RewriterVar* JitFragmentWriter::emitCreateSet(const llvm::ArrayRef<RewriterVar*> values) {
auto num = values.size();
if (num == 0)
return call(false, (void*)createSet);
else
return call(false, (void*)createSetHelper, imm(num), allocArgs(values));
}
RewriterVar* JitFragmentWriter::emitCreateDict(const llvm::ArrayRef<RewriterVar*> keys,
const llvm::ArrayRef<RewriterVar*> values) {
assert(keys.size() == values.size());
if (keys.empty())
return call(false, (void*)createDict);
else
return call(false, (void*)createDictHelper, imm(keys.size()), allocArgs(keys), allocArgs(values));
}
RewriterVar* JitFragmentWriter::emitCallattr(AST_expr* node, RewriterVar* obj, BoxedString* attr, CallattrFlags flags,
const llvm::ArrayRef<RewriterVar*> args,
std::vector<BoxedString*>* keyword_names) {
TypeRecorder* type_recorder = getTypeRecorderForNode(node);
#if ENABLE_BASELINEJIT_ICS
RewriterVar* attr_var = imm(attr);
RewriterVar* flags_var = imm(flags.asInt());
RewriterVar::SmallVector call_args;
call_args.push_back(obj);
call_args.push_back(attr_var);
call_args.push_back(flags_var);
call_args.push_back(args.size() > 0 ? args[0] : imm(0ul));
call_args.push_back(args.size() > 1 ? args[1] : imm(0ul));
call_args.push_back(args.size() > 2 ? args[2] : imm(0ul));
if (args.size() > 3) {
RewriterVar* scratch = allocate(args.size() - 3);
for (int i = 0; i < args.size() - 3; ++i)
scratch->setAttr(i * sizeof(void*), args[i + 3]);
call_args.push_back(scratch);
} else if (keyword_names) {
call_args.push_back(imm(0ul));
}
if (keyword_names)
call_args.push_back(imm(keyword_names));
return emitPPCall((void*)callattr, call_args, 2, 640, type_recorder);
#else
// We could make this faster but for now: keep it simple, stupid...
RewriterVar* attr_var = imm(attr);
RewriterVar* flags_var = imm(flags.asInt());
RewriterVar* keyword_names_var = keyword_names ? imm(keyword_names) : nullptr;
RewriterVar* args_array = nullptr;
if (args.size())
args_array = allocArgs(args);
else
RELEASE_ASSERT(!keyword_names_var, "0 args but keyword names are set");
RewriterVar::SmallVector call_args;
call_args.push_back(obj);
call_args.push_back(attr_var);
call_args.push_back(flags_var);
call_args.push_back(imm(type_recorder));
if (args_array)
call_args.push_back(args_array);
if (keyword_names_var)
call_args.push_back(keyword_names_var);
return call(false, (void*)callattrHelper, call_args);
#endif
}
RewriterVar* JitFragmentWriter::emitCreateTuple(const llvm::ArrayRef<RewriterVar*> values) {
auto num = values.size();
if (num == 0)
return imm(EmptyTuple);
else if (num == 1)
return call(false, (void*)BoxedTuple::create1, values[0]);
else if (num == 2)
return call(false, (void*)BoxedTuple::create2, values[0], values[1]);
else if (num == 3)
return call(false, (void*)BoxedTuple::create3, values[0], values[1], values[2]);
else
return call(false, (void*)createTupleHelper, imm(num), allocArgs(values));
}
RewriterVar* JitFragmentWriter::emitRuntimeCall(AST_expr* node, RewriterVar* obj, ArgPassSpec argspec,
const llvm::ArrayRef<RewriterVar*> args,
std::vector<BoxedString*>* keyword_names) {
TypeRecorder* type_recorder = getTypeRecorderForNode(node);
