tsv_reader.cpp

#include "tsv_reader.h"

/*
  htsFile* hp;
  kstring_t str;
  int32_t lstr;
  int32_t nfields;
  int32_t* fields;
  int32_t nlines;
*/

bool tsv_reader::open(const char* filename) {
  this->filename = filename;
  hp = hts_open(filename, "r");
  if ( hp == NULL ) {
    return false;
  }
  return true;
}

bool tsv_reader::close() {
  if ( hp == NULL ) return false;
  int32_t ret = hts_close(hp);
  hp = NULL;
  return ret == 0;
}

int32_t tsv_reader::read_line() {
  if ( itr == NULL ) {
    //if ( ( str.s != NULL ) && ( lstr > 0 ) ) free(str.s);
    lstr = hts_getline(hp, KS_SEP_LINE, &str);
  }
  else {
    lstr = tbx_itr_next(hp, tbx, itr, &str);
  }

  if ( lstr <= 0 ) {
    nfields = 0;
    fields = NULL;
    return 0; // lstr;
  }

  // need to free the previously allocated fields!!
  if ( fields != NULL ) { free(fields); fields = NULL; }  
  fields = ksplit(&str, delimiter, &nfields);

  //notice("lstr = %d, str = %s, delim = %d", lstr, str.s, delimiter);
    
  ++nlines;
  return nfields;
}

bool tsv_reader::jump_to(const char* chr, int32_t beg, int32_t end) {
  char buf[65536];
  sprintf(buf, "%s:%d-%d", chr, beg, end);
  return jump_to(buf);
}

bool tsv_reader::jump_to(const char* reg) {
  if ( tbx == NULL ) {
    tbx = tbx_index_load(filename.c_str());
    if ( !tbx ) error("[E:%s] Could not load .tbi/.csi index of %s\n", __PRETTY_FUNCTION__, filename.c_str());
  }

  if ( itr != NULL )
    tbx_itr_destroy(itr);

  itr = tbx_itr_querys(tbx, reg);
  
  if ( itr == NULL ) {
    notice("Failed jumping to %s, tbx = %x, itr = %x", reg, tbx, itr);
    return false;
  }
  else return true;
}

const char* tsv_reader::str_field_at(int32_t idx) {
  if ( idx >= nfields ) {
    error("[E:%s:%d %s] Cannot access field at %d >= %d", __FILE__, __LINE__, __FUNCTION__, idx, nfields);
    //return NULL;
  }
  return ( &str.s[fields[idx]] );
}

int32_t tsv_reader::int_field_at(int32_t idx) {
  if ( idx >= nfields )
    error("[E:%s:%d %s] Cannot access field at %d >= %d", __FILE__, __LINE__, __FUNCTION__, idx, nfields);    
  return ( atoi(&str.s[fields[idx]]) );
}

double tsv_reader::double_field_at(int32_t idx) {
  if ( idx >= nfields )
    error("[E:%s:%d %s] Cannot access field at %d >= %d", __FILE__, __LINE__, __FUNCTION__, idx, nfields);    
  return ( atof(&str.s[fields[idx]]) );
}

int32_t tsv_reader::store_to_vector(std::vector<std::string>& v) {
  v.resize(nfields);
  for(int32_t i=0; i < nfields; ++i) {
    v[i].assign(&str.s[fields[i]]);
  }
  return nfields;
}