *len_hist_clean;

  kmer_covgs_init      = ctx_calloc(DUMP_COVG_ARRSIZE, sizeof(uint64_t));
  kmer_covgs_clean    = ctx_calloc(DUMP_COVG_ARRSIZE, sizeof(uint64_t));
  unitig_covgs_init    = ctx_calloc(DUMP_COVG_ARRSIZE, sizeof(uint64_t));
  unitig_covg_clean  = ctx_calloc(DUMP_COVG_ARRSIZE, sizeof(uint64_t));
  len_hist_init        = ctx_calloc(DUMP_LEN_ARRSIZE,  sizeof(uint64_t));
  len_hist_clean     = ctx_calloc(DUMP_LEN_ARRSIZE,  sizeof(uint64_t));

  UnitigCleaner tmp = {.nthreads = nthreads,
                       .covg_threshold = covg_threshold,
                       .min_keep_tip = min_keep_tip,
                       .cbufs = cbufs,
                       .kmer_covgs_init   = kmer_covgs_init,
                       .kmer_covgs_clean  = kmer_covgs_clean,
                       .unitig_covgs_init = unitig_covgs_init,
                       .unitig_covg_clean = unitig_covg_clean,
                       .covg_arrsize      = DUMP_COVG_ARRSIZE,
                       .len_hist_init   = len_hist_init,
                       .len_hist_clean  = len_hist_clean,
                       .len_arrsize     = DUMP_LEN_ARRSIZE,
                       .keep_flags = keep_flags,
                       .num_tips = 0,
                       .num_low_covg_snodes = 0,
                       .num_tip_and_low_snodes = 0,
                       .num_tip_kmers = 0,
                       .num_low_covg_snode_kmers = 0,
                       .num_tip_and_low_snode_kmers = 0,
                       .db_graph = db_graph};

  memcpy(cl, &tmp, sizeof(UnitigCleaner));
}

static void unitig_cleaner_dealloc(UnitigCleaner *cl)
{
  size_t i;
  for(i = 0; i < cl->nthreads; i++)
    covg_buf_dealloc(&cl->cbufs[i]);
  ctx_free(cl->cbufs);
  ctx_free(cl->kmer_covgs_init);
  ctx_free(cl->kmer_covgs_clean);
  ctx_free(cl->unitig_covgs_init);
  ctx_free(cl->unitig_covg_clean);
  ctx_free(cl->len_hist_init);
  ctx_free(cl->len_hist_clean);
  memset(cl, 0, sizeof(UnitigCleaner));
}