SW# Documentation

Simple library usage can be seen in the following simple.c file. This short program aligns two nucleotide sequences in fasta format. The nucleotides paths are read from the command line as the first two arguments. This example is for the linux platform.

simple.c:

#include "swsharp/swsharp.h"

int main(int argc, char* argv[]) {

    Chain* query = NULL;
    Chain* target = NULL; 
    
    // read the query as the first command line argument
    readFastaChain(&query, argv[1]);
    
    // read the target as the first command line argument
    readFastaChain(&target, argv[2]);
    
    // use one CUDA card with index 0
    int cards[] = { 0 };
    int cardsLen = 1;
    
    // create a scorer object
    // match = 1
    // mismatch = -3
    // gap open = 5
    // gap extend = 2
    Scorer* scorer;
    scorerCreateScalar(&scorer, 1, -3, 5, 2);

    // do the pairwise alignment, use Smith-Waterman algorithm
    Alignment* alignment;
    alignPair(&alignment, SW_ALIGN, query, target, scorer, cards, cardsLen, NULL);
     
    // output the results in emboss stat-pair format
    outputAlignment(alignment, NULL, SW_OUT_STAT_PAIR);
    
    // clean the memory
    alignmentDelete(alignment);

    chainDelete(query);
    chainDelete(target);
    
    scorerDelete(scorer);
    
    return 0;
}

This code can be compiled with:

nvcc simple.c -I include/ -L lib/ -l swsharp -l pthread -o simple

And the executable can be run with:

./simple input1.fasta input2.fasta