#if ENABLE_BASELINEJIT_ICS
RewriterVar* argspec_var = imm(argspec.asInt());
RewriterVar::SmallVector call_args;
call_args.push_back(obj);
call_args.push_back(argspec_var);
call_args.push_back(args.size() > 0 ? args[0] : imm(0ul));
call_args.push_back(args.size() > 1 ? args[1] : imm(0ul));
call_args.push_back(args.size() > 2 ? args[2] : imm(0ul));
if (args.size() > 3) {
RewriterVar* scratch = allocate(args.size() - 3);
for (int i = 0; i < args.size() - 3; ++i)
scratch->setAttr(i * sizeof(void*), args[i + 3]);
call_args.push_back(scratch);
} else
call_args.push_back(imm(0ul));
if (keyword_names)
call_args.push_back(imm(keyword_names));
return emitPPCall((void*)runtimeCall, call_args, 2, 640, type_recorder);
#else
RewriterVar* argspec_var = imm(argspec.asInt());
RewriterVar* keyword_names_var = keyword_names ? imm(keyword_names) : nullptr;
RewriterVar* args_array = nullptr;
if (args.size()) {
args_array = allocArgs(args);
} else
RELEASE_ASSERT(!keyword_names_var, "0 args but keyword names are set");
RewriterVar::SmallVector call_args;
call_args.push_back(obj);
call_args.push_back(argspec_var);
call_args.push_back(imm(type_recorder));
if (args_array)
call_args.push_back(args_array);
if (keyword_names_var)
call_args.push_back(keyword_names_var);
return call(false, (void*)runtimeCallHelper, call_args);
#endif
}
//read program parameters
args *getArgsBambi(argStruct *arguments){
args *ret = allocArgs();
ret->inputfiles=angsd::getArg("-bam",ret->inputfiles,arguments);
ret->inputfile=angsd::getArg("-i",ret->inputfile,arguments);
if(ret->inputfiles==NULL && ret->inputfile==NULL)
return NULL;
if(ret->inputfiles!=NULL&&strcmp(ret->inputfiles,"-999")==0){//DRAGON fix this
ret->inputfiles=NULL;
printArg(stdout,ret);
exit(0);
}
remove_bads = angsd::getArg("-remove_bads",remove_bads,arguments);
uniqueOnly = angsd::getArg("-uniqueOnly",uniqueOnly,arguments);
only_proper_pairs =angsd::getArg("-only_proper_pairs",only_proper_pairs,arguments);
minMapQ = angsd::getArg("-minMapQ",minMapQ,arguments);
adjustMapQ = angsd::getArg("-C",adjustMapQ,arguments);
baq = angsd::getArg("-baq",baq,arguments);
ret->region =angsd::getArg("-r",ret->region,arguments);
ret->regionfile = angsd::getArg("-rf",ret->regionfile,arguments);
ret->nInd = angsd::getArg("-nInd",ret->nInd,arguments);
ret->nLines = angsd::getArg("-nLines",ret->nLines,arguments);
ret->type = angsd::getArg("-type",ret->type,arguments);
ret->show = angsd::getArg("-show",ret->show,arguments);
// minQ = angsd::getArg("-minQ",minQ,arguments);
if(ret->inputfile && ret->inputfile[0]=='-'){
fprintf(stderr,"[Error] Problem understanding inputfilename: %s\n",ret->inputfile);
return NULL;
}
char *tmp = "";
tmp = angsd::getArg("-ref",tmp,arguments);
if(strcmp(tmp,"")==0&&adjustMapQ!=0){
fprintf(stderr,"Must also supply -ref for adjusting the mapping quality\n");
exit(0);
}
if(strcmp(tmp,"")==0&&baq!=0){
fprintf(stderr,"Must also supply -ref for adjusting base qualities (baq)\n");
exit(0);
}
printArg(arguments->argumentFile,ret);
return ret;
}
void bamInfo(FILE *fp){
args *ret = allocArgs();
printArg(fp,ret);
}