function sPROFILER_main(fileName, newChipFileName)
fprintf('ChipName\tCallRate_GSEQ\tCallRate_sPROFILER\tNo-Calls_GSEQ\tNo-Calls_sPROFILER\tVariants_GSEQ\tVariants_sPROFILER\n');
fidChips=fopen(fileName,'r');
chips=textread(fileName, '%s','delimiter','\n','whitespace','');
firstChip=fgetl(fidChips);
numChips=length(chips);

fidNewChip=fopen(newChipFileName, 'r');
newChip=textread(newChipFileName, '%s','delimiter','\n','whitespace','');

callsFile=strcat(firstChip,'\',firstChip,'_calls.txt');
intFile=strcat(firstChip,'\',firstChip,'_int.txt');
fidCall = fopen(callsFile, 'r');
fidInt = fopen(intFile, 'r');
refSeq= fscanf(fidCall, '%s %s', [2 inf]);
refSeq = refSeq';
numBP=length(refSeq);
allCallsArray=refSeq(:,2);
refSeq=refSeq(:,1);
intFirst= fscanf(fidInt, '%g %g %g %g %g %g %g %g', [8 inf]);
allIntArray=intFirst';
fclose(fidInt);
fclose(fidCall);
fclose(fidChips);

fidChips=fopen(fileName,'r');
for index=2:numChips
    chipNum=fgetl(fidChips);
    callsFile=strcat(chipNum,'\',chipNum,'_calls.txt');
    intFile=strcat(chipNum,'\',chipNum,'_int.txt');
    fidCall = fopen(callsFile, 'r');
    fidInt = fopen(intFile, 'r');
    tempSeq= fscanf(fidCall, '%s %s', [2 inf]);
    tempSeq=tempSeq';
    tempSeq=tempSeq(:,2);
    allCallsArray=[allCallsArray, tempSeq];
    intArray= fscanf(fidInt, '%g %g %g %g %g %g %g %g', [8 inf]);
    allIntArray=[allIntArray, intArray'];
    fclose(fidCall);
    fclose(fidInt);
end
fclose(fidChips);
varChipRatio=zeros(numBP,3);

for numRows=1:numBP
    numWt=0;
    numCalls=0;
    for numCols=1:numChips
        if(allCallsArray(numRows, numCols)==refSeq(numRows))
            numWt=numWt+1;
            intMatFwd=allIntArray(numRows,numChips:numChips+3); intMatRev=allIntArray(numRows,numChips+4:numChips+7);
            sort(intMatFwd,2); sort(intMatRev,2);
            varChipRatio(numRows,1)=varChipRatio(numRows,1)+intMatFwd(4)/(numChips*intMatFwd(3));
            varChipRatio(numRows,2)=varChipRatio(numRows,2)+intMatRev(4)/(numChips*intMatRev(3));
        end
        if(allCallsArray(numRows, numCols)~='n')
            numCalls=numCalls+1;
        end
    end
    if(numWt>0)
        varChipRatio(numRows,3)=numWt/numCalls;
    else 
        varChipRatio(numRows,1)=1; varChipRatio(numRows,2)=1; varChipRatio(numRows,3)=1;
    end    
end
%========================================================================================================%

chipNum=fgetl(fidNewChip);
sPROFILER_call(chipNum, varChipRatio);
fclose(fidNewChip);

%XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

function BaseCallHetVal=BaseCallHetVal(chipNum, arrayPosRatio)
fprintf('%s\t', chipNum);
%================================================================================================================================%
%Read input files; create output files.
callsFile=strcat(chipNum,'\',chipNum,'_calls.txt');
intFile=strcat(chipNum,'\',chipNum,'_int.txt');
outFile=strcat(chipNum,'\',chipNum,'_OutCalls.txt');

%Read tiling information
tilingIndices=dlmread('Cincinnati_tiling.txt');

%Store intensities into nX8 matrix.
setInt = dlmread(intFile, '\t');
[numBP,colsBP]=size(setInt);

