build_fm_index.cpp

extern "C"{
#include "hash_cdbg/kseq.h"
#include <zlib.h>
};

#include <sdsl/sd_vector.hpp>
#include <sdsl/suffix_arrays.hpp>
#include "hash_cdbg/dna_alphabet.hpp"


KSEQ_INIT(gzFile, gzread)

using namespace std;
using namespace sdsl;

int main(int argc, char* argv[]) {

  if (argc < 3) {
    std::cerr << "Usage: " << argv[0] << " INPUT_FASTQ OUTPUT_PREFIX" << std::endl;
    return 1;
  }

  cache_config config(false, ".", "tmp");
  csa_wt<wt_huff<rrr_vector<127> >, 512, 1024> fm_index;

  uint8_t int_symbol;
  string output_file = cache_file_name(conf::KEY_TEXT, config);

  int_vector_buffer<8> int_text(output_file, std::ios::out, 1000000);

  gzFile fp;
  kseq_t *seq;
  int l;
  fp = gzopen(argv[1], "r");
  seq = kseq_init(fp);
  size_t i = 0;

  int_text[i] = dna_alphabet::char2comp['$'];
  i++;
  size_t cont=0;
  while ((l = kseq_read(seq)) >= 0) { // STEP 4: read sequence
    for (size_t j = 0; j < l; j++) {
      int_symbol = dna_alphabet::char2comp[seq->seq.s[j]];
      int_text[i] = int_symbol;
      i++;
    }
    int_text[i] = dna_alphabet::char2comp['$'];
    i++;
    cont++;
  }
  kseq_destroy(seq);
  gzclose(fp);
  int_text.close();

  construct(fm_index, cache_file_name(conf::KEY_TEXT, config)); // generate index
  store_to_file(fm_index, string(argv[2]) + ".fm_index"); // save it
}