gamgee::SamHeader Class Reference

Utility class to hold the header of a sam file. More...

#include <sam_header.h>

Public Member Functions
	SamHeader ()=default
	initializes a null SamHeader More...
	SamHeader (const std::shared_ptr< bam_hdr_t > &header)
	creates a SamHeader given htslib object. More...
	SamHeader (const SamHeader &other)
	makes a deep copy of a SamHeader. Shared pointers maintain state to all other associated objects correctly. More...
SamHeader &	operator= (const SamHeader &other)
	deep copy assignment of a SamHeader. Shared pointers maintain state to all other associated objects correctly. More...
	SamHeader (SamHeader &&other)=default
	moves SamHeader accordingly. Shared pointers maintain state to all other associated objects correctly. More...
SamHeader &	operator= (SamHeader &&other)=default
	move assignment of a SamHeader. Shared pointers maintain state to all other associated objects correctly. More...
uint32_t	n_sequences () const
	Returns the number of reference sequences in the header. More...
uint32_t	sequence_length (const std::string &sequence_name) const
	Returns the length of the given reference sequence as stored in the @SQ tag in the BAM header. More...
uint32_t	sequence_length (const uint32_t sequence_index) const
	Returns the length of the given reference sequence as stored in the @SQ tag in the BAM header. More...
std::string	sequence_name (const uint32_t sequence_index) const
	Returns the sequence name for the sequence with the given zero-based index. More...
std::vector< ReadGroup >	read_groups () const
	extracts read group objects from a SAM header More...

Friends
class	SamWriter
class	SamBuilder

Detailed Description

Utility class to hold the header of a sam file.

Constructor & Destructor Documentation

gamgee::SamHeader::SamHeader ( )

explicitdefault

initializes a null SamHeader

Warning

if you need to create a SamHeader from scratch, use the builder instead

gamgee::SamHeader::SamHeader ( const std::shared_ptr< bam_hdr_t > &  header )

explicit

creates a SamHeader given htslib object.

creates a SamHeader object that points to htslib memory already allocated

Note

used by all iterators

the resulting SamHeader object shares ownership of the pre-allocated memory via shared_ptr reference counting

gamgee::SamHeader::SamHeader

(

const SamHeader &

other

)

makes a deep copy of a SamHeader. Shared pointers maintain state to all other associated objects correctly.

creates a deep copy of a SamHeader object

Note

the copy will have exclusive ownership over the newly-allocated htslib memory

gamgee::SamHeader::SamHeader ( SamHeader &&  other )

default

moves SamHeader accordingly. Shared pointers maintain state to all other associated objects correctly.

Member Function Documentation

uint32_t gamgee::SamHeader::n_sequences ( ) const

inline

Returns the number of reference sequences in the header.

SamHeader & gamgee::SamHeader::operator=

(

const SamHeader &

other

)

deep copy assignment of a SamHeader. Shared pointers maintain state to all other associated objects correctly.

creates a deep copy of a SamHeader object

Note

the copy will have exclusive ownership over the newly-allocated htslib memory

< shared_ptr assignment will take care of deallocating old sam record if necessary

SamHeader& gamgee::SamHeader::operator= ( SamHeader &&  other )

default

move assignment of a SamHeader. Shared pointers maintain state to all other associated objects correctly.

vector< ReadGroup > gamgee::SamHeader::read_groups

(

)

const

extracts read group objects from a SAM header

uint32_t gamgee::SamHeader::sequence_length

(

const std::string &

sequence_name

)

const

Returns the length of the given reference sequence as stored in the @SQ tag in the BAM header.

Returns the length of the given sequence as stored in the @SQ tag in the BAM header, or 0 if the sequence name is not found.

uint32_t gamgee::SamHeader::sequence_length ( const uint32_t  sequence_index ) const

inline

Returns the length of the given reference sequence as stored in the @SQ tag in the BAM header.

std::string gamgee::SamHeader::sequence_name ( const uint32_t  sequence_index ) const

inline

Returns the sequence name for the sequence with the given zero-based index.

Friends And Related Function Documentation

friend class SamBuilder

friend

friend class SamWriter

friend

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The documentation for this class was generated from the following files:

• gamgee/sam/sam_header.h
• gamgee/sam/sam_header.cpp