Exemplo n.º 1
0
int
tmap_refseq_refinfo_main(int argc, char *argv[])
{
  int c, help=0;
  tmap_refseq_t *refseq = NULL;
  tmap_file_t *fp_anno = NULL;
  char *fn_anno = NULL;
  char *fn_fasta = NULL;

  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;
  }
  fn_fasta = argv[optind];

  // Note: 'tmap_file_stdout' should not have been previously modified
  tmap_file_stdout = tmap_file_fdopen(fileno(stdout), "wb", TMAP_FILE_NO_COMPRESSION);

  // allocate some memory 
  refseq = tmap_calloc(1, sizeof(tmap_refseq_t), "refseq");
  refseq->is_rev = 0;
  refseq->is_shm = 0;

  // read the annotation file
  fn_anno = tmap_get_file_name(fn_fasta, TMAP_ANNO_FILE);
  fp_anno = tmap_file_fopen(fn_anno, "rb", TMAP_ANNO_COMPRESSION);
  tmap_refseq_read_anno(fp_anno, refseq);
  tmap_file_fclose(fp_anno);
  free(fn_anno);

  // no need to read in the pac
  refseq->seq = NULL;

  // print the header
  tmap_refseq_print_header(tmap_file_stdout, refseq);

  // destroy
  tmap_refseq_destroy(refseq);

  // close the output
  tmap_file_fclose(tmap_file_stdout);

  return 0;
}
Exemplo n.º 2
0
int
tmap_vswbm_main(int argc, char *argv[])
{

  int32_t seq_len = 150;
  int32_t tlen = 256; 
  int32_t n_iter = 1000;
  int32_t n_sub_iter = 1;
  int32_t vsw_type = 0;
  int c;

  while((c = getopt(argc, argv, "q:t:n:N:H:h")) >= 0) {
      switch(c) {
        case 'q':
          seq_len = atoi(optarg); break;
        case 't':
          tlen = atoi(optarg); break;
        case 'n':
          n_iter = atoi(optarg); break;
        case 'N':
          n_sub_iter = atoi(optarg); break;
        case 'H':
          vsw_type = atoi(optarg); break;
        case 'h':
        default:
          return usage(seq_len, tlen, n_iter, n_sub_iter, vsw_type);
      }
  }
  if(argc != optind || seq_len > tlen) {
      return usage(seq_len, tlen, n_iter, n_sub_iter, vsw_type);
  }

  tmap_progress_set_verbosity(1);
  tmap_progress_print2("starting benchmark");

  tmap_vsw_bm_core(seq_len, tlen, n_iter, n_sub_iter, vsw_type);
  
  tmap_progress_print2("ending benchmark");

  return 0;
}
Exemplo n.º 3
0
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;
}
Exemplo n.º 4
0
int 
tmap_index(int argc, char *argv[])
{
  int c;
  tmap_index_opt_t opt;

  opt.fn_fasta = NULL;
  opt.occ_interval = TMAP_BWT_OCC_INTERVAL; 
  opt.hash_width = INT32_MAX;
  opt.sa_interval = TMAP_SA_INTERVAL; 
  opt.is_large = -1;
  opt.check_hash = 1;
      
  if(2 == argc && 0 == strcmp("--version", argv[1])) {
      tmap_file_stdout = tmap_file_fdopen(fileno(stdout), "wb", TMAP_FILE_NO_COMPRESSION);
      tmap_file_fprintf(tmap_file_stdout, "%s\n", tmap_refseq_get_version_format(PACKAGE_VERSION));
      tmap_file_fclose(tmap_file_stdout);
      return 0;
  }

  while((c = getopt(argc, argv, "f:o:i:w:a:hvH")) >= 0) {
      switch(c) {
        case 'f':
          opt.fn_fasta = tmap_strdup(optarg); break;
        case 'o':
          opt.occ_interval = atoi(optarg); break;
        case 'i':
          opt.sa_interval = atoi(optarg); break;
        case 'w':
          opt.hash_width = atoi(optarg); break;
        case 'a':
          if(0 == strcmp("is", optarg)) opt.is_large = 0;
          else if(0 == strcmp("bwtsw", optarg)) opt.is_large = 1;
          else tmap_error("Option -a value not correct", Exit, CommandLineArgument); 
          break; 
        case 'v':
          tmap_progress_set_verbosity(1); break;
        case 'h':
          return usage(&opt);
        case 'H':
          opt.check_hash = 0; break;
        default:
          return usage(&opt);
      }
  }

  if(argc != optind || 1 == argc) {
      return usage(&opt);
  }
  if(NULL == opt.fn_fasta) {
      tmap_error("required option -f", Exit, CommandLineArgument);
  }
  if(opt.occ_interval < TMAP_BWT_OCC_MOD || 0 != (opt.occ_interval % 2) || 0 != (opt.occ_interval % TMAP_BWT_OCC_MOD)) {
      tmap_error("option -o out of range", Exit, CommandLineArgument);
  }
  if(opt.hash_width < 0) {
      tmap_error("option -w out of range", Exit, CommandLineArgument);
  }
  if(opt.sa_interval <= 0 || (1 < opt.sa_interval && 0 != (opt.sa_interval % 2))) {
      tmap_error("option -i out of range", Exit, CommandLineArgument);
  }

  tmap_index_core(&opt);

  free(opt.fn_fasta);
  
  tmap_progress_print2("terminating successfully");

  return 0;
}
Exemplo n.º 5
0
int
tmap_seqs_io_sff2sam_main(int argc, char *argv[])
{
  int c, help = 0;
  tmap_seqs_io_t *io_in = NULL;
  tmap_seqs_t *seqs = NULL;
  char **sam_rg = NULL;
  int32_t sam_rg_num = 0;
  int bidirectional = 0, sam_flowspace_tags = 0;
  int out_type = 0;
  tmap_sam_io_t *io_out = NULL;
  bam_header_t *header = NULL; // BAM Header
  int32_t i;