%Store quality scores into nX1 matrix.
qualFile=strcat(chipNum,'\',chipNum,'_qualScores.txt');
qualArray=dlmread(qualFile);

%Read Ref and GDAS sequences.
fid = fopen(callsFile, 'r');
setCalls = fscanf(fid, '%s %s', [2 inf]);
setCalls = setCalls';
fclose(fid);

newCalls=zeros(numBP,1); score=zeros(numBP,1); model=zeros(numBP,1);
bases=['a' 'c' 'g' 't']; hets=['x' 'm' 'r' 'w'; 'm' 'x' 's' 'y'; 'r' 's' 'x' 'k'; 'w' 'y' 'k' 'x'];

fid = fopen(outFile, 'wt');
fprintf(fid, 'Index\tRef\tNew\tScore\tGSEQ\tGSEQQual\tModel\tFlag\tA\tC\tG\tT\tA"\tC"\tG"\tT"\n');

numCallsOld=0; numCalls=0;
oldHet=0; oldSnp=0;
oldHetWithSeq=0; oldSnpWithSeq=0;
newHet=0; newSnp=0;
newHetWithSeq=0; newSnpWithSeq=0;
varToN=0; varToNWithSeq=0;
%=========================================================================================================================
intMatFwd=setInt(:,1:4); intMatRev=setInt(:,5:8);
sort(intMatFwd,2); sort(intMatRev,2);
peak43F=0; peak43R=0;
peak32F=0; peak32R=0;
meanRatioFwd=0; meanRatioRev=0; 
numForThresh=0;

for temp=1:numBP
    if (setCalls(temp,2)~='n')
        if(setCalls(temp,2)=='a'|setCalls(temp,2)=='c'|setCalls(temp,2)=='g'|setCalls(temp,2)=='t')
            peak43F=peak43F+intMatFwd(temp,4)/intMatFwd(temp,3);
            peak43R=peak43R+intMatRev(temp,4)/intMatRev(temp,3);
            peak32F=peak32F+intMatFwd(temp,3)/intMatFwd(temp,2);
            peak32R=peak32R+intMatRev(temp,3)/intMatRev(temp,2);
            numForThresh=numForThresh+1;
        end
    end
end

peak43F=peak43F/numForThresh; peak43R=peak43R/numForThresh;
peak32F=peak32F/numForThresh; peak32R=peak32R/numForThresh;
%=========================================================================================================================
NCWt=0; NCHet=0; NCSnp=0;
%==========================================%
for temp=1:numBP   
    
    %Check if >75% calls are N in +/-12-bp window
    tilingIndex=tilingIndices(temp);
    nCallsInWindow=0;
    windowLenFwd=1; 
    windowLenRev=1;
    tilingFlagRev=1;
    tilingFlagFwd=1;
    
    if(temp>=13 & temp<=numBP-13)
        while(tilingFlagRev | tilingFlagFwd)
            if((tilingIndices(temp-windowLenRev)==tilingIndex-windowLenRev) & windowLenRev<=11 & tilingFlagRev)
                if(setCalls(temp-windowLenRev,2)~=setCalls(temp-windowLenRev,1))
                    nCallsInWindow=nCallsInWindow+1;
                end
                windowLenRev=windowLenRev+1;
            else
                tilingFlagRev=0;
            end
            
            if((tilingIndices(temp+windowLenFwd)==tilingIndex+windowLenFwd) & windowLenFwd<=11 & tilingFlagFwd)
                if(setCalls(temp+windowLenFwd,2)~=setCalls(temp+windowLenFwd,1))
                    nCallsInWindow=nCallsInWindow+1;
                end
                windowLenFwd=windowLenFwd+1;
            else
                tilingFlagFwd=0;
            end
        end
    end
    
    if(nCallsInWindow/(windowLenFwd+windowLenRev)>=0.60 | (setCalls(temp,2)~='n' & qualArray(temp)<55 & (setCalls(temp,1) ~= setCalls(temp,2))))
        newCalls(temp,1)='n'; 
        
