alignments.cpp

#include "alignments.hpp"
#include"utils.hpp"
gpu_alignments::gpu_alignments(int max_alignments){
    cudaErrchk(cudaMalloc(&offset_query_gpu, (max_alignments) * sizeof(int)));
    cudaErrchk(cudaMalloc(&offset_ref_gpu, (max_alignments) * sizeof(int)));
    cudaErrchk(cudaMalloc(&ref_start_gpu, (max_alignments) * sizeof(short)));
    cudaErrchk(cudaMalloc(&ref_end_gpu, (max_alignments) * sizeof(short)));
    cudaErrchk(cudaMalloc(&query_end_gpu, (max_alignments) * sizeof(short)));
    cudaErrchk(cudaMalloc(&query_start_gpu, (max_alignments) * sizeof(short)));
    cudaErrchk(cudaMalloc(&scores_gpu, (max_alignments) * sizeof(short)));
}

gpu_alignments::~gpu_alignments(){
    cudaErrchk(cudaFree(offset_ref_gpu));
    cudaErrchk(cudaFree(offset_query_gpu));
    cudaErrchk(cudaFree(ref_start_gpu));
    cudaErrchk(cudaFree(ref_end_gpu));
    cudaErrchk(cudaFree(query_start_gpu));
    cudaErrchk(cudaFree(query_end_gpu));
}