Detailed description

a read batch in host memory

Definition at line 415 of file reads.h.

#include <reads.h>

Inheritance diagram for nvbio::io::ReadDataRAM:

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

Public Types inherited from nvbio::io::ReadData
typedef ReadDataView< uint32 , uint32 , char , char >	plain_view_type

typedef ReadDataView< const uint32 , const uint32 , const char , const char >	const_plain_view_type

Public Types inherited from nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >
typedef IndexIterator	index_iterator
	the index iterator More...

typedef to_const < index_iterator >::type	const_index_iterator
	the const index iterator More...

typedef ReadStorageIterator	read_storage_iterator
	the read storage iterator More...

typedef to_const < read_storage_iterator > ::type	const_read_storage_iterator
	the const read storage iterator More...

typedef QualStorageIterator	qual_storage_iterator
	the qualities iterator More...

typedef to_const < qual_storage_iterator > ::type	const_qual_storage_iterator
	the const qualities iterator More...

typedef NameStorageIterator	name_storage_iterator
	the names string iterator More...

typedef to_const < name_storage_iterator > ::type	const_name_storage_iterator
	the names string iterator More...

typedef PackedStream < read_storage_iterator, uint8, READ_BITS, READ_BIG_ENDIAN >	read_stream_type
	the packed read-stream type More...

typedef PackedStream < const_read_storage_iterator, uint8, READ_BITS, READ_BIG_ENDIAN >	const_read_stream_type
	the const packed read-stream type More...

typedef read_stream_type::iterator	read_stream_iterator
	the read-stream iterator More...

typedef const_read_stream_type::iterator	const_read_stream_iterator
	the const read-stream iterator More...

typedef vector_view < read_stream_iterator >	read_string
	the read string type More...

typedef vector_view < const_read_stream_iterator >	const_read_string
	the const read string type More...

typedef ConcatenatedStringSet < read_stream_iterator, index_iterator >	read_string_set_type
	string-set type More...

typedef ConcatenatedStringSet < const_read_stream_iterator, const_index_iterator >	const_read_string_set_type
	const string-set type More...

typedef ConcatenatedStringSet < qual_storage_iterator, index_iterator >	qual_string_set_type
	quality string-set type More...

typedef ConcatenatedStringSet < const_qual_storage_iterator, const_index_iterator >	const_qual_string_set_type
	const quality string-set type More...

typedef ConcatenatedStringSet < name_storage_iterator, index_iterator >	name_string_set_type
	name string-set type More...

typedef ConcatenatedStringSet < const_name_storage_iterator, const_index_iterator >	const_name_string_set_type
	const name string-set type More...

Public Methods
	ReadDataRAM ()

void	reserve (const uint32 n_reads, const uint32 n_bps)

void	push_back (uint32 read_len, const char name, const uint8 base_pairs, const uint8 *quality, const QualityEncoding quality_encoding, const uint32 truncate_read_len, const StrandOp conversion_flags)

void	end_batch (void)

Public Methods inherited from nvbio::io::ReadData
	ReadData ()

virtual	~ReadData ()

Public Methods inherited from nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	ReadDataView ()

template<typename InIndexIterator , typename InReadIterator , typename InQualIterator , typename InNameIterator >
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	ReadDataView (const ReadDataView< InIndexIterator, InReadIterator, InQualIterator, InNameIterator > &in)

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE index_iterator	name_index ()

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE index_iterator	read_index ()

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE name_storage_iterator	name_stream ()

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE read_storage_iterator	read_stream_storage ()

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE read_stream_type	read_stream ()

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE qual_storage_iterator	qual_stream ()

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_index_iterator	const_name_index () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_index_iterator	const_read_index () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_name_storage_iterator	const_name_stream () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_storage_iterator	const_read_stream_storage () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_stream_type	const_read_stream () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_qual_storage_iterator	const_qual_stream () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_index_iterator	name_index () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_index_iterator	read_index () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_name_storage_iterator	name_stream () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_storage_iterator	read_stream_storage () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_stream_type	read_stream () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_qual_storage_iterator	qual_stream () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	size () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	bps () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	words () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	name_stream_len () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	max_read_len () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	min_read_len () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	avg_read_len () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint2	get_range (const uint32 i) const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE read_string_set_type	read_string_set ()

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_string_set_type	read_string_set () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_string_set_type	const_read_string_set () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE read_string	get_read (const uint32 i)

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE read_string	get_read (const uint32 i) const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE qual_string_set_type	qual_string_set ()

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_qual_string_set_type	qual_string_set () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_qual_string_set_type	const_qual_string_set () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE name_string_set_type	name_string_set ()

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_name_string_set_type	name_string_set () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_name_string_set_type	const_name_string_set () const

Public Members
std::vector< uint32 >	m_read_vec

std::vector< uint32 >	m_read_index_vec

std::vector< char >	m_qual_vec

std::vector< char >	m_name_vec

std::vector< uint32 >	m_name_index_vec

Additional Inherited Members
Static Public Members inherited from nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >
static const uint32	READ_BITS = 4

static const bool	HI_BITS = false

static const bool	READ_BIG_ENDIAN = false

static const uint32	READ_SYMBOLS_PER_WORD = (4*sizeof(uint32))/READ_BITS

Member Enumeration Documentation

enum nvbio::io::ReadDataRAM::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 419 of file reads.h.

Constructor & Destructor Documentation

nvbio::io::ReadDataRAM::ReadDataRAM ( )

Definition at line 275 of file reads.cpp.

Member Function Documentation

void nvbio::io::ReadDataRAM::end_batch ( void )

signals that the batch is complete

Definition at line 322 of file reads.cpp.

void nvbio::io::ReadDataRAM::push_back	(	uint32	read_len,
		const char *	name,
		const uint8 *	base_pairs,
		const uint8 *	quality,
		const QualityEncoding	quality_encoding,
		const uint32	truncate_read_len,
		const StrandOp	conversion_flags
	)

add a read to the end of this batch

Parameters

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

Definition at line 466 of file reads.cpp.

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

reserve enough storage for a given number of reads and bps

Definition at line 303 of file reads.cpp.

Member Data Documentation

std::vector<uint32> nvbio::io::ReadDataRAM::m_name_index_vec

Definition at line 459 of file reads.h.

std::vector<char> nvbio::io::ReadDataRAM::m_name_vec

Definition at line 458 of file reads.h.

std::vector<char> nvbio::io::ReadDataRAM::m_qual_vec

Definition at line 457 of file reads.h.

std::vector<uint32> nvbio::io::ReadDataRAM::m_read_index_vec

Definition at line 456 of file reads.h.

std::vector<uint32> nvbio::io::ReadDataRAM::m_read_vec

Definition at line 455 of file reads.h.

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

E:/git/nvbio/nvbio/io/reads/reads.h
E:/git/nvbio/nvbio/io/reads/reads.cpp

Detailed description

Public Types

Public Methods

Public Members

Additional Inherited Members

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation