// ==========================================================================
//                SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2016, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
//     * Redistributions of source code must retain the above copyright
//       notice, this list of conditions and the following disclaimer.
//     * Redistributions in binary form must reproduce the above copyright
//       notice, this list of conditions and the following disclaimer in the
//       documentation and/or other materials provided with the distribution.
//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
//       its contributors may be used to endorse or promote products derived
//       from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// DAMAGE.
//
// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// Concatenate multiple files from soft-masked FASTA (masked sequence is
// lower case) to hard-masked FASTA (replaced by Ns) and write to stdout.
//
// USAGE: soft_to_hard_masking IN1.fa [IN2.fa ...] > out.fa
// ==========================================================================

#include <iostream>
#include <cctype>

#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/seq_io.h>

using namespace seqan;

template <typename TStream>
void convertToHardMasked(TStream & stream, char const * filename)
{
    SeqFileIn inFile(filename);

    String<char> meta;
    String<char> seq;

    while (!atEnd(inFile))
    {
        clear(meta);
        clear(seq);

        readRecord(meta, seq, inFile);

        // Header lines are not touched.
        if (front(seq) != '>')
        {
            typedef typename Iterator<CharString, Rooted>::Type TIter;
            for (TIter it = begin(seq, Rooted()); !atEnd(it); goNext(it))
                if (std::islower(*it))
                    *it = 'N';
        }

        stream << meta << '\n' << seq << '\n';
    }
}

int main(int argc, char const ** argv)
{
    for (int i = 1; i < argc; ++i)
    {
        std::cerr << argv[i] << '\n';
        convertToHardMasked(std::cout, argv[i]);
    }

    return 0;
}
