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#include<cstdlib>
#include<fstream>
#include<iomanip>
#include<vector>
using namespace std;
#include "FileHeader.h"
#include "transposeFiles.h"
#include "common.h"
bool transposeFiles(vector<string> inFileNames, string outFileName, bool verbose, string message){
long M=0,fileN=1,i,j,bufMax,bufN,m,n,totalN,maxN=0,f;
bool trans=false,transposed=false;
vector<long> N;
bufMax=BUFFER_DEFAULT;
ofstream outFile(outFileName.c_str());
if(!outFile.is_open()){//{{{
error("TransposeFile: Unable to open output file\n");
return 0;
}//}}}
//{{{ Opening input
fileN = inFileNames.size();
ifstream *inFile = new ifstream[fileN];
totalN=0;
FileHeader fh;
for(i=0;i<fileN;i++){
inFile[i].open(inFileNames[i].c_str());
fh.setFile(&inFile[i]);
m = n = 0;
if((!fh.samplesHeader(&n,&m,&trans)) || (m == 0) || (n == 0)){
error("TransposeFile: Unable to read header of file: %s\n",(inFileNames[i]).c_str());
return false;
}
if(N.size()==0){
M=m;
transposed=trans;
maxN=n;
}else if((M!=m)||(transposed!=trans)){
error("TransposeFile: Different number of transcripts or file %s is in wrong format.\n",(inFileNames[i]).c_str());
return false;
}
outFile<<"# "<<inFileNames[i]<<" "<<n<<endl;
N.push_back(n);
if(n>maxN)maxN=n;
totalN+=n;
}
if(bufMax>M)bufMax=M;
//}}}
outFile<<message;
if(!trans)
outFile<<"# T (M rows,N cols)";
else
outFile<<"# (N rows,M cols)";
outFile<<"\n# M "<<M<<"\n# N "<<totalN<<endl;
outFile.precision(9);
outFile<<scientific;
if(verbose)message("Transposing files:\n Samples: %ld Transcripts: %ld Buffer size: %ld\n",totalN,M,bufMax);
if(!trans){ // {{{
vector< vector<long> > seeks(fileN,vector<long>(maxN,-1));
vector<vector<string> > valueBuf(bufMax,vector<string>(totalN));
long lastBuf = 0, done=0;
bufN=bufMax;
if(verbose)messageF("(r");
for(f=0;f<fileN;f++){
for(i=0;i<N[f];i++){
for(j=0;j<bufN;j++) inFile[f]>>valueBuf[j][lastBuf];
lastBuf++;
seeks[f][i]=inFile[f].tellg();
inFile[f].ignore(10000000,'\n');
}
}
if(verbose)messageF(">w.");
for(j=0;j<bufN;j++){
for(i=0;i < lastBuf - 1;i++)
outFile<<valueBuf[j][i]<<" ";
// Write last value without space.
outFile<<valueBuf[j][i]<<endl;
}
lastBuf=0;
done=bufN;
while(done<M){
bufN=bufMax;
if(M-done<bufMax)bufN=M-done;
if(verbose)messageF("r");
for(f=0;f<fileN;f++){
for(i=0;i<N[f];i++){
inFile[f].seekg(seeks[f][i]);
for(j=0;j<bufN;j++) inFile[f]>>valueBuf[j][lastBuf];
lastBuf++;
seeks[f][i]=inFile[f].tellg();
}
}
if(verbose)messageF(">w.");
for(j=0;j<bufN;j++){
for(i=0;i < lastBuf - 1;i++)
outFile<<valueBuf[j][i]<<" ";
// Write last value without space.
outFile<<valueBuf[j][i]<<endl;
}
lastBuf=0;
done+=bufN;
}
for(f=0;f<fileN;f++)inFile[f].close();
if(verbose)message(")\n");
} // }}}
else{ // if(trans) {{{
vector<long> seeks(M,-1);
vector<vector<string> > valueBuf(M,vector<string>(bufMax));
long done;
if(verbose)message("(");
for(f=0;f<fileN;f++){
seeks.assign(M,-1);
done = 0;
while(done<N[f]){
bufN=bufMax;
if(bufN>N[f]-done)bufN=N[f]-done;
if(verbose)messageF("r");
for(j=0;j<M;j++){
if(seeks[j]!=-1)inFile[f].seekg(seeks[j]);
for(i=0;i<bufN;i++){
inFile[f]>>valueBuf[j][i];
}
seeks[j]=inFile[f].tellg();
if((j+1<M)&&(seeks[j+1]==-1))inFile[f].ignore(100000000,'\n');
}
if(verbose)messageF(">w.");
for(i=0;i<bufN;i++){
for(j=0;j < M - 1;j++)
outFile<<valueBuf[j][i]<<" ";
// Write last value without space.
outFile<<valueBuf[j][i]<<endl;
}
done+=bufN;
}
inFile[f].close();
}
if(verbose)message(")\n");
} //}}}
delete[] inFile;
outFile.close();
return true;
}
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