        %Only no-calls are analyzed.
    elseif(setCalls(temp,2)=='n')
        [fwdVal, fwdIndex] = sort(setInt(temp,1:4),2);
        [revVal, revIndex] = sort(setInt(temp,5:8),2);
        fwdTwin=[fwdIndex(3) fwdIndex(4)]; revTwin=[revIndex(3) revIndex(4)];
        
        %If peak on either strand exceeds next highest by
        %peakDiff*2ndpeak AND it corresponts to RefSeq, assign it as RefSeq. Model = 3.
        if(arrayPosRatio(temp,1)==1)
            arrayPosRatio(temp,1)=peak43F;
        end
        if(arrayPosRatio(temp,2)==1)
            arrayPosRatio(temp,2)=peak43R;
        end
        
        if (((bases(revIndex(4))==setCalls(temp,1))&(revVal(4)>=revVal(3)*mean([peak43R/arrayPosRatio(temp,3)])))|((bases(5-fwdIndex(4))==setCalls(temp,1))&(fwdVal(4)>=fwdVal(3)*mean([peak43F/arrayPosRatio(temp,3)])))) 
            newCalls(temp,1)=setCalls(temp,1);
            score(temp,1)=(fwdVal(4)*revVal(4)*fwdVal(4)*revVal(4))/(fwdVal(3)*revVal(3)*mean(fwdVal(1:3))*mean(revVal(1:3)));
            model(temp,1)=3;
            else newCalls(temp,1)='n';
        end        
    else newCalls(temp,1)=setCalls(temp,2);        
    end    
    %========================================================================================================================   
    %Compute new call rate
    if(char(newCalls(temp,1))~='n')
        numCalls=numCalls+1;
    end
    if (setCalls(temp,2)~='n')
        numCallsOld=numCallsOld+1;
    end
    
    %Calculate Var calls converted to N
    if(char(newCalls(temp,1))=='n'& setCalls(temp,2)~='n'& setCalls(temp,2)~=setCalls(temp,1))
        varToN=varToN+1;
    end
    %Matches with reference seq.
    if(newCalls(temp,1)==setCalls(temp,1) & newCalls(temp,1)==setCalls(temp,2))
        snpType=0;
        %No-call converted to refseq.
    elseif(newCalls(temp,1)==setCalls(temp,1) & setCalls(temp,2)=='n')
        snpType=1;
        NCWt=NCWt+1;
        %Hets from GDAS (old Hets)
    elseif(setCalls(temp,2)~='a'&setCalls(temp,2)~='c'&setCalls(temp,2)~='g'&setCalls(temp,2)~='t'&setCalls(temp,2)~='n')
        snpType=2;
        oldHet=oldHet+1;
        %SNP's from GDAS (old SNPs)
    elseif((setCalls(temp,2)=='a'|setCalls(temp,2)=='c'|setCalls(temp,2)=='g'|setCalls(temp,2)=='t')&setCalls(temp,2)~=setCalls(temp,1))
        snpType=3;
        oldSnp=oldSnp+1;
        %Still a no-call.
    elseif(newCalls(temp,1)=='n')
        snpType=4;
    end
    
    fprintf(fid, '%d\t%c\t%c\t%g\t%c\t%g\t%d\t%d\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\n', temp, setCalls(temp,1), newCalls(temp,1), score(temp,1), setCalls(temp,2), qualArray(temp), model(temp,1), snpType, setInt(temp, 1), setInt(temp,2), setInt(temp,3), setInt(temp,4), setInt(temp,5), setInt(temp,6), setInt(temp,7), setInt(temp,8));
end
fclose(fid); 
%CallRate
fprintf('%g\t%g\t',100*numCallsOld/(numBP),100*numCalls/(numBP));
%No-calls
fprintf('%g\t%g\t',numBP-numCallsOld, numBP-numCalls);
%Variants
fprintf('%d\t%d\t',oldSnp+oldHet,oldSnp+oldHet-varToN);
%=========================================================================================================================