BaseUtilities.cpp
/*
* Copyright (C) 2010-2012 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include "BaseUtilities.h"
#include <ctype.h>
#include "BaseAsciiMap.h"
bool BaseUtilities::isAmbiguous(char base)
{
switch(base)
{
case 'N':
case 'n':
case '.':
return(true);
default:
break;
};
// Not 'N', 'n', or '.', so return false.
return(false);
}
bool BaseUtilities::areEqual(char base1, char base2)
{
// If they are the same, return true.
if(base1 == base2)
{
return(true);
}
// If one of the bases is '=', return true.
if((base1 == '=') || (base2 == '='))
{
return(true);
}
// Check both in upercase.
if(toupper(base1) == toupper(base2))
{
// same in upper case.
return(true);
}
// The bases are different.
return(false);
}
// Get phred base quality from the specified ascii quality.
uint8_t BaseUtilities::getPhredBaseQuality(char charQuality)
{
if(charQuality == UNKNOWN_QUALITY_CHAR)
{
return(UNKNOWN_QUALITY_INT);
}
return(charQuality - 33);
}
char BaseUtilities::getAsciiQuality(uint8_t phredQuality)
{
if(phredQuality == UNKNOWN_QUALITY_INT)
{
return(UNKNOWN_QUALITY_CHAR);
}
return(phredQuality + 33);
}
void BaseUtilities::reverseComplement(std::string& sequence)
{
int start = 0;
int end = sequence.size() - 1;
char tempChar;
while(start < end)
{
tempChar = sequence[start];
sequence[start] = BaseAsciiMap::base2complement[(int)(sequence[end])];
sequence[end] = BaseAsciiMap::base2complement[(int)tempChar];
// Move both pointers.
++start;
--end;
}
// there was an odd number of entries, complement the middle one.
if(start == end)
{
tempChar = sequence[start];
sequence[start] = BaseAsciiMap::base2complement[(int)tempChar];
}
}
BaseUtilities::isAmbiguous
static bool isAmbiguous(char base)
Returns whether or not the specified bases is an indicator for ambiguity.
Definition: BaseUtilities.cpp:23
BaseUtilities::UNKNOWN_QUALITY_CHAR
static const char UNKNOWN_QUALITY_CHAR
Character used when the quality is unknown.
Definition: BaseUtilities.h:49
BaseUtilities::getPhredBaseQuality
static uint8_t getPhredBaseQuality(char charQuality)
Get phred base quality from the specified ascii quality.
Definition: BaseUtilities.cpp:65
BaseUtilities::UNKNOWN_QUALITY_INT
static const uint8_t UNKNOWN_QUALITY_INT
Int value used when the quality is unknown.
Definition: BaseUtilities.h:51
BaseUtilities::areEqual
static bool areEqual(char base1, char base2)
Returns whether or not two bases are equal (case insensitive), if one of the bases is '=',...
Definition: BaseUtilities.cpp:39
BaseAsciiMap::base2complement
static unsigned char base2complement[]
This table maps 5' base space to the 3' complement base space values, as well as 5' color space value...
Definition: BaseAsciiMap.h:41
BaseUtilities::getAsciiQuality
static char getAsciiQuality(uint8_t phredQuality)
Get ascii quality from the specified phred quality.
Definition: BaseUtilities.cpp:76