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#include <mpi.h>
#include <sys/time.h>
#include <iostream>
#include <functional>
#include <algorithm>
#include <vector>
#include <sstream>
#include "CombBLAS/CombBLAS.h"
using namespace std;
using namespace combblas;
#define myidlen 35
#define myseqlen 150
template <unsigned int IDLEN, unsigned int SEQLEN>
class ShortRead
{
public:
ShortRead(){ id[0] = '\0'; seq[0] = '\0'; qual[0] = '\0'; };
ShortRead(const string & s_id, const string & s_seq, const string & s_qual)
{
s_id.copy(id, IDLEN);
s_seq.copy(seq, SEQLEN);
s_qual.copy(qual, SEQLEN);
id[IDLEN] = '\0';
seq[SEQLEN] = '\0';
qual[SEQLEN] = '\0';
}
template <unsigned int NS_IDLEN, unsigned int NS_SEQLEN>
friend ostream& operator<<( ostream& os, const ShortRead<NS_IDLEN,NS_SEQLEN> & sread);
private:
char id[IDLEN+1]; // (+1)s are for null termination
char seq[SEQLEN+1];
char qual[SEQLEN+1];
template <typename IT,unsigned int NS_IDLEN, unsigned int NS_SEQLEN> // NS: no-shadow
friend class ShortReadSaveHandler;
};
template <unsigned int IDLEN, unsigned int SEQLEN>
ostream& operator<<(ostream& os, const ShortRead<IDLEN, SEQLEN> & sread )
{
os << sread.id << " " << sread.seq << " " << sread.qual << endl;
return os;
};
template <class IT, unsigned int IDLEN, unsigned int SEQLEN>
class ShortReadSaveHandler
{
public:
ShortReadSaveHandler() {};
ShortRead<IDLEN,SEQLEN> getNoNum(IT ind) { return ShortRead<IDLEN,SEQLEN>(); }
MPI_Datatype getMPIType()
{
return MPIType< ShortRead<IDLEN,SEQLEN> >(); // utilize the MPI type cache
}
void binaryfill(FILE * rFile, IT & ind, ShortRead<IDLEN,SEQLEN> & val)
{
size_t entryLength = fread (&ind,sizeof(ind),1,rFile); // read the index first
entryLength += fread (&val,sizeof(ShortRead<IDLEN,SEQLEN>),1,rFile);
if(entryLength != 2)
cout << "Not enough bytes read in binaryfill " << endl;
}
size_t entrylength() { return sizeof(ShortRead<IDLEN,SEQLEN>); }
template <typename c, typename t>
ShortRead<IDLEN,SEQLEN> read(std::basic_istream<c,t>& is, IT ind)
{
string s_id, s_seq, s_qual, s_null;
getline (is,s_id);
getline (is,s_seq);
getline (is,s_null); // basically the '+' sign
getline (is,s_qual);
return ShortRead<IDLEN,SEQLEN>(s_id, s_seq, s_qual);
}
template <typename c, typename t>
void save(std::basic_ostream<c,t>& os, const ShortRead<IDLEN,SEQLEN> & tw, IT ind)
{
// make it compatible with read...
}
};
int main(int argc, char* argv[])
{
int nprocs, myrank;
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
MPI_Comm_rank(MPI_COMM_WORLD,&myrank);
if(argc < 4)
{
if(myrank == 0)
{
cout << "Usage: ./VectorIOPermute <VectorFile>" << endl;
cout << "<VectorFile> is a binary file" << endl;
}
MPI_Finalize();
return -1;
}
{
FullyDistSpVec<int64_t, ShortRead<myidlen, myseqlen> > ShortReads;
ShortReads.ReadDistribute(string(argv[1]), 0, ShortReadSaveHandler<int64_t, myidlen, myseqlen>(), true); // read it from binary file in parallel
}
MPI_Finalize();
return 0;
}
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