BamReadFilter.h

#ifndef theplu_yat_omic_bam_read_filter
#define theplu_yat_omic_bam_read_filter

// $Id: BamReadFilter.h 3363 2014-11-25 10:42:54Z peter $

/*
  Copyright (C) 2013, 2014 Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  The yat library 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.

  The yat library 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 "config_bam.h"
#include YAT_SAM_HEADER

#include <functional>

// this flag was defined in bam.h but has disappeared in htslib
#ifndef BAM_DEF_MASK
#define BAM_DEF_MASK (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP)
#endif

namespace theplu {
namespace yat {
namespace omic {

  class BamRead;

  class BamReadFilter : public std::unary_function<const BamRead&, bool>
  {
  public:
    BamReadFilter(unsigned char mapQ, unsigned int filtered_flags=BAM_DEF_MASK,
                  unsigned int required_flags=0);

    bool operator()(const BamRead& bam) const;
  private:
    unsigned char mapQ_;
    unsigned int filtered_;
    unsigned int required_;
  };

}}}
#endif