C++ (Cpp) tmap_refseq_fasta2pacの例

コード例 #1

ファイル: tmap_index.c プロジェクト: vivekgopalan/TMAP

static void 
tmap_index_core(tmap_index_opt_t *opt)
{
  uint64_t ref_len = 0;

  // pack the reference sequence
  ref_len = tmap_refseq_fasta2pac(opt->fn_fasta, TMAP_FILE_NO_COMPRESSION, 0);
      
  if(TMAP_INDEX_TOO_BIG_GENOME <= ref_len) { // too big (2^32 - 1)!
      tmap_error("Reference sequence too large", Exit, OutOfRange);
  }

  // check returned genome size
  if(opt->is_large < 0) {
      if(TMAP_INDEX_LARGE_GENOME <= ref_len) { 
          opt->is_large = 1;
          tmap_progress_print("defaulting to \"bwtsw\" BWT construction algorithm");
      }
      else {
          opt->is_large = 0;
          tmap_progress_print("defaulting to \"is\" BWT construction algorithm");
      }
  }

  // create the bwt 
  tmap_bwt_pac2bwt(opt->fn_fasta, opt->is_large, opt->occ_interval, opt->hash_width, opt->check_hash);

  // create the suffix array
  tmap_sa_bwt2sa(opt->fn_fasta, opt->sa_interval);

  // pack the reference sequence
  ref_len = tmap_refseq_fasta2pac(opt->fn_fasta, TMAP_FILE_NO_COMPRESSION, 1);
}

コード例 #2

ファイル: tmap_refseq.c プロジェクト: edvenson/TMAP

int
tmap_refseq_fasta2pac_main(int argc, char *argv[])
{
  int c, help=0;

  while((c = getopt(argc, argv, "vh")) >= 0) {
      switch(c) {
        case 'v': tmap_progress_set_verbosity(1); break;
        case 'h': help = 1; break;
        default: return 1;
      }
  }
  if(1 != argc - optind || 1 == help) {
      tmap_file_fprintf(tmap_file_stderr, "Usage: %s %s [-vh] <in.fasta>\n", PACKAGE, argv[0]);
      return 1;
  }

  tmap_refseq_fasta2pac(argv[optind], TMAP_FILE_NO_COMPRESSION);

  return 0;
}