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#pragma once
#ifndef SHORT_READ_UTIL_H
#define SHORT_READ_UTIL_H
#include <ctype.h>
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <iostream>
using namespace std;
//TODO separate inline functions for single base and functions for short Read.
#define NT_SIZE 4
inline bool isACGT(char nt)
{
switch (nt) {
case 'a':
case 'c':
case 'g':
case 't':
case 'A':
case 'C':
case 'G':
case 'T':
return(true);
#ifdef DIPLOID
case 'R':
// G or A as puRine
case 'Y':
// T or C as pYrimidine
case 'M':
// aMino
case 'K':
// Keto
case 'S':
// Strong interaction
case 'W':
// Weak interaction
return(true);
#endif
default:
return(false);
}
}
inline int nt2Id(char nt)
{
switch (nt) {
case 'A':
case 'a':
return(0);
case 'C':
case 'c':
return(1);
case 'G':
case 'g':
return(2);
case 'T':
case 't':
return(3);
default:
return(4);
}
}
inline bool is0123(char nt)
{
switch (nt) {
case '0':
case '1':
case '2':
case '3':
return true;
default:
return false;
}
}
inline
bool isNucleotide(char nt)
{
switch (nt) {
case 'a':
case 'c':
case 'g':
case 't':
case 'A':
case 'C':
case 'G':
case 'T':
case 'U':
case 'u':
case 'R': // G or A as puRine
case 'r':
case 'Y': // T or C as pYrimidine
case 'y':
case 'M': // aMino
case 'm':
case 'N': // unknown
case 'n':
case 'K': // Keto
case 'k':
case 'S': // Strong interaction
case 's':
case 'W': // Weak interaction
case 'w':
case 'B': // GTC
case 'b':
case 'D': // GAT
case 'd':
case 'H': // ACT
case 'h':
case 'V': // GCA
case 'v':
return(true);
default:
return(false);
}
}
/* Perform the WildCard comparison between two base. If match return true */
inline bool diNtWildCardComp(char nt1, char nt2)
{
if (nt1 == nt2)
return true;
switch (nt1) {
case 'R':
if (nt2 == 'G' || nt2 == 'A' || nt2 == 'R')
return true;
break;
case 'Y':
if (nt2 == 'T' || nt2 == 'C' || nt2 == 'Y')
return true;
break;
case 'M':
if (nt2 == 'A' || nt2 == 'C' || nt2 == 'M')
return true;
break;
case 'K':
if (nt2 == 'G' || nt2 == 'T' || nt2 == 'K')
return true;
break;
case 'S':
if (nt2 == 'G' || nt2 == 'C' || nt2 == 'S')
return true;
break;
case 'W':
if (nt2 == 'T' || nt2 == 'A' || nt2 == 'W')
return true;
break;
default:
return false;
}
return false;
}
unsigned int diNtStrWildCardComp(char* read1, char* read2, unsigned int readlength);
unsigned int strComp(char* str1, char* str2, int l);
unsigned int strCompMarkDiff(char* str1, char* str2);
inline char complimentBase(char ntbase)
{
switch (ntbase) {
case 'a':
return('t');
case 'c':
return('g');
case 'g':
return('c');
case 't':
return('a');
case 'A':
return('T');
case 'C':
return('G');
case 'G':
return('C');
case 'T':
return('A');
default:
return('N');
}
}
inline char base2color(char nt, char color)
{
switch (color) {
case '1':
switch (color) {
case 'A':
return('C');
case 'C':
return('A');
case 'G':
return('T');
case 'T':
return('G');
default:
return(nt);
}
case '2':
switch (color) {
case 'A':
return('G');
case 'C':
return('T');
case 'G':
return('A');
case 'T':
return('C');
default:
return(nt);
}
case '3':
switch (color) {
case 'A':
return('T');
case 'C':
return('G');
case 'G':
return('C');
case 'T':
return('A');
default:
return(nt);
}
default: // include color 0
return(nt);
}
}
char getBaseFromColors(char nt, const char* colors, int pos);
void toUpperCase(char* caArray, int length);
void mutateBase(char* Base);
char* mutateRead(char* Kmer , unsigned int No_of_mutation);
char* mutatePairsOfConsecutiveBases(char* Kmer, unsigned int no_of_mutated_pairs);
bool isBadRead(const char* tkmer, unsigned int KmerLength);
bool isBadSOLiDRead(const char* Read, unsigned int ReadLength);
bool isBadRead(bool isSOLiD, const char* Read, unsigned int ReadLength);
//return the complement kmer from 5'->3', destroy the original kmer
char* reverseComplementKmer(char* Kmer);
char* reverseKmer(char* Kmer);
#endif
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