Detailed description

Base class to encode a host-side SequenceData object. The alphabet is provided to this class as a run-time parameter.

Definition at line 39 of file sequence_encoder.h.

#include <sequence_encoder.h>

Inheritance diagram for nvbio::io::SequenceDataEncoder:

Public Types
enum	StrandOp { NO_OP = 0x0000, REVERSE_OP = 0x0001, COMPLEMENT_OP = 0x0002, REVERSE_COMPLEMENT_OP = 0x0003 }

Public Methods
	SequenceDataEncoder (const Alphabet alphabet)

virtual	~SequenceDataEncoder ()

virtual void	reserve (const uint32 n_reads, const uint32 n_bps)

virtual void	push_back (const uint32 in_sequence_len, const char name, const uint8 base_pairs, const uint8 *quality, const QualityEncoding quality_encoding, const uint32 max_sequence_len, const uint32 trim3, const uint32 trim5, const StrandOp conversion_flags)

virtual void	begin_batch (void)

virtual void	end_batch (void)

virtual const SequenceDataInfo *	info () const

Alphabet	alphabet () const

Member Enumeration Documentation

enum nvbio::io::SequenceDataEncoder::StrandOp

a set of flags describing the operators to apply to a given strand

Enumerator
NO_OP	default, no operator applied
REVERSE_OP	reverse operator
COMPLEMENT_OP	complement operator
REVERSE_COMPLEMENT_OP	convenience definition, same as StrandOp( REVERSE_OP \| COMPLEMENT_OP )

Definition at line 43 of file sequence_encoder.h.

Constructor & Destructor Documentation

nvbio::io::SequenceDataEncoder::SequenceDataEncoder ( const Alphabet alphabet)

inline

constructor

Definition at line 53 of file sequence_encoder.h.

virtual nvbio::io::SequenceDataEncoder::~SequenceDataEncoder ( )

inlinevirtual

destructor

Definition at line 57 of file sequence_encoder.h.

Member Function Documentation

Alphabet nvbio::io::SequenceDataEncoder::alphabet ( ) const

inline

get the alphabet

Definition at line 109 of file sequence_encoder.h.

virtual void nvbio::io::SequenceDataEncoder::begin_batch ( void )

inlinevirtual

signals that a batch is to begin

Reimplemented in nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET >.

Definition at line 97 of file sequence_encoder.h.

virtual void nvbio::io::SequenceDataEncoder::end_batch ( void )

inlinevirtual

signals that the batch is complete

Reimplemented in nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET >.

Definition at line 101 of file sequence_encoder.h.

virtual const SequenceDataInfo* nvbio::io::SequenceDataEncoder::info ( ) const

inlinevirtual

return the sequence data info

Reimplemented in nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET >.

Definition at line 105 of file sequence_encoder.h.

virtual void nvbio::io::SequenceDataEncoder::push_back	(	const uint32	in_sequence_len,
		const char *	name,
		const uint8 *	base_pairs,
		const uint8 *	quality,
		const QualityEncoding	quality_encoding,
		const uint32	max_sequence_len,
		const uint32	trim3,
		const uint32	trim5,
		const StrandOp	conversion_flags
	)

inlinevirtual

add a read to the end of this batch

Parameters

sequence_len	input read length
name	read name
base_pairs	list of base pairs
quality	list of base qualities
quality_encoding	quality encoding scheme
max_sequence_len	truncate the read if longer than this
conversion_flags	conversion operators applied to the strand

Reimplemented in nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET >.

Definition at line 73 of file sequence_encoder.h.

virtual void nvbio::io::SequenceDataEncoder::reserve	(	const uint32	n_reads,
		const uint32	n_bps
	)

inlinevirtual

reserve enough storage for a given number of reads and bps

Reimplemented in nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET >.

Definition at line 61 of file sequence_encoder.h.

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

E:/git/nvbio/nvbio/io/sequence/sequence_encoder.h

Detailed description

Public Types

Public Methods

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation