bitscode.h

#pragma once
#ifndef BITSCODE_H_
#define BITSCODE_H_

#include "stdafx.h"

typedef struct {
  WORD_SIZE ub;
  WORD_SIZE lb;
} InBits;

//1000000000000000000000000000000000000000000000000000000000000000000000000000
//static const unsigned short getonebit[66];

void EncodeRead(const char * strReads, InBits * readsInBits, int len);
void DecodeRead(char * strReads, int readLen, const InBits * readsInBits);
void DecodeReadReverse(char * strReads, int readLen,
                       const InBits * readsInBits);

void printWORD(WORD_SIZE word, SIZE_T len);
void printWORD2File(FILE * fout, WORD_SIZE word, SIZE_T len);

void Swap(char * strVal, int len);
char complimentBase(char nt);
SIZE_T bitsStrNCompare(InBits r1, InBits r2, SIZE_T N);

char getNT(const int & nt);

#endif /* BITSCODE_H_ */