/usr/include/pbbam/SequenceInfo.h is in libpbbam-dev 0.7.4+ds-1build2.
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.
//
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// 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
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// 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,
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
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// 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 SequenceInfo.h
/// \brief Defines the SequenceInfo class.
//
// Author: Derek Barnett
#ifndef SEQUENCEINFO_H
#define SEQUENCEINFO_H
#include "pbbam/Config.h"
#include <map>
#include <string>
namespace PacBio {
namespace BAM {
/// \brief The SequenceInfo class represents a program entry (\@SQ) in the SAM
/// header.
///
class PBBAM_EXPORT SequenceInfo
{
public:
/// \name Conversion & Validation
///
/// \brief Creates a SequenceInfo object from SAM-formatted text.
///
/// \param[in] sam SAM-formatted text
/// \returns program info object
///
static SequenceInfo FromSam(const std::string& sam);
/// \brief Converts a SequenceInfo object to its SAM-formatted text.
///
/// \param[in] seq input SequenceInfo object
/// \returns SAM-formatted text (no trailing newline)
///
static std::string ToSam(const SequenceInfo& seq);
/// \}
public:
/// \name Constructors & Related Methods
/// \{
/// \brief Creates an empty sequence info object.
SequenceInfo(void);
/// \brief Creates a sequence info object with name & (optional) length.
///
/// \param[in] name sequence name (\@SQ:SN)
/// \param[in] length sequence length (\@SQ:LN)
///
SequenceInfo(const std::string& name,
const std::string& length = "0");
SequenceInfo(const SequenceInfo& other);
SequenceInfo(SequenceInfo&& other);
SequenceInfo& operator=(const SequenceInfo& other);
SequenceInfo& operator=(SequenceInfo&& other);
~SequenceInfo(void);
/// \}
public:
/// \name Operators
/// \{
bool operator==(const SequenceInfo& other) const;
bool operator!=(const SequenceInfo& other) const;
/// \}
public:
/// \name Conversion & Validation
///
/// \returns true if sequence info is valid
///
/// Currently this checks to see that Name is non-empty and Length is within
/// the accepted range.
///
bool IsValid(void) const;
/// \brief Converts this object to its SAM-formatted text.
///
/// \returns SAM-formatted text (no trailing newline)
///
std::string ToSam(void) const;
/// \}
public:
/// \name Attributes
/// \{
/// \returns string value of \@SQ:AS
std::string AssemblyId(void) const;
/// \returns string value of \@SQ:M5
std::string Checksum(void) const;
/// \returns any non-standard tags added to the \@PG entry
///
/// Result map consists of {tagName => value}.
///
std::map<std::string, std::string> CustomTags(void) const;
/// \returns string value of \@SQ:LN
std::string Length(void) const;
/// \returns string value of \@SQ:SN
std::string Name(void) const;
/// \returns string value of \@SQ:SP
std::string Species(void) const;
/// \returns string value of \@SQ:UR
std::string Uri(void) const;
/// \}
public:
/// \name Attributes
/// \{
/// \brief Sets the value for \@SQ:AS
///
/// \param[in] id new value
/// \returns reference to this object
///
SequenceInfo& AssemblyId(const std::string& id);
/// \brief Sets the value for \@SQ:M5
///
/// \param[in] checksum new value
/// \returns reference to this object
///
SequenceInfo& Checksum(const std::string& checksum);
/// \brief Sets a new collection of non-standard tags.
///
/// Custom tag map entries should consist of {tagName => value}.
///
/// \param[in] custom new tags
/// \returns reference to this object
///
SequenceInfo& CustomTags(const std::map<std::string, std::string>& custom);
/// \brief Sets the value for \@SQ:LN
///
/// \param[in] length new value
/// \returns reference to this object
///
SequenceInfo& Length(const std::string& length);
/// \brief Sets the value for \@SQ:SN
///
/// \param[in] name new value
/// \returns reference to this object
///
SequenceInfo& Name(const std::string& name);
/// \brief Sets the value for \@SQ:SP
///
/// \param[in] species new value
/// \returns reference to this object
///
SequenceInfo& Species(const std::string& species);
/// \brief Sets the value for \@SQ:UR
///
/// \param[in] uri new value
/// \returns reference to this object
///
SequenceInfo& Uri(const std::string& uri);
/// \}
private:
std::string name_; // SN:<Name> * must be unique for valid SAM *
std::string length_; // LN:<Length> * must be within [0 - 2^31-1] *
std::string assemblyId_; // AS:<AssemblyId>
std::string checksum_; // M5:<Checksum>
std::string species_; // SP:<Species>
std::string uri_; // UR:<URI>
// custom attributes
std::map<std::string, std::string> custom_; // tag => value
};
} // namespace BAM
} // namespace PacBio
#include "pbbam/internal/SequenceInfo.inl"
#endif // SEQUENCEINFO_H
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