Detailed Description

This module contains a series of functions to build a Q-Group Index, as described in:

: Massively parallel read mapping on GPUs with PEANUT
Johannes Koester and Sven Rahmann
http://arxiv.org/pdf/1403.1706v1.pdf
this data-structure requires O(A^q) bits of storage in the alphabet-size A and the q-gram length q (to be precise, 2*A^q bits + (min(A^q,|T|) + |T|) words), and provides O(1) query time;

Classes
struct	nvbio::QGroupIndexViewCore< index_iterator >

struct	nvbio::QGroupIndexHost

struct	nvbio::QGroupIndexDevice

struct	nvbio::plain_view_subtype< QGroupIndexHost >

struct	nvbio::plain_view_subtype< QGroupIndexDevice >

struct	nvbio::plain_view_subtype< const QGroupIndexHost >

struct	nvbio::plain_view_subtype< const QGroupIndexDevice >

Typedefs
typedef QGroupIndexViewCore < uint32 * >	nvbio::QGroupIndexView

typedef QGroupIndexViewCore < const uint32 * >	nvbio::ConstQGroupIndexView

Functions
QGroupIndexView	nvbio::plain_view (const QGroupIndexView qgram)

ConstQGroupIndexView	nvbio::plain_view (const ConstQGroupIndexView qgram)

QGroupIndexView	nvbio::plain_view (QGroupIndexDevice &qgroup)

ConstQGroupIndexView	nvbio::plain_view (const QGroupIndexDevice &qgroup)

Typedef Documentation

typedef QGroupIndexViewCore<const uint32*> nvbio::ConstQGroupIndexView

Definition at line 160 of file qgroup.h.

typedef QGroupIndexViewCore<uint32*> nvbio::QGroupIndexView

Definition at line 159 of file qgroup.h.

QGroupIndexView nvbio::plain_view ( const QGroupIndexView qgram)

inline

return the plain view of a QGroupIndexView, i.e. the object itself

Definition at line 254 of file qgroup.h.

ConstQGroupIndexView nvbio::plain_view ( const ConstQGroupIndexView qgram)

inline

return the plain view of a QGroupIndexView, i.e. the object itself

Definition at line 259 of file qgroup.h.

QGroupIndexView nvbio::plain_view ( QGroupIndexDevice & qgroup)

inline

return the plain view of a QGroupIndex

Definition at line 264 of file qgroup.h.

ConstQGroupIndexView nvbio::plain_view ( const QGroupIndexDevice & qgroup)

inline

return the plain view of a QGroupIndex

Definition at line 280 of file qgroup.h.