int main(int argc, char **argv) {
FILE *output;
ibis::horometer timer1,timer2;
timer1.start();
timer2.start();
int CHOP=1;
const rlim_t STACK_SIZE = 1000*1024*1024;
struct rlimit rl;
rl.rlim_cur = STACK_SIZE;
int ret = setrlimit(RLIMIT_STACK,&rl);
map<int, string> Calls;
Calls[0]="AA";
Calls[1]="AT";
Calls[2]="AC";
Calls[3]="AG";
Calls[4]="AN";
Calls[5]="TA";
Calls[6]="TT";
Calls[7]="TC";
Calls[8]="TG";
Calls[9]="TN";
Calls[10]="CA";
Calls[11]="CT";
Calls[12]="CC";
Calls[13]="CG";
Calls[14]="CN";
Calls[15]="GA";
Calls[16]="GT";
Calls[17]="GC";
Calls[18]="GG";
Calls[19]="GN";
Calls[20]="NA";
Calls[21]="NT";
Calls[22]="NC";
Calls[23]="NG";
Calls[24]="NN";
Calls[25]="--";
parseArgs(argc, argv);
if(datafile.empty() || pos.empty() || varName.empty() || varPath.empty() || outfile.empty()){
std::cerr << "Usage:\n" << *argv
<< " -f data-file-name"
<< " -n variable-name"
<< " -p variable-path"
<< " -r ref&row indices ('x|y:z' where x=ref sample,x:y as row range) "
<< " -r snp bounds (x:y, where x=start, y=end)"
<< " -d variable-dimension (e.g. 2:2)"
<< " -o output-file"
<< std::endl;
}
#ifndef FQ_NOMPI
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
#endif
FQ::FileFormat model = FQ::FQ_HDF5;
bool berr = true;
QueryProcessor* queryProcessor = new QueryProcessor(datafile, model, "", 0, "","");
if (queryProcessor->isValid() == false) {
printf("ERROR: Failed to initiate query processor for file.\n");
berr = false;
}
string variable;
vector<uint64_t> dims;
FQ::DataType type;
if (! queryProcessor->getVariableInfo(varName, variable, dims, &type, varPath)) {
printf("ERROR: Failed to get the information for variable\n");
berr = false;
} else {
if(dims.size()!=2){ /*dims is derived from the data*/
printf("ERROR: The data has an invalid dimension. SNP data should be in 2D matrix only.\n");
berr=false;
}
string str,param;
vector<uint64_t> sample;
vector<uint64_t> row; //snps
int prePos = 0, idx = 0,blocksize=1;
FastQuery* fq = new FastQuery(datafile, model, "", 0, "","");
int *refdata=NULL, *data=NULL, *consensus=NULL;
ostringstream paramtemp,ref;
/*Get the index for reference sample and subrows*/
idx = pos.find('|',prePos);
if(idx!=pos.npos && idx!=pos.length()-1){
str = pos.substr(prePos,idx - prePos);
sample.push_back(atoi(str.c_str())); /*get the ref. sample index*/
prePos=idx+1;
idx=pos.find(':',prePos);
if(idx!=pos.npos){ /*indicates multiple comparison*/
if(idx==pos.length()-1){ /*string ends with ':'*/
printf("ERROR: Incomplete indices specified for sample comparison.\n");
return 0;
}
str = pos.substr(prePos,idx - prePos);
sample.push_back(atoi(str.c_str())); /*get the start index*/
prePos=idx+1;
str = pos.substr(prePos,pos.length() - prePos);
sample.push_back(atoi(str.c_str())); /*get the end index*/
if(sample[2]<0 || sample[2]>=dims[1] || sample[1]>=sample[2]){
printf("ERROR: Indices out of bounds/invalid range.\n");
return 0;
}
}else{
str = pos.substr(prePos,idx - prePos);
sample.push_back(atoi(str.c_str())); /*get the index of another sample*/
}
if(sample[0]<0 || sample[0]>=dims[1] || sample[1]<0 || sample[1]>=dims[1]){
printf("ERROR: Indices out of bounds.\n");
return 0;
}
}else{
printf("ERROR: Invalid indices specified for sample comparison.\n");
return 0;
}
/*Get the SNP bounds for subset sample*/
if(!snpbound.empty()){
idx=snpbound.find(':',0);
if(idx==snpbound.npos || idx==snpbound.length()-1){
printf("ERROR: Invalid SNP bounds.");
return 1;
}
str = snpbound.substr(0,idx);
row.push_back(atoi(str.c_str()));
str= snpbound.substr(idx+1,snpbound.length()-idx+1);
row.push_back(atoi(str.c_str()));
if(row[0]<0 || row[1]>=dims[0] || row[1]<0 || row[0]>=row[1]){
printf("ERROR: Invalid SNP bounds.\n");
return 0;
}
dims[0]=row[1]-row[0]+1; /*dims is now the SNP bounds for subregion*/
}
if(sample.size()==3){
