Exemplos de tmap_seq_get_bases_length em C++ (Cpp)

Exemplo n.º 1

Arquivo: tmap_map1.c Projeto: Brainiarc7/TS

tmap_map_sams_t*
tmap_map1_thread_map(void **data, tmap_seq_t **seqs, tmap_index_t *index, tmap_bwt_match_hash_t *hash, tmap_rand_t *rand, tmap_map_opt_t *opt)
{
  int32_t seq_len = 0;;
  tmap_map_sams_t *sams = NULL;

  // sequence length
  seq_len = tmap_seq_get_bases_length(seqs[0]);

  // sequence length not in range
  if((0 < opt->min_seq_len && seq_len < opt->min_seq_len)
     || (0 < opt->max_seq_len && opt->max_seq_len < seq_len)) {
      return tmap_map_sams_init(NULL);
  }

  // not enough bases, ignore
  if(0 < opt->seed_length && seq_len < opt->seed_length){
      return tmap_map_sams_init(NULL);
  }

  // core algorithm; use the reverse
  sams = tmap_map1_thread_map_core(data, seqs, seq_len, index, hash, opt);

  return sams;
}

Exemplo n.º 2

Arquivo: tmap_map_vsw.c Projeto: edvenson/TMAP

tmap_map_sams_t*
tmap_map_vsw_thread_map(void **data, tmap_seq_t **seqs, tmap_index_t *index, tmap_map_stats_t *stat, tmap_rand_t *rand, tmap_bwt_match_hash_t *hash[2], tmap_map_opt_t *opt)
{
  int32_t seq_len = 0;;
  tmap_seq_t *seqs_tmp[2]={NULL, NULL};
  tmap_map_sams_t *sams = NULL;

  // sequence length
  seq_len = tmap_seq_get_bases_length(seqs[0]);

  // sequence length not in range
  if((0 < opt->min_seq_len && seq_len < opt->min_seq_len)
     || (0 < opt->max_seq_len && opt->max_seq_len < seq_len)) {
      return tmap_map_sams_init(NULL);
  }

  // clone the sequence 
  seqs_tmp[0] = seqs[0];
  seqs_tmp[1] = seqs[1];

  // core algorithm
  sams = tmap_map_vsw_thread_map_core(data, seqs_tmp, seq_len, index, opt);

  return sams;
}

Exemplo n.º 3

Arquivo: tmap_map3_aux.c Projeto: a1aks/TMAP

// TODO: memory pools?
tmap_map_sams_t *
tmap_map3_aux_core(tmap_seq_t *seq, 
                   uint8_t *flow_order,
                   int32_t flow_order_len,
                   tmap_refseq_t *refseq,
                   tmap_bwt_t *bwt,
                   tmap_sa_t *sa,
                   tmap_bwt_match_hash_t *hash,
                   tmap_map_opt_t *opt)
{
  int32_t i, j, n, seed_length, hp_diff = 0;
  int32_t seq_len;
  tmap_string_t *bases;
  uint8_t *query;
  uint8_t *flow=NULL;
  tmap_map3_aux_seed_t *seeds;
  int32_t m_seeds, n_seeds;
  tmap_map_sams_t *sams = NULL;

  if(0 < opt->hp_diff) {
      // set up the flow order to be used
      if(NULL == flow_order) {
          hp_diff = 0;
      }
      else {
          flow = tmap_malloc(sizeof(uint8_t)*flow_order_len, "flow[0]");
          for(i=0;i<flow_order_len;i++) {
              flow[i] = flow_order[i]; // forward
          }
      }
  }

  // init
  sams = tmap_map_sams_init(NULL);

  // update the seed length based on the read length
  seed_length = opt->seed_length;
  if(0 == opt->seed_length_set) {
      i = tmap_seq_get_bases_length(seq);
      while(0 < i) {
          seed_length++;
          i >>= 1; // divide by two
      }
  }