FastxInputStream< Reader > Class Template Reference

#include <genesis/sequence/formats/fastx_input_stream.hpp>

Detailed Description

template<class Reader>
class genesis::sequence::FastxInputStream< Reader >

Stream through an input source and parse it as Fasta or Fastq sequences.

This class allows to iterate over an input source, interpreting it as Fasta or Fastq sequences, and yielding one such sequence per iteration step. This is useful for processing large files without having to keep them fully in memory.

Example:

for( auto const& s : FastaInputStream( from_file( "/path/to/large_file.fastq" ))) {
    std::cout << s.length() << "\n";
}

Use functions such as utils::from_file() and utils::from_string() to conveniently get an input source that can be used here.

See FastaReader and FastqReader for a description of the expected formats. In order to change the reading behaviour, a reader object can be handed over from which the settings are copied. The reader instance can also be modified before starting the iteration, if needed.

Thread safety: No thread safety. The common use case for this iterator is to loop over a file. Thus, guarding induces unnecessary overhead. If multiple threads read from this iterator, both dereferencing and incrementing need to be guarded.

Definition at line 55 of file fastx_input_stream.hpp.

Public Member Functions
	FastxInputStream ()
	Create a default instance, with no input. More...
	FastxInputStream (self_type &&)=default
	FastxInputStream (self_type const &)=default
	FastxInputStream (std::shared_ptr< utils::BaseInputSource > source)
	Create an instance that reads from an input source, using a default FastaReader or FastqReader. More...
	FastxInputStream (std::shared_ptr< utils::BaseInputSource > source, Reader const &reader)
	Create an instance that reads from an input source, using the settings of a given FastaReader oder FastqReader. More...
	~FastxInputStream ()=default
Iterator	begin () const
Iterator	end () const
std::shared_ptr< utils::BaseInputSource >	input_source () const
self_type &	operator= (self_type &&)=default
self_type &	operator= (self_type const &)=default
Reader &	reader ()
Reader const &	reader () const

Public Types
using	difference_type = std::ptrdiff_t
using	iterator_category = std::input_iterator_tag
using	pointer = value_type *
using	reference = value_type &
using	self_type = FastxInputStream
using	value_type = Sequence

Classes
class	Iterator
	Internal iterator over the sequences. More...

Constructor & Destructor Documentation

FastxInputStream() [1/5]

FastxInputStream ( )

inline

Create a default instance, with no input.

Definition at line 279 of file fastx_input_stream.hpp.

FastxInputStream() [2/5]

FastxInputStream ( std::shared_ptr< utils::BaseInputSource >  source )

inlineexplicit

Create an instance that reads from an input source, using a default FastaReader or FastqReader.

Definition at line 288 of file fastx_input_stream.hpp.

FastxInputStream() [3/5]

FastxInputStream ( std::shared_ptr< utils::BaseInputSource >  source, Reader const &  reader  )

inline

Create an instance that reads from an input source, using the settings of a given FastaReader oder FastqReader.

Definition at line 299 of file fastx_input_stream.hpp.

~FastxInputStream()

~FastxInputStream ( )

default

FastxInputStream() [4/5]

FastxInputStream ( self_type const &  )

default

FastxInputStream() [5/5]

FastxInputStream ( self_type &&  )

default

Member Function Documentation

begin()

Iterator begin ( ) const

inline

Definition at line 319 of file fastx_input_stream.hpp.

end()

Iterator end ( ) const

inline

Definition at line 324 of file fastx_input_stream.hpp.

input_source()

std::shared_ptr<utils::BaseInputSource> input_source ( ) const

inline

Definition at line 333 of file fastx_input_stream.hpp.

operator=() [1/2]

self_type& operator= ( self_type &&  )

default

operator=() [2/2]

self_type& operator= ( self_type const &  )

default

reader() [1/2]

Reader& reader ( )

inline

Definition at line 338 of file fastx_input_stream.hpp.

reader() [2/2]

Reader const& reader ( ) const

inline

Definition at line 343 of file fastx_input_stream.hpp.

Member Typedef Documentation

difference_type

using difference_type = std::ptrdiff_t

Definition at line 101 of file fastx_input_stream.hpp.

iterator_category

using iterator_category = std::input_iterator_tag

Definition at line 102 of file fastx_input_stream.hpp.

pointer

using pointer = value_type*

Definition at line 99 of file fastx_input_stream.hpp.

reference

using reference = value_type&

Definition at line 100 of file fastx_input_stream.hpp.

self_type

using self_type = FastxInputStream

Definition at line 97 of file fastx_input_stream.hpp.

value_type

using value_type = Sequence

Definition at line 98 of file fastx_input_stream.hpp.

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

• fastx_input_stream.hpp