blocksize=sample[2]-sample[1]+1; /*block of data*/
}
if((dims[0]+(dims[0]*blocksize)+dims[0])*sizeof(int)>(1000*1024*1024)){
//printf("Error: Insufficient memory to handle huge block.\nREPORT: Failed to complete comparing data.\n");
//return 1;
printf("\nData is greater than the available/alloted memory space.\n");
CHOP=10;
}
printf("Running with %d thread/s.\n",NUMTHREADS);
int rowchunk=dims[0]/CHOP, offset; /*CHOP is 1 if data fits in memory*/
float com_time=0;
ostringstream outtext;
pthread_t threads[NUMTHREADS];
threadData *thread_data = (threadData*)malloc(NUMTHREADS*sizeof(threadData));
refdata=(int*)malloc(rowchunk*sizeof(int));
data=(int*)malloc((rowchunk*blocksize)*sizeof(int));
consensus=(int*)calloc(rowchunk,sizeof(int));
output=fopen(outfile.c_str(),"w");
/*Print output header*/
if(sample.size()==3)
fprintf(output,"Reference:%lu\nBlock samples:%lu-%lu\n",sample[0],sample[1],sample[2]);
else
fprintf(output,"Reference:%lu\nSample:%lu\n",sample[0],sample[1]);
fprintf(output,"SNPIdx\tRef\t");
for(int i=sample[1];i<sample[1]+blocksize;i++){
fprintf(output,"%d\t",i);
}
fprintf(output,"\n");
if(!snpbound.empty()){ /*set start position if bounded*/
offset=(int)row[0];
}
int rem=0;
if(dims[0]%CHOP!=0){
rem = dims[0]%CHOP;
CHOP++; /*another chunk for the remainder*/
}
for(int h=0;h<CHOP;h++){
if(h+1==CHOP && rem!=0){
rowchunk=rem;
free(data);
free(refdata);
free(consensus);
data=(int*)malloc((rowchunk*blocksize)*sizeof(int));
refdata=(int*)malloc(rowchunk*sizeof(int));
consensus=(int*)calloc(rowchunk,sizeof(int));
printf("Remainder chunk.%d\n",rowchunk);
}
if(!snpbound.empty()){
ref << variable << "[" << offset <<":"<< offset+rowchunk << "," << sample[0] << "]";
if(sample.size()==3)
paramtemp << variable << "[" << offset <<":"<< offset+rowchunk << "," << sample[1] << ":" << sample[2]+1 <<"]";
else
paramtemp << variable << "[" << offset <<":"<< offset+rowchunk << "," << sample[1] << "]";
}else{
ref << variable << "[:," << sample[0] << "]";
if(sample.size()==3)
paramtemp << variable << "[:," << sample[1] << ":" << sample[2]+1 << "]";
else
paramtemp << variable << "[:," << sample[1] << "]";
}
param = ref.str();
fq->getData(param,refdata);
param = paramtemp.str();
cout << h << "Ref:"<< ref.str() <<"\tParam:"<<paramtemp.str()<<"\n\n";
fq->getData(param,data); /*param=var[:,0:2]*/
/*printf("Reference Row:\n");
for(int i=0; i<rowchunk;i++) printf("%d ",refdata[i]);
printf("\n\n");
printf("Comparison Row Block:\n");
for(int x=0;x<(blocksize*rowchunk);x++){
printf("%d ",data[x]);
if((x+1)%blocksize==0) printf("\n\n");
}*/
/*THREADING of the comparison*/
for(int i=0;i<NUMTHREADS; i++){
thread_data[i].refdata = refdata;
thread_data[i].data = data;
thread_data[i].consensus=consensus;
thread_data[i].snpcount = rowchunk;
thread_data[i].blocksize = blocksize;
thread_data[i].tid = i;
thread_data[i].tcount = NUMTHREADS;
pthread_create(&threads[i],NULL,compareSample, (void*) &thread_data[i]);
}
for(int i=0;i<NUMTHREADS;i++){
pthread_join(threads[i],NULL);
}
/*RESULT printing*/
timer1.stop();
for(int i=0;i<rowchunk;i++){
if(consensus[i]==1){
outtext << i+offset << "\t" << Calls[refdata[i]] << "\t";
for(int x=0;x<blocksize;x++){
outtext << Calls[data[i*blocksize+x]] << "\t";
}
fprintf(output,"%s\n",outtext.str().c_str());
outtext.str("");
}
}
offset+=rowchunk;
paramtemp.str("");
ref.str("");
outtext.str("");
timer1.resume();
}
timer1.stop();
printf("Comparison Time:%f\n", timer1.realTime());
free(data);
free(refdata);
free(consensus);
free(thread_data);
fclose(output);
}
delete(queryProcessor);
#ifndef FQ_NOMPI
MPI_Finalize();
#endif
timer2.stop();
if (berr) {
printf("REPORT: Successfully completed comparing data.\n Total time elapsed:%f\n", timer2.realTime());
return 0;
} else {
printf("REPORT: Failed to complete comparing data.\n");
return -1;
}
}
