/usr/include/pbbam/IndexedFastaReader.h is in libpbbam-dev 0.7.4+ds-1build2.
This file is owned by root:root, with mode 0o644.
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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 IndexedFastaReader.h
/// \brief Defines the IndexedFastaReader class.
//
// Author: David Alexander
#ifndef INDEXEDFASTAREADER_H
#define INDEXEDFASTAREADER_H
#include "pbbam/Orientation.h"
#include "pbbam/Position.h"
#include <htslib/faidx.h>
#include <string>
#include <iostream>
#include <stdexcept>
namespace PacBio {
namespace BAM {
class GenomicInterval;
class BamRecord;
/// \brief The IndexedFastaReader class provides random-access to FASTA file
/// data.
///
class IndexedFastaReader {
public:
/// \name Constructors & Related Methods
/// \{
IndexedFastaReader(void) = delete;
IndexedFastaReader(const std::string& filename);
IndexedFastaReader(const IndexedFastaReader& src);
IndexedFastaReader& operator=(const IndexedFastaReader& rhs);
~IndexedFastaReader(void);
/// \}
public:
/// name Sequence Access
/// \{
/// \brief Fetches FASTA sequence for desired interval.
///
/// \param[in] id reference sequence name
/// \param[in] begin start position
/// \param[in] end end position
///
/// \returns sequence string at desired interval
///
/// \throws std::runtime_error on failure to fetch sequence
///
std::string Subsequence(const std::string& id,
Position begin,
Position end) const;
/// \brief Fetches FASTA sequence for desired interval.
///
/// \param[in] interval desired interval
///
/// \returns sequence string at desired interval
///
/// \throws std::runtime_error on failure to fetch sequence
///
std::string Subsequence(const GenomicInterval& interval) const;
/// \brief Fetches FASTA sequence for desired interval.
///
/// \param[in] htslibRegion htslib/samtools-formatted REGION string
/// representing the desired interval
///
/// \returns sequence string at desired interval
///
/// \throws std::runtime_error on failure to fetch sequence
///
std::string Subsequence(const char* htslibRegion) const;
/// \brief Fetches FASTA sequence corresponding to a BamRecord, oriented and
/// gapped as requested.
///
/// For example, "native" orientation and "gapped" will return the reference
/// sequence with gaps inserted, as would align against the read in "native"
/// orientation.
///
/// \param[in] bamRecord input BamRecord to derive interval/CIGAR
/// data
/// \param[in] orientation orientation of output
/// \param[in] gapped if true, gaps/padding will be inserted, per
/// record's CIGAR info.
/// \param[in] exciseSoftClips if true, any soft-clipped positions will be
/// removed from query ends
///
/// \returns sequence string over the record's interval
///
/// \throws std::runtime_error on failure to fetch sequence
///
std::string ReferenceSubsequence(const BamRecord& bamRecord,
const Orientation orientation=Orientation::GENOMIC,
const bool gapped=false,
const bool exciseSoftClips=false) const;
/// \}
public:
/// \name File Attributes
/// \{
/// \returns true if FASTA file contains a sequence matching \p name
bool HasSequence(const std::string& name) const;
/// \returns number of sequences stored in FASTA file
int NumSequences(void) const;
/// \returns length of FASTA sequence
///
/// \throws std::runtime_error if length could not be determined
///
int SequenceLength(const std::string& name) const;
/// \}
private:
std::string filename_;
faidx_t* handle_;
private:
void Close(void);
bool Open(const std::string& filename);
};
} // namespace BAM
} // namespace PacBio
#endif // INDEXEDFASTAREADER_H
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