libpbbam-dev 0.7.4+ds-1 / usr / include / pbbam / BamHeader.h

// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
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// File Description
/// \file BamHeader.h
/// \brief Defines the BamHeader class.
//
// Author: Derek Barnett

#ifndef BAMHEADER_H
#define BAMHEADER_H

#include "pbbam/Config.h"
#include "pbbam/ProgramInfo.h"
#include "pbbam/ReadGroupInfo.h"
#include "pbbam/SequenceInfo.h"
#include <stdexcept>
#include <string>
#include <vector>

namespace PacBio {
namespace BAM {

namespace internal { class BamHeaderPrivate; }

/// \brief The BamHeader class represents the header section of the %BAM file.
///
/// It provides metadata about the file including file version, reference
/// sequences, read groups, comments, etc.
///
/// A BamHeader may be fetched from a BamFile to view an existing file's
/// metadata. Or one may be created/edited for use with writing to a new file
/// (via BamWriter).
///
/// \note A particular BamHeader is likely to be re-used in lots of places
///       throughout the library, for read-only purposes. For this reason, even
///       though a BamHeader may be returned by value, it is essentially a thin
///       wrapper for a shared-pointer to the actual data. This means, though,
///       that if you need to edit an existing BamHeader for use with a
///       BamWriter, please consider using BamHeader::DeepCopy. Otherwise any
///       modifications will affect all BamHeaders that are sharing its
///       underlying data.
///
class PBBAM_EXPORT BamHeader
{
public:
    /// \name Constructors & Related Methods
    /// \{

    BamHeader(void);
    BamHeader(const std::string& samHeaderText);
    BamHeader(const BamHeader& other);
    BamHeader(BamHeader&& other);
    BamHeader& operator=(const BamHeader& other);
    BamHeader& operator=(BamHeader&& other);
    ~BamHeader(void);

    /// \brief Detaches underlying data from the shared-pointer, returning a
    ///        independent copy of the header contents.
    ///
    /// This ensures that any modifications to the newly returned BamHeader do
    /// not affect other BamHeader objects that were sharing its underlying data.
    ///
    BamHeader DeepCopy(void) const;

    /// \}

public:
    /// \name Operators
    /// \{

    /// \brief Merges another header with this one.
    ///
    /// Headers must be compatible for merging. This means that their Version,
    /// SortOrder, PacBioBamVersion (and in the case of aligned BAM data,
    /// Sequences) must all match. If not, an exception will be thrown.
    ///
    /// \param[in] other  header to merge with this one
    /// \returns reference to this header
    ///
    /// \throws std::runtime_error if the headers are not compatible
    ///
    BamHeader& operator+=(const BamHeader& other);

    /// \brief Creates a new, merged header.
    ///
    /// Headers must be compatible for merging. This means that their Version,
    /// SortOrder, PacBioBamVersion (and in the case of aligned BAM data,
    /// Sequences) must all match. If not, an exception will be thrown.
    ///
    /// Both original headers (this header and \p other) will not be modified.
    ///
    /// \param[in] other  header to merge with this one
    /// \returns merged header
    ///
    /// \throws std::runtime_error if the headers are not compatible
    ///
    BamHeader operator+(const BamHeader& other) const;

    /// \}

public:
    /// \name General Attributes
    /// \{

    /// \returns the %PacBio %BAM version number (\@HD:pb)
    ///
    /// \note This is different from the SAM/BAM version number
    /// \sa BamHeader::Version.
    ///
    std::string PacBioBamVersion(void) const;

    /// \returns the sort order used
    ///
    /// Valid values: "unknown", "unsorted", "queryname", or "coordinate"
    ///
    std::string SortOrder(void) const;

    /// \returns the SAM/BAM version number (\@HD:VN)
    ///
    /// \note This is different from the %PacBio %BAM version number
    /// \sa BamHeader::PacBioBamVersion
    ///
    std::string Version(void) const;

    /// \}

public:
    /// \name Read Groups
    /// \{

    /// \returns true if the header contains a read group with \p id (\@RG:ID)
    bool HasReadGroup(const std::string& id) const;

    /// \returns a ReadGroupInfo object representing the read group matching
    ///          \p id (\@RG:ID)
    /// \throws std::runtime_error if \p id is unknown
    ///
    ReadGroupInfo ReadGroup(const std::string& id) const;

    /// \returns vector of read group IDs listed in this header
    std::vector<std::string> ReadGroupIds(void) const;

    /// \returns vector of ReadGroupInfo objects, representing all read groups
    ///          listed in this header
    ///
    std::vector<ReadGroupInfo> ReadGroups(void) const;

    /// \}

public:
    /// \name Sequences
    /// \{

    /// \returns true if header contains a sequence with \p name (\@SQ:SN)
    bool HasSequence(const std::string& name) const;

    /// \returns number of sequences (\@SQ entries) stored in this header
    size_t NumSequences(void) const;

    /// \returns numeric ID for sequence matching \p name (\@SQ:SN)
    ///
    /// This is the numeric ID used elsewhere throughout the API.
    ///
    /// \throws std::runtime_error if \p name is unknown
    /// \sa BamReader::ReferenceId, PbiReferenceIdFilter,
    ///     PbiRawMappedData::tId_
    ///
    int32_t SequenceId(const std::string& name) const;

    /// \returns the length of the sequence (\@SQ:LN, e.g. chromosome length) at
    ///          index \p id
    ///
    /// \sa SequenceInfo::Length, BamHeader::SequenceId
    ///
    std::string SequenceLength(const int32_t id) const;

