Built with -O3 optimization. Install this if you do not want to compile ncbi-c++ libs from source
remotes::install_local("QuickBLAST_1.0_R_x86_64-pc-linux-gnu.tar.gz", build=F)
tblastx_ptr <- QuickBLAST::CreateNewBLASTInstance(seq_info = list(0,0,F), program = "tblastx", options = list("evalue"=1e-05, "pident"=0.75, "qcovhsp_perc"=0.75))
blastn_ptr <- QuickBLAST::CreateNewBLASTInstance(seq_info = list(0,0,F), program = "blastn", options = "")
QuickBLAST::BLAST2Files(ptr=tblastx_ptr, query="ungrouped.cds", subject="ungrouped.cds", out_file="out.tmp", seq_limit=1000, show_progress=T,return_values=F, num_threads=5)
QuickBLAST::BLAST2Seqs(ptr=tblastx_ptr, query="AAAAAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGG", subject="TTTTTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC")
QuickBLAST::BLAST2Seqs(ptr=blastn_ptr, query=">i11166\nTGGCACGTCTGGTAGCAGTTTGCAGGGAAGGGGAAGAGGAATACCCGTTTCTCGCCAGACAGATCC", subject=">i11167\nATGGCACGTCTGGTAGCAGTTTGCAGGGAAGGGGAAGAGGAATACCCGTTTCTCGCCAGACAGATCCCCCTCTTCATCGATGACACTCTCACGATGGTGATGGAGTTTTCCGATAGCGTCATGG")
QuickBLAST::BLAST1Folder(ptr = tblastx_ptr, input_folder="test", extension= ".cds", out_folder="test_out", num_threads=7, reciprocal_hits=F)
QuickBLAST::BLAST2Folders(ptr=blastn_ptr, query="query", subject="subject", extension = ".cds", out_folder="test2_out", num_threads=8, reciprocal_hits=F)