/usr/include/pbbam/internal/QueryBase.h is in libpbbam-dev 0.7.4+ds-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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//
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted (subject to the limitations in the
// disclaimer below) 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 Pacific Biosciences nor the names of its
// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
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// SUCH DAMAGE.
// Author: Derek Barnett
#ifndef QUERYBASE_H
#define QUERYBASE_H
#include "pbbam/BamFile.h"
#include "pbbam/BamRecord.h"
#include "pbbam/DataSet.h"
#include <memory>
#include <vector>
#include <cassert>
namespace PacBio {
namespace BAM {
namespace internal {
template<typename T>
class QueryBase;
template<typename T>
class QueryIteratorBase
{
public:
virtual ~QueryIteratorBase(void);
bool operator==(const QueryIteratorBase<T>& other) const;
bool operator!=(const QueryIteratorBase<T>& other) const;
protected:
QueryIteratorBase(void);
QueryIteratorBase(QueryBase<T>& query);
void ReadNext(void);
protected:
QueryBase<T>* query_;
T record_;
};
template<typename T>
class QueryIterator : public QueryIteratorBase<T>
{
public:
QueryIterator(void);
QueryIterator(QueryBase<T>& query);
T& operator*(void);
T* operator->(void);
QueryIterator<T>& operator++(void);
QueryIterator<T> operator++(int);
};
template<typename T>
class QueryConstIterator : public QueryIteratorBase<T>
{
public:
QueryConstIterator(void);
QueryConstIterator(const QueryBase<T>& query);
const T& operator*(void) const;
const T* operator->(void) const;
QueryConstIterator<T>& operator++(void);
QueryConstIterator<T> operator++(int);
};
template<typename T>
class QueryBase {
public:
typedef QueryIterator<T> iterator;
typedef QueryConstIterator<T> const_iterator;
public:
virtual ~QueryBase(void);
public:
QueryConstIterator<T> begin(void) const;
QueryConstIterator<T> cbegin(void) const;
QueryIterator<T> begin(void);
QueryConstIterator<T> end(void) const;
QueryConstIterator<T> cend(void) const;
QueryIterator<T> end(void);
public:
virtual bool GetNext(T& r) =0;
protected:
QueryBase(void);
};
typedef QueryBase<BamRecord> IQuery;
typedef QueryBase<std::vector<BamRecord> > IGroupQuery;
} // namespace internal
} // namespace BAM
} // namespace PacBio
#include "pbbam/internal/QueryBase.inl"
#endif // QUERYBASE_H
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