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/*
* 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/>.
*/
#ifndef __BASE_UTILITIES_H__
#define __BASE_UTILITIES_H__
#include <stdint.h>
#include <string>
/// This class contains static utilities for performing
/// basic operations on bases.
class BaseUtilities
{
public:
/// Returns whether or not the specified bases is
/// an indicator for ambiguity.
/// \return true if base = 'n' or 'N' or '.'
static bool isAmbiguous(char base);
/// Returns whether or not two bases are equal (case insensitive),
/// if one of the bases is '=', the bases are consided
/// to be equal.
static bool areEqual(char base1, char base2);
/// Get phred base quality from the specified ascii quality.
static uint8_t getPhredBaseQuality(char charQuality);
/// Get ascii quality from the specified phred quality.
static char getAsciiQuality(uint8_t phredQuality);
static void reverseComplement(std::string& sequence);
/// Character used when the quality is unknown.
static const char UNKNOWN_QUALITY_CHAR = ' ';
/// Int value used when the quality is unknown.
static const uint8_t UNKNOWN_QUALITY_INT = 0xFF;
};
#endif
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