  /*
  uint8_t *key_seq = NULL;
  int key_seq_len = 0;
  */

  while((c = getopt(argc, argv, "DGR:Yvh")) >= 0) {
      switch(c) {
        case 'D': bidirectional = 1; break;
        case 'G': break;
        case 'R':
                  sam_rg = tmap_realloc(sam_rg, (1+sam_rg_num) * sizeof(char*), "sam_rg");
                  sam_rg[sam_rg_num] = tmap_strdup(optarg);
                  sam_rg_num++;
                  break;
        case 'Y': sam_flowspace_tags = 1; break;
        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 [-R -Y -v -h] <in.sff>\n", PACKAGE, argv[0]);
      return 1; 
  }

  // input
  io_in = tmap_seqs_io_init(&argv[optind], 1, TMAP_SEQ_TYPE_SFF, TMAP_FILE_NO_COMPRESSION, 0l, 0l);

  // BAM Header
  header = tmap_seqs_io_to_bam_header(NULL, io_in, sam_rg, sam_rg_num, argc, argv);

  // open the output file
  switch(out_type) {
    case 0: // SAM
      io_out = tmap_sam_io_init2("-", "wh", header);
      break;
    case 1:
      io_out = tmap_sam_io_init2("-", "wb", header);
      break;
    case 2:
      io_out = tmap_sam_io_init2("-", "wbu", header);
      break;
    default:
      tmap_bug();
  }

  // destroy the BAM Header
  bam_header_destroy(header);
  header = NULL;

  seqs = tmap_seqs_init(TMAP_SEQ_TYPE_SFF);
  while(0 < tmap_seqs_io_read(io_in, seqs, io_out->fp->header->header)) {
      bam1_t *b = NULL;
      tmap_seq_t *seq = seqs->seqs[0];
      b = tmap_sam_convert_unmapped(seq, sam_flowspace_tags, bidirectional, NULL,
                                    0, 0, 0,
                                    0, 0, 0,
                                    "\tlq:i:%d\trq:i:%d\tla:i:%d\trq:i:%d",
                                    seq->data.sff->rheader->clip_qual_left,
                                    seq->data.sff->rheader->clip_qual_right,
                                    seq->data.sff->rheader->clip_adapter_left,
                                    seq->data.sff->rheader->clip_adapter_right);
      if(samwrite(io_out->fp, b) <= 0) {
          tmap_error("Error writing the SAM file", Exit, WriteFileError);
      }
      bam_destroy1(b); 
      tmap_seqs_destroy(seqs);
      seqs = tmap_seqs_init(TMAP_SEQ_TYPE_SFF);
  }
  tmap_seqs_destroy(seqs);

  // free memory
  tmap_seqs_io_destroy(io_in);
  tmap_sam_io_destroy(io_out);
  for(i=0;i<sam_rg_num;i++) {
      free(sam_rg[i]);
  }
  free(sam_rg);

  return 0;
}
Exemplo n.º 6
0
int
tmap_refseq_pac2fasta_main(int argc, char *argv[])
{
  int c, help=0, amb=0;
  uint32_t i, j, k;
  char *fn_fasta = NULL;
  tmap_refseq_t *refseq = NULL;

  while((c = getopt(argc, argv, "avh")) >= 0) {
      switch(c) {
        case 'a': amb = 1; break;
        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 [-avh] <in.fasta>\n", PACKAGE, argv[0]);
      return 1;
  }

  fn_fasta = argv[optind];

  // Note: 'tmap_file_stdout' should not have been previously modified
  tmap_file_stdout = tmap_file_fdopen(fileno(stdout), "wb", TMAP_FILE_NO_COMPRESSION);

  // read in the reference sequence
  refseq = tmap_refseq_read(fn_fasta, 0);

  for(i=0;i<refseq->num_annos;i++) {
      tmap_file_fprintf(tmap_file_stdout, ">%s", refseq->annos[i].name->s); // new line handled later
      for(j=k=0;j<refseq->annos[i].len;j++) {
          if(0 == (j % TMAP_REFSEQ_FASTA_LINE_LENGTH)) {
              tmap_file_fprintf(tmap_file_stdout, "\n");
          }
          if(1 == amb && 0 < refseq->annos[i].num_amb) {
              // move the next ambiguous region
              while(k < refseq->annos[i].num_amb && refseq->annos[i].amb_positions_end[k] < j+1) {
                  k++;
              }
              // check for the ambiguous region
              if(k < refseq->annos[i].num_amb
                 && 0 == tmap_interval_overlap(j+1, j+1, refseq->annos[i].amb_positions_start[k], refseq->annos[i].amb_positions_end[k])) {
                  tmap_file_fprintf(tmap_file_stdout, "%c", tmap_iupac_int_to_char[refseq->annos[i].amb_bases[k]]);
              }
              else {
                  tmap_file_fprintf(tmap_file_stdout, "%c", "ACGTN"[(int)tmap_refseq_seq_i(refseq, j + refseq->annos[i].offset)]);
              }
          }
          else {
              tmap_file_fprintf(tmap_file_stdout, "%c", "ACGTN"[(int)tmap_refseq_seq_i(refseq, j + refseq->annos[i].offset)]);
          }
      }
      tmap_file_fprintf(tmap_file_stdout, "\n");
  }

  // destroy
  tmap_refseq_destroy(refseq);

  // close the output
  tmap_file_fclose(tmap_file_stdout);

  return 0;
}