Mapping of sequence intervals from positions in the genome to positions in the alignment and vice versa. More...

#include <liftover.hh>

Public Member Functions
	LiftOver (Alignment *a, vector< int > &o)

template<typename T >
void	projectToAli (vector< map< int_fast64_t, T * > > &seqints, map< int_fast64_t, list< pair< int, T * > > > &alignedSIs)

template<typename T >
void	projectToGenome (map< int_fast64_t, list< pair< int, T * > > > &alignedSIs, vector< AnnoSequence * > const &seqRanges, vector< map< int_fast64_t, T * > > &seqints, bool insertMissingSIs=true)

Detailed Description

Mapping of sequence intervals from positions in the genome to positions in the alignment and vice versa.

A sequence interval can be any object T for which functions

int_fast64_ T::getKey() // returns a SeqIntKey encoding start position and length of the SI
T* create(int_fast64_t key , const char* dna) // creates a new SI from a SeqIntKey after verification (e.g. if SI is an // intron, check whether splice sites are present in the sequence)

exist. Sequence positions can be encoded as zero-length SIs.
Purpose: lifting over of exons, introns and non-canonical SS to other species (is it possible to generalize this class to lifting over whole gene structures?)

Author: Stefanie Koenig

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

include/liftover.hh

Public Member Functions

Detailed Description