wrapper class around struct faidx_t in libhts More...

#include <yat/omic/Fasta.h>

Classes
class	Sequence

Public Member Functions
	Fasta (const std::string &fn)

bool	present (const std::string &name) const

std::string	name (size_t i) const

int	nseq (void) const

int	sequence_length (const std::string &name) const

Sequence	sequence (const std::string &chr) const

Sequence	sequence (const std::string &chr, int beg, int end) const

Detailed Description

wrapper class around struct faidx_t in libhts

Class handling a fasta file. Class assumes the fasta file has an index file created by e.g. 'samtools faidx'.

Since: New in yat 0.14

Constructor & Destructor Documentation

◆ Fasta()

theplu::yat::omic::Fasta::Fasta ( const std::string & fn )

Tries to open index for fasta file fn. It is assumed that the index file is called fn + ".fai". If open fails, constructor tries to create an index file from fasta file fn (see fai_build in htslib). If that also fails, an exception is thrown.

Exceptions

utility::runtime_error if open fails

Member Function Documentation

◆ name()

std::string theplu::yat::omic::Fasta::name ( size_t i ) const

Returns: name of sequence i

◆ nseq()

int theplu::yat::omic::Fasta::nseq ( void ) const

Returns: number of sequences

◆ present()

bool theplu::yat::omic::Fasta::present ( const std::string & name ) const

Returns: true if there exist a sequence called name

◆ sequence() [1/2]

Sequence theplu::yat::omic::Fasta::sequence ( const std::string & chr ) const

Returns: entire sequence from sequence chr

◆ sequence() [2/2]

Sequence theplu::yat::omic::Fasta::sequence	(	const std::string &	chr,
		int	beg,
		int	end
	)		const

Parameters

chr	sequence name
beg	beginning position (0-based)
end	end position (0-based)

Returns: sub-sequence of chr starting at beg and with last base end (length of sequence is end-begin+1).

◆ sequence_length()

int theplu::yat::omic::Fasta::sequence_length ( const std::string & name ) const

Returns: length of sequence with name name