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];
    }
}