bool Compiler::CreateEngine() {
auto module = cs_.module_.get();
auto engine = llvm::EngineBuilder(cs_.module_.release())
.setErrorStr(&error_)
.setOptLevel(OPT_LEVEL)
.setEngineKind(llvm::EngineKind::JIT)
#ifdef LLL_USE_MCJIT
.setUseMCJIT(true)
#else
.setUseMCJIT(false)
#endif
.create();
if (engine) {
engine->finalizeObject();
engine_.reset(new Engine(engine, module, cs_.function_));
return true;
} else {
return false;
}
}
static void _finalizeObject(GC_PTR addr, GC_PTR client_data) {
Object* obj = (Object*) addr;
Env* env = rvmGetEnv();
assert(env != NULL);
finalizeObject(env, obj);
}
/**
* Compile many queries, then arrange them into a chain and squirt reads
* through it.
*/
int main(int argc, char *const *argv) {
const char *input_filename = nullptr;
bool binary = false;
ChainPattern chain = known_chains["parallel"];
bool help = false;
bool ignore_index = false;
int c;
while ((c = getopt(argc, argv, "bc:f:hI")) != -1) {
switch (c) {
case 'b':
binary = true;
break;
case 'c':
if (known_chains.find(optarg) == known_chains.end()) {
std::cerr << "Unknown chaining method: " << optarg << std::endl;
return 1;
} else {
chain = known_chains[optarg];
}
break;
case 'h':
help = true;
break;
case 'I':
ignore_index = true;
break;
case 'f':
input_filename = optarg;
break;
case '?':
fprintf(stderr, "Option -%c is not valid.\n", optopt);
return 1;
default:
abort();
}
}
if (help) {
std::cout << argv[0] << " [-b] [-c] [-I] [-v] -f input.bam "
" query1 output1.bam ..." << std::endl;
std::cout << "Filter a BAM/SAM file based on the provided query. For "
"details, see the man page." << std::endl;
std::cout << "\t-b\tThe input file is binary (BAM) not text (SAM)."
<< std::endl;
std::cout << "\t-c\tChain the queries, rather than use them independently."
<< std::endl;
std::cout << "\t-I\tDo not use the index, even if it exists." << std::endl;
std::cout << "\t-v\tPrint some information along the way." << std::endl;
return 0;
}
if (optind >= argc) {
std::cout << "Need a query and a BAM file." << std::endl;
return 1;
}
if ((argc - optind) % 2 != 0) {
std::cout << "Queries and BAM files must be paired." << std::endl;
return 1;
}
if (input_filename == nullptr) {
std::cout << "An input file is required." << std::endl;
return 1;
}
// Create a new LLVM module and JIT
LLVMInitializeNativeTarget();
llvm::InitializeNativeTargetAsmParser();
llvm::InitializeNativeTargetAsmPrinter();
std::unique_ptr<llvm::Module> module(
new llvm::Module("bamql", llvm::getGlobalContext()));
auto generator = std::make_shared<bamql::Generator>(module.get(), nullptr);
auto engine = bamql::createEngine(std::move(module));
if (!engine) {
return 1;
}
// Prepare a chain of wranglers.
std::shared_ptr<OutputWrangler> output;
for (auto it = argc - 2; it >= optind; it -= 2) {
// Prepare the output file.
std::shared_ptr<htsFile> output_file;
if (strcmp("-", argv[it + 1]) != 0) {
output_file =
std::shared_ptr<htsFile>(hts_open(argv[it + 1], "wb"), hts_close);
if (!output_file) {
perror(optarg);
return 1;
}
}
// Parse the input query.
std::string query(argv[it]);
auto ast =
bamql::AstNode::parseWithLogging(query, bamql::getDefaultPredicates());
if (!ast) {
return 1;
}
// Add the link to the chain.
std::stringstream function_name;
function_name << "filter" << it;
output = std::make_shared<OutputWrangler>(engine,
generator,
query,
ast,
function_name.str(),
chain,
std::string(argv[it + 1]),
output_file,
output);
}
engine->finalizeObject();
output->prepareExecution();
// Run the chain.
if (output->processFile(input_filename, binary, ignore_index)) {
output->write_summary();
return 0;
} else {
return 1;
}
}
