C++ (Cpp) tmap_sa_read Examples

Example #1

File: tmap_index.c Project: vivekgopalan/TMAP

tmap_index_t*
tmap_index_init(const char *fn_fasta, key_t shm_key, int32_t mm)
{
  tmap_index_t *index = NULL;

  index = tmap_calloc(1, sizeof(tmap_index_t), "index");

  index->shm_key = shm_key;
  index->mm      = mm;

  // get the reference information
  // primary 65380; sa_intv: 32
  // seq_len = 97004
  //n_sa = 3032, sa 67973 .. 18446744073709551615

  if (1 == index->mm) {
      tmap_progress_print("Retrieving reference data from memory map");
      index->refseq = tmap_refseq_mm_read(fn_fasta);
      index->bwt = tmap_bwt_mm_read(fn_fasta);
      index->sa = tmap_sa_mm_read(fn_fasta);
      tmap_progress_print2("Reference data retrieved from memory map");
  } else if(0 == index->shm_key) {
      tmap_progress_print("reading in reference data");
      index->refseq = tmap_refseq_read(fn_fasta);
      index->bwt = tmap_bwt_read(fn_fasta);
      index->sa = tmap_sa_read(fn_fasta);
      tmap_progress_print2("reference data read in");
  }
  else {
      tmap_progress_print("retrieving reference data from shared memory");
      index->shm = tmap_shm_init(index->shm_key, 0, 0);
      if(NULL == (index->refseq = tmap_refseq_shm_unpack(tmap_shm_get_buffer(index->shm, TMAP_SHM_LISTING_REFSEQ)))) {
          tmap_error("the packed reference sequence was not found in shared memory", Exit, SharedMemoryListing);
      }
      if(NULL == (index->bwt = tmap_bwt_shm_unpack(tmap_shm_get_buffer(index->shm, TMAP_SHM_LISTING_BWT)))) {
          tmap_error("the BWT string was not found in shared memory", Exit, SharedMemoryListing);
      }
      if(NULL == (index->sa = tmap_sa_shm_unpack(tmap_shm_get_buffer(index->shm, TMAP_SHM_LISTING_SA)))) {
          tmap_error("the SA was not found in shared memory", Exit, SharedMemoryListing);
      }
      tmap_progress_print2("reference data retrieved from shared memory");
  }

  if((index->refseq->len << 1) != index->bwt->seq_len) {
      tmap_error("refseq and bwt lengths do not match", Exit, OutOfRange);
  }
  if((index->refseq->len << 1) != index->sa->seq_len) {
      tmap_error("refseq and sa lengths do not match", Exit, OutOfRange);
  }
  
  return index;
}

Example #2

File: tmap_index.c Project: Lingrui/TS

tmap_index_t*
tmap_index_init(const char *fn_fasta, key_t shm_key)
{
  tmap_index_t *index = NULL;

  index = tmap_calloc(1, sizeof(tmap_index_t), "index");

  index->shm_key = shm_key;

  // get the reference information
  if(0 == index->shm_key) {
      tmap_progress_print("reading in reference data");
      index->refseq = tmap_refseq_read(fn_fasta);
      index->bwt = tmap_bwt_read(fn_fasta);
      index->sa = tmap_sa_read(fn_fasta);
      tmap_progress_print2("reference data read in");
  }
  else {
      tmap_progress_print("retrieving reference data from shared memory");
      index->shm = tmap_shm_init(index->shm_key, 0, 0);
      if(NULL == (index->refseq = tmap_refseq_shm_unpack(tmap_shm_get_buffer(index->shm, TMAP_SHM_LISTING_REFSEQ)))) {
          tmap_error("the packed reference sequence was not found in shared memory", Exit, SharedMemoryListing);
      }
      if(NULL == (index->bwt = tmap_bwt_shm_unpack(tmap_shm_get_buffer(index->shm, TMAP_SHM_LISTING_BWT)))) {
          tmap_error("the BWT string was not found in shared memory", Exit, SharedMemoryListing);
      }
      if(NULL == (index->sa = tmap_sa_shm_unpack(tmap_shm_get_buffer(index->shm, TMAP_SHM_LISTING_SA)))) {
          tmap_error("the SA was not found in shared memory", Exit, SharedMemoryListing);
      }
      tmap_progress_print2("reference data retrieved from shared memory");
  }

  if((index->refseq->len << 1) != index->bwt->seq_len) {
      tmap_error("refseq and bwt lengths do not match", Exit, OutOfRange);
  }
  if((index->refseq->len << 1) != index->sa->seq_len) {
      tmap_error("refseq and sa lengths do not match", Exit, OutOfRange);
  }
  
  return index;
}