Usage

Dynamic loading

Building versalignLib creates shared objects for each Kernel implementation in the bin/Versalign-0.1.0/lib subfolder. These can be dynamically loaded and directly used in your program. An example how to do this can be found in the reference implementation.

Library interface

Each shared object exports the following functions.

void set_parameters(AlignmentParameters * parameters)

Sets parameters for alignment.

void set_logger(AlignmentLogger * logger)

Sets logger for alignment.

AlignmentKernel * spawn_alignment_kernel()

Creates alignment.

 void delete_alignment_kernel(AlignmentKernel * instance)

Deletes alignment.

Execution order

Caveat: Before instantiating an AlignmentKernel, all parameters and loggers have to be set using set_parameters and set_logger functions!

Library classes

All Kernels implement the AlignmentKernel interface in include/AlignmentKernel.h providing two functions:

Score alignments

This function will return an alignment score for each sequence pair.

void score_alignments(int const & opt, int const & aln_number, char const * const * const reads,
			char const * const * const refs, short * const scores)

Arguments

Argument	Type	Description
opt	int	Type of alignment (0 Smith-Waterman, 1 Needleman-Wunsch)
aln_number	int	Number of reads vs refs pairs
reads	char * []	Array of sequences to align to refs
refs	char * []	Array of sequences to align to reads
scores	short []	One score for each pair in reads vs refs

Calculate alignments

This function will return an alignment struct object for each sequence pair.

void compute_alignments(int const & opt, int const & aln_number, char const * const * const reads,
			char const * const * const refs, Alignment * const alignments)

Arguments

Argument	Type	Description
opt	int	Type of alignment (0 Smith-Waterman, 1 Needleman-Wunsch)
aln_number	int	Number of reads vs refs pairs
reads	char * []	Array of sequences to align to refs
refs	char * []	Array of sequences to align to reads
alignments	Alignment []	One Alignment object for each pair in reads vs refs

Setting parameters

It is required to set the alignment parameters (scoring schema, number of threads...) before instantiating any of the Kernel shared objects. This can be done using an object implementing the AlignmentParameters interface defined in include/AlignmentParameters.h. An example is shown in the reference implementation.

Available parameters

The following table lists the minimal set of parameters that needs to be available.

Parameter	Type	Description
score_match	int	Score for base match
score_mismatch	int	Score for base mismatch
score_gap_read	int	Score for introducing a gap in the first sequence
score_gap_ref	int	Score for introducing a gap in the second sequence
read_length	int	Maximum length of first sequence
ref_length	int	Maximum length of second sequence
num_threads	int	Number of threads to use

Logging

Logging of Kernels is also supported by implementing the AlignmentLogger interface defined in include/AlignmentLogger.h. An example implementation can be found in the reference implementation.