/usr/include/pbbam/CompositeBamReader.h is in libpbbam-dev 0.7.4+ds-1.
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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
// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
// SUCH DAMAGE.
//
// File Description
/// \file CompositeBamReader.h
/// \brief Defines the composite BAM readers, for working with multiple input
/// files.
//
// Author: Derek Barnett
#ifndef COMPOSITEBAMREADER_H
#define COMPOSITEBAMREADER_H
#include "pbbam/BaiIndexedBamReader.h"
#include "pbbam/BamFile.h"
#include "pbbam/BamHeader.h"
#include "pbbam/BamReader.h"
#include "pbbam/BamRecord.h"
#include "pbbam/Config.h"
#include "pbbam/DataSet.h"
#include "pbbam/GenomicInterval.h"
#include "pbbam/PbiIndexedBamReader.h"
#include <deque>
#include <functional>
#include <memory>
#include <string>
#include <vector>
namespace PacBio {
namespace BAM {
namespace internal {
/// \internal
/// \brief The CompositeMergeItem class provides a helper struct for composite
/// readers, containing a single-file reader and its "next" record.
///
struct CompositeMergeItem
{
public:
std::unique_ptr<BamReader> reader;
BamRecord record;
public:
CompositeMergeItem(std::unique_ptr<BamReader>&& rdr);
CompositeMergeItem(std::unique_ptr<BamReader>&& rdr, BamRecord&& rec);
CompositeMergeItem(CompositeMergeItem&& other);
CompositeMergeItem& operator=(CompositeMergeItem&& other);
~CompositeMergeItem(void);
};
/// \internal
/// \brief The CompositeMergeItemSorter class provides a helper function object
/// for ordering composite reader results.
///
/// Essentially just exracts a BamRecord from its parent CompositeMergeItem for
/// further checks.
///
template<typename CompareType>
struct CompositeMergeItemSorter : public std::function<bool(const CompositeMergeItem&,
const CompositeMergeItem&)>
{
bool operator()(const CompositeMergeItem& lhs,
const CompositeMergeItem& rhs);
};
} // namespace internal
/// \brief The GenomicIntervalCompositeBamReader class provides read access to
/// multipe %BAM files, limiting results to a genomic region.
///
/// Requires a ".bai" file for each input %BAM file.
///
/// Results will be returned in order of genomic coordinate (first by reference
/// ID, then by position).
///
class PBBAM_EXPORT GenomicIntervalCompositeBamReader
{
public:
/// \name Contstructors & Related Methods
/// \{
GenomicIntervalCompositeBamReader(const GenomicInterval& interval,
const std::vector<BamFile>& bamFiles);
GenomicIntervalCompositeBamReader(const GenomicInterval& interval,
std::vector<BamFile>&& bamFiles);
GenomicIntervalCompositeBamReader(const GenomicInterval& interval,
const DataSet& dataset);
/// \}
public:
/// \name Data Access
/// \{
/// Fetches next BAM record in the interval specified, storing in \p record
///
/// \param[out] record
/// \returns true on success, false if no more data available.
///
bool GetNext(BamRecord& record);
/// Sets a new genomic interval of interest.
///
/// \returns reference to this reader
///
GenomicIntervalCompositeBamReader& Interval(const GenomicInterval& interval);
/// \returns the current specified interval
///
const GenomicInterval& Interval(void) const;
/// \}
private:
void UpdateSort(void);
private:
GenomicInterval interval_;
std::deque<internal::CompositeMergeItem> mergeItems_;
std::vector<std::string> filenames_;
};
/// \brief Provides read access to multipe %BAM files, limiting results to those
/// passing a PbiFilter.
///
/// Requires a ".pbi" file for each input %BAM file.
///
/// \note The template parameter OrderByType is not fully implemented at this
/// time. Use of comparison functor (e.g. Compare::Zmw) for this will
/// currently result in the proper "next" value <b> at each iteration
/// step, independently, but not over the full data set. </b> If all
/// files' "order-by" data values are accessible in increasing order
/// within each file, then the expected ordering will be observed,
/// However, if these data are not sorted within a file, the final results
/// will appear unordered. \n
/// \n
/// Example:\n
/// file 1: { 1, 5, 2, 6 } \n
/// file 2: { 3, 8, 4, 7 } \n
/// results: { 1, 3, 5, 2, 6, 8, 4, 7 } \n
/// \n
/// This a known issue and will be addressed in a future update. But in
/// the meantime, use of Compare::None as the OrderByType is recommended,
/// to explicitly indicate that no particular ordering is expected.
///
template<typename OrderByType>
class PBBAM_EXPORT PbiFilterCompositeBamReader
{
public:
typedef internal::CompositeMergeItem value_type;
typedef internal::CompositeMergeItemSorter<OrderByType> merge_sorter_type;
typedef std::deque<value_type> container_type;
typedef typename container_type::iterator iterator;
typedef typename container_type::const_iterator const_iterator;
public:
/// \name Contstructors & Related Methods
/// \{
PbiFilterCompositeBamReader(const PbiFilter& filter,
const std::vector<BamFile>& bamFiles);
PbiFilterCompositeBamReader(const PbiFilter& filter,
std::vector<BamFile>&& bamFiles);
PbiFilterCompositeBamReader(const PbiFilter& filter,
const DataSet& dataset);
/// \}
public:
/// \name Data Access
/// \{
/// Fetches next BAM record in the interval specified.
///
/// \returns true on success, false if no more data available.
///
bool GetNext(BamRecord& record);
/// Sets a new PBI filter
///
/// \returns reference to this reader
///
PbiFilterCompositeBamReader& Filter(const PbiFilter& filter);
/// \}
private:
void UpdateSort(void);
private:
container_type mergeQueue_;
std::vector<std::string> filenames_;
};
/// \brief The SequentialCompositeBamReader class provides read access to
/// multiple %BAM files, reading through the entire contents of each
/// file.
///
/// Input files will be accessed in the order provided to the constructor. Each
/// file's contents will be exhausted before moving on to the next one (as
/// opposed to a "round-robin" scheme).
///
class PBBAM_EXPORT SequentialCompositeBamReader
{
public:
/// \name Contstructors & Related Methods
/// \{
SequentialCompositeBamReader(const std::vector<BamFile>& bamFiles);
SequentialCompositeBamReader(std::vector<BamFile>&& bamFiles);
SequentialCompositeBamReader(const DataSet& dataset);
/// \}
public:
/// \name Data Access
/// \{
/// Fetches next BAM record from the .
///
/// \returns true on success, false if no more data available.
///
bool GetNext(BamRecord& record);
/// \}
private:
std::deque<std::unique_ptr<BamReader> > readers_;
};
} // namespace BAM
} // namespace PacBio
#include "pbbam/internal/CompositeBamReader.inl"
#endif // COMPOSITEBAMREADER_H
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