td element

th element

A 4-way uint8 SIMD type

An adapter implementation of the \ref SmithWatermanScoringScheme model producing the edit distance scoring

Wrapper struct to keep CIGAR arrays and CIGAR coords in one place. This is the device version.

add functor

Utility struct to gather all data related to a given alignment. This breaks out the alignment data for a given alignment by setting up pointers to the

A simple data-structure to hold the best 2 alignments

generic implementation of a move function for WorkUnit's This class is responsible for moving any external payload bound to a work-unit, and gets inv

A simple POD struct to represent a read id and its top flag status in a packed uint32

A simple POD struct to represent a seed's information in a packed uint32: - position in read - FM-index direction - reverse-complement flag - top flag

A simple data-structure to hold the best 2 paired alignments

a null type, useful to represent unbound template arguments

a set of flags describing what to load

a tag to define the device architecture

return the size of a given range

A binary functor implementing some custom logic to remove singletons from a set of segment-flags

A tight 16-bit CIGAR element representation

A functor to transform a global suffix index into a DCS-local index

A simple data-structure to hold paired alignments

A POD type encapsulating basic sequence information

Global statistics

A functor dividing all integers by the given constant

extract the string set sequence id from the kmer coordinates

extract the kmer size from the kmer coordinates

maps from the id of a kmer to the global id of its prefix

maps from the id of a kmer to the global id of its suffix

maps kmer global id to its UID

A functor to cast from one type into another

equality based on kmer key and region id coordinate

equality based on kmer key only

A functor adding the given constant to all intergers

pack-read functor, converting an integer read id into a packed_read

A trivial implementation of a quality string, constantly zero; This class has both a string and an iterator interface, as it is used as its own iterat

A trivial implementation of a quality string set, constantly zero

A simple data-structure to represent an alignment

Encapsulates all sequence data required for alignment. This is a simple convenience wrapper for FMIndexData.

A data structure to hold a Difference Cover Sample

A non-POD structure holding all of nvBowtie's parameters plus a few extra string options

LRU cache. The template parameter CacheManager should supply the following interface: bool acquire(const uint32 item); try to acquire/load an element

collapse kmers that start at the same position and belong to the same sequence by just returning the one with max length

implements a simple inter-CTA condition variable The condition variable is actually an integer, and the interface offers the possibility to test if /

a class to view a set of conditions from the device