missing.h

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#ifndef gamgee__missing__guard
#define gamgee__missing__guard

#include "sam/sam_tag.h"
#include "utils/utils.h"

#include "htslib/vcf.h"

#include <vector>
#include <string>
#include <cmath>

namespace gamgee {

namespace missing_values {
  constexpr auto int8 = bcf_int8_missing;                                                                                       
  constexpr auto int16 = bcf_int16_missing;                                                                                     
  constexpr auto int32 = bcf_int32_missing;                                                                                     
  constexpr auto string_empty = "";                                                                                             
  constexpr auto string_dot = ".";                                                                                              
}

inline bool missing (const bool value) { return !value; }                                                                       
inline bool missing (const float value) { return bcf_float_is_missing(value); }                                                 
inline bool missing (const int8_t value)  { return value == missing_values::int8; }                                             
inline bool missing (const int16_t value) { return value == missing_values::int16; }                                            
inline bool missing (const int32_t value) { return value == missing_values::int32; }                                            
inline bool missing (const std::string& value) { return value.empty() || value == missing_values::string_dot;}                  
inline bool missing (const char* value) { return value == missing_values::string_empty || value == missing_values::string_dot;} 

template <class MISSING_TYPE>
inline bool missing(const MISSING_TYPE& value) {
  return value.missing();
}

template <class VALUE>
inline bool missing(const std::vector<VALUE>& v) { return v.empty(); }

}

#endif // gamgee__missing__guard