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//
// Lookup tables that are too annoying to initialize with array expressions.
// These includes things like complements of bases, numerical values, etc.
//
// To avoid having an init() function that everyone must call, we stow these
// in a special class and have one static instance of that class and variables
// pointing to it to ensure that the initializer (class constructor) is run.
//
#pragma once
class Tables
{
char complement[256];
char isN[256];
int baseValue[256];
int baseValueNoN[256]; // Same as above but N maps to 0 instead of 4
char valueBase[5];
unsigned char value4RC[256]; // reverse complement of 4 bases/byte
unsigned isLowerCaseOrDot[256];
char toUpperCaseDotToN[256];
char packedBaseValue[256];
char packedQualityMask[256];
char packedValueBase[256];
char packedValueBaseRC[256];
char cigarQualToSam[256];
public:
Tables();
const char *getComplement() const { return complement; }
const char *getIsN() const { return isN; }
const int *getBaseValue() const { return baseValue; }
const int *getBaseValueNoN() const { return baseValueNoN; }
const char *getValueBase() const { return valueBase; }
const unsigned char *getValue4RC() const { return value4RC; }
const char* getPackedBaseValue() const { return packedBaseValue; }
const char* getPackedQualityMask() const { return packedQualityMask; }
const char* getPackedValueBase() const { return packedValueBase; }
const char* getPackedValueBaseRC() const { return packedValueBaseRC; }
const unsigned *getIsLowerCaseOrDot() const {return isLowerCaseOrDot; }
const char *getToUpperCaseDotToN() const { return toUpperCaseDotToN; }
const char *getCigarQualToSam() const { return cigarQualToSam; }
};
extern const char *COMPLEMENT;
extern const char *IS_N;
extern const int *BASE_VALUE;
extern const char *VALUE_BASE;
extern const unsigned char *VALUE4_RC;
extern const char *PACKED_BASE_VALUE;
extern const char *PACKED_QUALITY_MASK;
extern const char *PACKED_VALUE_BASE;
extern const char *PACKED_VALUE_BASE_RC;
extern const int *BASE_VALUE_NO_N;
extern const unsigned *IS_LOWER_CASE_OR_DOT;
extern const char *TO_UPPER_CASE_DOT_TO_N;
extern const char *CIGAR_QUAL_TO_SAM;
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