NCBI C++ ToolKit
Public Types | Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
CBamHeader Class Reference

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#include <sra/readers/bam/bamindex.hpp>

+ Collaboration diagram for CBamHeader:

Public Types

typedef map< string, stringTSBamTags
 
typedef pair< string, TSBamTagsTSBamRecord
 
typedef list< TSBamRecordTSBamRecords
 
typedef vector< SBamHeaderRefInfoTRefs
 

Public Member Functions

 CBamHeader ()
 
 CBamHeader (const string &bam_file_name)
 
 ~CBamHeader ()
 
void Read (CBGZFStream &stream)
 
void Read (const string &bam_file_name)
 
const stringGetText () const
 
size_t GetSBamRecords (TSBamRecords &records) const
 
const TRefsGetRefs () const
 
size_t GetRefCount () const
 
const SBamHeaderRefInfoGetRef (size_t ref_index) const
 
size_t GetRefIndex (const string &name) const
 
const stringGetRefName (size_t index) const
 
TSeqPos GetRefLength (size_t index) const
 
CBGZFPos GetAlignStart () const
 

Static Public Member Functions

static SBamHeaderRefInfo ReadRef (CBGZFStream &in)
 

Private Attributes

string m_Text
 
map< string, size_t > m_RefByName
 
TRefs m_Refs
 
CBGZFPos m_AlignStart
 

Detailed Description

Definition at line 56 of file bamindex.hpp.

Member Typedef Documentation

◆ TRefs

Definition at line 78 of file bamindex.hpp.

◆ TSBamRecord

Definition at line 73 of file bamindex.hpp.

◆ TSBamRecords

Definition at line 74 of file bamindex.hpp.

◆ TSBamTags

Definition at line 72 of file bamindex.hpp.

Constructor & Destructor Documentation

◆ CBamHeader() [1/2]

CBamHeader::CBamHeader ( )

Definition at line 1548 of file bamindex.cpp.

◆ CBamHeader() [2/2]

CBamHeader::CBamHeader ( const string bam_file_name)
explicit

Definition at line 1553 of file bamindex.cpp.

References Read().

◆ ~CBamHeader()

CBamHeader::~CBamHeader ( )

Definition at line 1559 of file bamindex.cpp.

Member Function Documentation

◆ GetAlignStart()

CBGZFPos CBamHeader::GetAlignStart ( ) const
inline

Definition at line 101 of file bamindex.hpp.

References m_AlignStart.

Referenced by CBamFileRangeSet::AddWhole().

◆ GetRef()

const SBamHeaderRefInfo & CBamHeader::GetRef ( size_t  ref_index) const

Definition at line 1598 of file bamindex.cpp.

References GetRefCount(), m_Refs, and NCBI_THROW.

Referenced by CBamIndex::SetLengthFromHeader().

◆ GetRefCount()

size_t CBamHeader::GetRefCount ( ) const
inline

Definition at line 84 of file bamindex.hpp.

References m_Refs.

Referenced by GetRef(), CBamRawDb::GetRefCount(), and CBamIndex::SetLengthFromHeader().

◆ GetRefIndex()

size_t CBamHeader::GetRefIndex ( const string name) const

◆ GetRefLength()

TSeqPos CBamHeader::GetRefLength ( size_t  index) const
inline

◆ GetRefName()

const string& CBamHeader::GetRefName ( size_t  index) const
inline

Definition at line 90 of file bamindex.hpp.

References m_Refs.

Referenced by CBamRawDb::GetRefName().

◆ GetRefs()

const TRefs& CBamHeader::GetRefs ( void  ) const
inline

Definition at line 79 of file bamindex.hpp.

References m_Refs.

◆ GetSBamRecords()

size_t CBamHeader::GetSBamRecords ( TSBamRecords records) const

Definition at line 1617 of file bamindex.cpp.

References CTempString::assign(), eNone, m_Text, and string.

◆ GetText()

const string& CBamHeader::GetText ( void  ) const
inline

Definition at line 67 of file bamindex.hpp.

References m_Text.

Referenced by CBamCoverageGraphPanel::SetBamFiles().

◆ Read() [1/2]

void CBamHeader::Read ( CBGZFStream stream)

◆ Read() [2/2]

void CBamHeader::Read ( const string bam_file_name)

Definition at line 1573 of file bamindex.cpp.

References file, and Read().

◆ ReadRef()

static SBamHeaderRefInfo CBamHeader::ReadRef ( CBGZFStream in)
static

Member Data Documentation

◆ m_AlignStart

CBGZFPos CBamHeader::m_AlignStart
private

Definition at line 110 of file bamindex.hpp.

Referenced by GetAlignStart(), and Read().

◆ m_RefByName

map<string, size_t> CBamHeader::m_RefByName
private

Definition at line 108 of file bamindex.hpp.

Referenced by GetRefIndex(), and Read().

◆ m_Refs

TRefs CBamHeader::m_Refs
private

Definition at line 109 of file bamindex.hpp.

Referenced by GetRef(), GetRefCount(), GetRefLength(), GetRefName(), GetRefs(), and Read().

◆ m_Text

string CBamHeader::m_Text
private

Definition at line 107 of file bamindex.hpp.

Referenced by GetSBamRecords(), GetText(), and Read().


The documentation for this class was generated from the following files:
Modified on Sat May 25 14:16:21 2024 by modify_doxy.py rev. 669887