theplu::yat::omic::BamHeader Class Reference

Wrapper around bam_hdr_t struct. More...

#include <yat/omic/BamHeader.h>

Public Types
typedef boost::transform_iterator < utility::PairFirst< const strMap2::value_type > , strMap2::const_iterator >	read_group_iterator

Public Member Functions
	BamHeader (void)
	Default constructor.
	~BamHeader (void)
	Destructor.
	BamHeader (const BamHeader &)
	Copy constructor.
void	parse_region (const std::string &reg, int &tid, int &begin, int &end) const
const std::string &	program_group (const std::string &id, const std::string &key) const
	Access value in @PG lines. More...
const std::string &	read_group (const std::string &id, const std::string &key) const
	Access value in @RG lines. More...
const std::map< std::string, std::string > &	read_group (const std::string &id) const
read_group_iterator	read_group_begin (void) const
read_group_iterator	read_group_end (void) const
void	swap (BamHeader &other)
	Exchanges the content in *this and other. More...
const char *	target_name (size_t tid) const
uint32_t	target_length (size_t tid) const
std::string	text (void) const
void	text (const std::string &txt)
	set text in header More...
int32_t	tid (const std::string &name) const
	inverse of target_name(size_t) More...
int32_t	n_targets (void) const
BamHeader &	operator= (const BamHeader &rhs)
	assignment operator

Friends
class	InBamFile
class	OutBamFile

Related Functions
(Note that these are not member functions.)
void	swap (BamHeader &lhs, BamHeader &rhs)

Detailed Description

Wrapper around bam_hdr_t struct.

Class is typically created via InBamFile::header().

It is possible to copy and assign a BamHeader, but note that a BamHeader does not own underlying data. The underlying data is owned by the InBamFile and the BamHeader is thus invalid after the corresponding InBamFile has been destroyed.

Since

New in yat 0.10

Member Typedef Documentation

typedef boost::transform_iterator< utility::PairFirst<const strMap2::value_type>, strMap2::const_iterator> theplu::yat::omic::BamHeader::read_group_iterator

read_group_iterator is used to iterate through read groups

See Also

read_group_begin

read_group_end

Since

New in yat 0.14

Member Function Documentation

int32_t theplu::yat::omic::BamHeader::n_targets

(

void

)

const

Returns

Number of chromosomes

void theplu::yat::omic::BamHeader::parse_region	(	const std::string &	reg,
		int &	tid,
		int &	begin,
		int &	end
	)		const

Parse a region in the format: 'chr2:100,000-200,000 and return values in variables tid, begin and end. reg is 1-based and begin and end are 0-based, i.e., "chr2:100,000-200,000" will set begin = 99999 and end = 200000.

Exceptions

utility::runtime_error

on failure

Since

new in yat 0.11

const std::string& theplu::yat::omic::BamHeader::program_group	(	const std::string &	id,
		const std::string &	key
	)		const

Access value in @PG lines.

A program group line in the header typically looks like

@PG ID:bwa  PN:bwa  VN:0.6.1-r104 

and for this line program_group("bwa", "VN") returns "0.6.1-r104"

Returns

value for key for line with ID id.

Since

New in yat 0.13

const std::string& theplu::yat::omic::BamHeader::read_group	(	const std::string &	id,
		const std::string &	key
	)		const

Access value in @RG lines.

A read group line in the header typically looks like

@RG ID:foo  PL:ILLUMINA SM:Tumour 

and for this line read_group("foo", "SM") returns "Tumour"

To see which IDs are available in the header, iterate through the set of IDs with read_group_begin() (and read_group_end()).

Returns

value for key for line with ID id.

Since

New in yat 0.13

const std::map<std::string, std::string>& theplu::yat::omic::BamHeader::read_group

(

const std::string &

id

)

const

Returns

a map describing an @RG line such as

@RG ID:foo  PL:ILLUMINA SM:Tumour 

for which the returned map contains two entries: one with key PL and value ILLUMINA, and one with key SM and value Tumour.

Since

New in yat 0.14

read_group_iterator theplu::yat::omic::BamHeader::read_group_begin

(

void

)

const

Returns

first of available RG IDs

Since

New in yat 0.14

read_group_iterator theplu::yat::omic::BamHeader::read_group_end

(

void

)

const

Returns

end of range of available RG IDs

See Also

read_group_begin()

Since

New in yat 0.14

void theplu::yat::omic::BamHeader::swap

(

BamHeader &

other

)

Exchanges the content in *this and other.

Since

New in yat 0.13

uint32_t theplu::yat::omic::BamHeader::target_length

(

size_t

tid

)

const

Length of chromosome with ID tid

const char* theplu::yat::omic::BamHeader::target_name

(

size_t

tid

)

const

Name of chromosome with ID tid

std::string theplu::yat::omic::BamHeader::text

(

void

)

const

Returns

text in header

Since

New in yat 0.13

void theplu::yat::omic::BamHeader::text

(

const std::string &

txt

)

set text in header

This function parses txt and updates fields.

Function invalidates object's iterators and reference returned from read_group(const std::string&).

Since

New in yat 0.13

int32_t theplu::yat::omic::BamHeader::tid

(

const std::string &

name

)

const

inverse of target_name(size_t)

If compiled against libbam and name does not exist, behavious is undefined. If compiled against htslib, a utility::runtime_error is thrown.

Since

new in yat 0.11

Friends And Related Function Documentation

void swap ( BamHeader &  lhs, BamHeader &  rhs  )

related

Exchanges the content in the headers.

Since

New in yat 0.13

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

• yat/omic/BamHeader.h