/**
 ** Copyright (c) 2007-2009 Illumina, Inc.
 **
 ** This software is covered by the "Illumina Genome Analyzer Software
 ** License Agreement" and the "Illumina Source Code License Agreement",
 ** and certain third party copyright/licenses, and any user of this
 ** source file is bound by the terms therein (see accompanying files
 ** Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
 ** Illumina_Source_Code_License_Agreement.pdf and third party
 ** copyright/license notices).
 **
 ** This file is part of the Consensus Assessment of Sequence And VAriation
 ** (CASAVA) software package.
 **
 ** \file MatchDescriptor.cpp
 **
 ** \brief Commonly used functions and definitions
 **
 ** \author Richard Shaw
 **/

#include <cassert>

#include "alignment/MatchDescriptor.hh"

/*****************************************************************************/

MatchDescriptor::MatchDescriptor(const std::string& refStr,
                                 const std::string& readStr)
{
    assert(readStr.length() == refStr.length());

    unsigned int matchRunLen(0);
    typedef std::string::const_iterator ChCIter;

    ChCIter readChCIter(readStr.begin());

    for (ChCIter refChCIter(refStr.begin());
         refChCIter != refStr.end(); ++refChCIter, ++readChCIter) {
        if (*readChCIter == *refChCIter) {
            ++matchRunLen;
        } else {
            if (matchRunLen != 0) {
                ostrm_ << matchRunLen;
                matchRunLen = 0;
            }

            ostrm_ << *refChCIter;
        }
    }

    if (matchRunLen != 0) {
        ostrm_ << matchRunLen;
    }
}

/*****************************************************************************/