    /// \returns the name of the sequence (\@SQ:SN) at index \p id
    ///
    /// \sa SequenceInfo::Name, BamHeader::SequenceId
    ///
    std::string SequenceName(const int32_t id) const;

    /// \returns vector of sequence names (\@SQ:SN) stored in this header
    ///
    /// Position in the vector is equivalent to SequenceId.
    ///
    std::vector<std::string> SequenceNames(void) const;

    /// \returns SequenceInfo object at index \p id
    ///
    /// \throws std::out_of_range if \p is an invalid or unknown index
    /// \sa BamHeader::SequenceId
    ///
    SequenceInfo Sequence(const int32_t id) const;

    /// \returns SequenceInfo for the sequence matching \p name
    SequenceInfo Sequence(const std::string& name) const;

    /// \returns vector of SequenceInfo objects representing the sequences
    ///          (\@SQ entries) stored in this header
    ///
    std::vector<SequenceInfo> Sequences(void) const;

    /// \}

public:
    /// \name Programs
    /// \{

    /// \returns true if this header contains a program entry with ID (\@PG:ID)
    ///          matching \p id
    ///
    bool HasProgram(const std::string& id) const;

    /// \returns ProgramInfo object for the program entry matching \p id
    /// \throws std::runtime_error if \p id is unknown
    ///
    ProgramInfo Program(const std::string& id) const;

    /// \returns vector of program IDs (\@PG:ID)
    std::vector<std::string> ProgramIds(void) const;

    /// \returns vector of ProgramInfo objects representing program entries
    ///          (\@PG) stored in this heder
    ///
    std::vector<ProgramInfo> Programs(void) const;

    /// \}

public:
    /// \name Comments
    /// \{

    /// \returns vector of comment (\@CO) strings
    std::vector<std::string> Comments(void) const;

    /// \}

public:
    /// \name Conversion Methods
    /// \{

    /// \returns SAM-header-formatted string representing this header's data
    std::string ToSam(void) const;

    /// \}

public:

    /// \name General Attributes
    /// \{

    /// \brief Sets this header's PacBioBAM version number (\@HD:pb).
    ///
    /// \returns reference to this object
    /// \throws std::runtime_error if version number cannot be parsed or
    ///         is less than the minimum version allowed.
    ///
    BamHeader& PacBioBamVersion(const std::string& version);

    /// \brief Sets this header's sort order label (\@HD:SO).
    ///
    /// Valid values: "unknown", "unsorted", "queryname", or "coordinate"
    ///
    /// \returns reference to this object
    ///
    BamHeader& SortOrder(const std::string& order);

    /// \brief Sets this header's SAM/BAM version number (\@HD:VN).
    ///
    /// \returns reference to this object
    ///
    BamHeader& Version(const std::string& version);

    /// \}

public:
    /// \name Read Groups
    /// \{

    /// \brief Appends a read group entry (\@RG) to this header.
    ///
    /// \returns reference to this object
    ///
    BamHeader& AddReadGroup(const ReadGroupInfo& readGroup);

    /// \brief Removes all read group entries from this header.
    ///
    /// \returns reference to this object
    ///
    BamHeader& ClearReadGroups(void);

    /// \brief Replaces this header's list of read group entries with those in
    ///        \p readGroups.
    ///
    /// \returns reference to this object
    ///
    BamHeader& ReadGroups(const std::vector<ReadGroupInfo>& readGroups);

    /// \}

public:
    /// \name Sequences
    /// \{

    /// \brief Appends a sequence entry (\@SQ) to this header.
    ///
    /// \returns reference to this object
    ///
    BamHeader& AddSequence(const SequenceInfo& sequence);

    /// \brief Removes all sequence entries from this header.
    ///
    /// \returns reference to this object
    ///
    BamHeader& ClearSequences(void);

    /// \brief Replaces this header's list of sequence entries with those in
    ///       \p sequences.
    ///
    /// \returns reference to this object
    ///
    BamHeader& Sequences(const std::vector<SequenceInfo>& sequences);

    /// \}

public:
    /// \name Programs
    /// \{

    /// \brief Appends a program entry (\@PG) to this header.
    ///
    /// \returns reference to this object
    ///
    BamHeader& AddProgram(const ProgramInfo& pg);

    /// \brief Removes all program entries from this header.
    ///
    /// \returns reference to this object
    ///
    BamHeader& ClearPrograms(void);

    /// \brief Replaces this header's list of program entries with those in
    ///        \p programs.
    ///
    /// \returns reference to this object
    ///
    BamHeader& Programs(const std::vector<ProgramInfo>& programs);

    /// \}

public:
    /// \name Comments
    /// \{

    /// \brief Appends a comment (\@CO) to this header.
    ///
    /// \returns reference to this object
    ///
    BamHeader& AddComment(const std::string& comment);

    /// \brief Removes all comments from this header.
    ///
    /// \returns reference to this object
    ///
    BamHeader& ClearComments(void);

    /// \brief Replaces this header's list of comments with those in \p comments.
    ///
    /// \returns reference to this object
    ///
    BamHeader& Comments(const std::vector<std::string>& comments);

    /// \}

private:
    PBBAM_SHARED_PTR<internal::BamHeaderPrivate> d_;
};

} // namespace BAM
} // namespace PacBio

#include "pbbam/internal/BamHeader.inl"

#endif // BAMHEADER_H