fixed bugg in shhh.seqs command

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 39a27d593abd1a3da6d9f93ab89e79b893c72089..b2b4de0559feff2074fb6269b6e18a8dafb9d6e4 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -32,7 +32,7 @@
 vector<string> ShhherCommand::getValidParameters(){    
        try {
                string Array[] =  {     
-                       "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors"       
+                       "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors", "maxiter", "mindelta"        
                };
                
                vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
@@ -111,7 +111,7 @@ ShhherCommand::ShhherCommand(string option) {
                        
                        //valid paramters for this command
                        string AlignArray[] =  {
-                               "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors"       
+                               "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors", "maxiter", "mindelta"        
                        };
                        
                        vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
@@ -294,8 +294,8 @@ int ShhherCommand::execute(){
                                
                                m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(numFiles) + ")\t<<<<<\n");
                                m->mothurOut("Reading flowgrams...\n");
-                               
                                getFlowData();
+
                                m->mothurOut("Identifying unique flowgrams...\n");
                                getUniques();
 
@@ -704,6 +704,10 @@ int ShhherCommand::execute(){
                        double begClock = clock();
                        unsigned long int begTime = time(NULL);
 
+                       
+                       cout << numOTUs << endl;
+                       
+                       
                        m->mothurOut("\nDenoising flowgrams...\n");
                        m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");
                        
@@ -1210,7 +1214,7 @@ void ShhherCommand::getOTUData(string listFileName){
                otuData.assign(numSeqs, 0);
                cumNumSeqs.assign(numOTUs, 0);
                nSeqsPerOTU.assign(numOTUs, 0);
-               aaP.resize(numOTUs);
+               aaP.clear();aaP.resize(numOTUs);
                
                seqNumber.clear();
                aaI.clear();
@@ -1266,6 +1270,8 @@ void ShhherCommand::getOTUData(string listFileName){
                        for(int j=nSeqsPerOTU[i];j<numSeqs;j++){
                                aaP[i].push_back(0);
                        }
+                       
+                       
                }
                
                for(int i=1;i<numOTUs;i++){
@@ -1275,6 +1281,13 @@ void ShhherCommand::getOTUData(string listFileName){
                seqIndex = seqNumber;
                
                listFile.close();       
+               
+               for(int i=0;i<seqNumber.size();i++){
+                       cout << seqNumber[i] << ' ';
+               }
+               cout << endl;
+               
+               
        }
        catch(exception& e) {
                m->errorOut(e, "ShhherCommand", "getOTUData");
@@ -1295,6 +1308,8 @@ void ShhherCommand::initPyroCluster(){
                nSeqsBreaks.assign(processors+1, 0);
                nOTUsBreaks.assign(processors+1, 0);
 
+               cout << numSeqs << '\t' << numOTUs << '\t' << processors << endl;
+               
                nSeqsBreaks[0] = 0;
                for(int i=0;i<processors;i++){
                        nSeqsBreaks[i+1] = nSeqsBreaks[i] + (int)((double) numSeqs / (double) processors);
@@ -1393,6 +1408,10 @@ void ShhherCommand::calcCentroidsDriver(int start, int finish){
        
        try{
                
+//             for(int i=0;i<seqNumber.size();i++){
+//                     cout << seqNumber[i] << ' ';
+//             }cout << endl;
+               
                for(int i=start;i<finish;i++){
                        
                        double count = 0;
@@ -1404,7 +1423,7 @@ void ShhherCommand::calcCentroidsDriver(int start, int finish){
                        for(int j=0;j<nSeqsPerOTU[i];j++){
                                count += singleTau[seqNumber[cumNumSeqs[i] + j]];
                        }
-                       
+
                        if(nSeqsPerOTU[i] > 0 && count > MIN_COUNT){
                                vector<double> adF(nSeqsPerOTU[i]);
                                vector<int> anL(nSeqsPerOTU[i]);