int main(int argc, char** argv)
{
if(argc <= 1)
{
std::cout << SGA_USAGE_MESSAGE;
return 0;
}
else
{
std::string command(argv[1]);
if(command == "help" || command == "--help")
{
std::cout << SGA_USAGE_MESSAGE;
return 0;
}
else if(command == "version" || command == "--version")
{
std::cout << SGA_VERSION_MESSAGE;
return 0;
}
if(command == "preprocess")
preprocessMain(argc - 1, argv + 1);
else if(command == "index")
indexMain(argc - 1, argv + 1);
else if(command == "merge")
mergeMain(argc - 1, argv + 1);
else if(command == "filter")
filterMain(argc - 1, argv + 1);
else if(command == "stats")
statsMain(argc - 1, argv + 1);
else if(command == "rmdup")
rmdupMain(argc - 1, argv + 1);
else if(command == "fm-merge")
FMMergeMain(argc - 1, argv + 1);
else if(command == "overlap")
overlapMain(argc - 1, argv + 1);
else if(command == "overlap-long")
overlapLongMain(argc - 1, argv + 1);
else if(command == "correct")
correctMain(argc - 1, argv + 1);
else if(command == "assemble")
assembleMain(argc - 1, argv + 1);
else if(command == "connect")
connectMain(argc - 1, argv + 1);
else if(command == "gmap")
gmapMain(argc - 1, argv + 1);
else if(command == "subgraph")
subgraphMain(argc - 1, argv + 1);
else if(command == "walk")
walkMain(argc - 1, argv + 1);
else if(command == "oview")
oviewMain(argc - 1, argv + 1);
else if(command == "scaffold")
scaffoldMain(argc - 1, argv + 1);
else if(command == "scaffold2fasta")
scaffold2fastaMain(argc - 1, argv + 1);
else if(command == "filterBAM")
filterBAMMain(argc - 1, argv + 1);
else if(command == "cluster")
clusterMain(argc - 1, argv + 1);
else if(command == "gen-ssa")
genSSAMain(argc - 1, argv + 1);
else if(command == "bwt2fa")
bwt2faMain(argc - 1, argv + 1);
else if(command == "graph-diff")
graphDiffMain(argc - 1, argv + 1);
else if(command == "gapfill")
gapfillMain(argc - 1, argv + 1);
else if(command == "variant-detectability")
variantDetectabilityMain(argc - 1, argv + 1);
else if(command == "rewrite-evidence-bam")
rewriteEvidenceBAMMain(argc - 1, argv + 1);
else if(command == "preqc")
preQCMain(argc - 1, argv + 1);
else if(command == "haplotype-filter")
haplotypeFilterMain(argc - 1, argv + 1);
else if(command == "graph-concordance")
graphConcordanceMain(argc - 1, argv + 1);
else if(command == "somatic-variant-filters")
somaticVariantFiltersMain(argc - 1, argv + 1);
else if(command == "kmer-count")
kmerCountMain(argc - 1, argv + 1);
else
{
std::cerr << "Unrecognized command: " << command << "\n";
return 1;
}
}
return 0;
}
int main ()
{
clusterMain();
return 0;
}
