added order=A or order=B to trim.flows and shhh.flows commands. added load balancing...

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 87d26cea75033c911d4db315265123fdd3dd49de..92f0e486898f80b2c6f85bb984a5b7662bc18340 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -947,7 +947,7 @@ vector<string>  ClusterSplitCommand::createProcesses(vector< map<string, string>
             if ((processToAssign-1) == 1) { m->mothurOut(distName[i].begin()->first + "\n"); }
         }
         
-        //not lets reverse the order of ever other process, so we balance big files running with little ones
+        //now lets reverse the order of ever other process, so we balance big files running with little ones
         for (int i = 0; i < processors; i++) {
             //cout << i << endl;
             int remainder = ((i+1) % processors);

diff --git a/flowdata.cpp b/flowdata.cpp
index 5dc7dc3e6c780171f1ee5cacdb1d766864f18a18..f4605b6dbe1613fdb3e1a6beb1929a3585ff5fe7 100644 (file)
--- a/flowdata.cpp
+++ b/flowdata.cpp
@@ -50,7 +50,7 @@ bool FlowData::getNext(ifstream& flowFile){
             translateFlow();
             m->gobble(flowFile);
                }
-            
+           
                if(flowFile){   return 1;       }
                else            {       return 0;       }
        }
@@ -86,16 +86,18 @@ string FlowData::getSequenceName(ifstream& flowFile) {
 void FlowData::updateEndFlow(){
        try{
                
+        if (baseFlow.length() > 4) { return; }
+        
                //int currLength = 0;
                float maxIntensity = (float) maxHomoP + 0.49;
                
                int deadSpot = 0;
-                               
+                       
                while(deadSpot < endFlow){
                        int signal = 0;
                        int noise = 0;
                        
-                       for(int i=0;i<4;i++){
+                       for(int i=0;i<baseFlow.length();i++){
                                float intensity = flowData[i + deadSpot];
                                if(intensity > signalIntensity){
                                        signal++;
@@ -110,7 +112,7 @@ void FlowData::updateEndFlow(){
                                break;
                        }
                
-                       deadSpot += 4;
+                       deadSpot += baseFlow.length();
                }
                endFlow = deadSpot;
 
@@ -129,13 +131,13 @@ void FlowData::translateFlow(){
                sequence = "";
                for(int i=0;i<endFlow;i++){
                        int intensity = (int)(flowData[i] + 0.5);
-                       char base = baseFlow[i % 4];
+                       char base = baseFlow[i % baseFlow.length()];
                        
                        for(int j=0;j<intensity;j++){
                                sequence += base;
                        }
                }
-
+        
                if(sequence.size() > 4){
                        sequence = sequence.substr(4);
                }

diff --git a/pcrseqscommand.h b/pcrseqscommand.h
index 5ac6437bb730cf03e6e69a8bf7d1562be4aad595..16c1e29be5f9cbba00180a55a746bbe923b3cbdb 100644 (file)
--- a/pcrseqscommand.h
+++ b/pcrseqscommand.h
@@ -77,14 +77,14 @@ struct pcrData {
        unsigned long long fend;
        int count, start, end, length, pdiffs;
        MothurOut* m;
-       vector<string> primers;
+       map<string, int> primers;
     vector<string> revPrimer;
     set<string> badSeqNames;
     bool keepprimer, keepdots;
        
        
        pcrData(){}
-       pcrData(string f, string gf, string bfn, MothurOut* mout, string ol, string ec, vector<string> pr, vector<string> rpr, string nm, bool kp, bool kd, int st, int en, int l, int pd, unsigned long long fst, unsigned long long fen) {
+       pcrData(string f, string gf, string bfn, MothurOut* mout, string ol, string ec, map<string, int> pr, vector<string> rpr, string nm, bool kp, bool kd, int st, int en, int l, int pd, unsigned long long fst, unsigned long long fen) {
                filename = f;
         goodFasta = gf;
         badFasta = bfn;
@@ -132,7 +132,7 @@ static DWORD WINAPI MyPcrThreadFunction(LPVOID lpParam){
         set<int> lengths;
         //pdiffs, bdiffs, primers, barcodes, revPrimers
         map<string, int> faked;
-        TrimOligos trim(pdiffs, 0, primers, faked, revPrimer);
+        TrimOligos trim(pDataArray->pdiffs, 0, pDataArray->primers, faked, pDataArray->revPrimer);
                
                for(int i = 0; i < pDataArray->fend; i++){ //end is the number of sequences to process
             pDataArray->count++;

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index a859d145b49e261bace85fb973d3aa9466bc1123..30815a077c19ff7663d498223c49e73ddc268809 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -21,8 +21,7 @@ vector<string> ShhherCommand::setParameters(){
         CommandParameter plarge("large", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(plarge);
                CommandParameter psigma("sigma", "Number", "", "60", "", "", "","",false,false); parameters.push_back(psigma);
                CommandParameter pmindelta("mindelta", "Number", "", "0.000001", "", "", "","",false,false); parameters.push_back(pmindelta);
-               CommandParameter porder("order", "String", "", "", "", "", "","",false,false); parameters.push_back(porder);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+        CommandParameter porder("order", "Multiple", "A-B", "A", "", "", "","",false,false, true); parameters.push_back(porder);               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
@@ -39,6 +38,11 @@ string ShhherCommand::getHelpString(){
        try {
                string helpString = "";
                helpString += "The shhh.flows command reads a file containing flowgrams and creates a file of corrected sequences.\n";
+        helpString += "The shhh.flows command parameters are flow, file, lookup, cutoff, processors, large, maxiter, sigma, mindelta and order.\n";
+        helpString += "The flow parameter is used to input your flow file.\n";
+        helpString += "The file parameter is used to input the *flow.files file created by trim.flows.\n";
+        helpString += "The lookup parameter is used specify the lookup file you would like to use. http://www.mothur.org/wiki/Lookup_files.\n";
+        helpString += "The order parameter options are A or B.  A = TACG and B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC.\n";
                return helpString;
        }
        catch(exception& e) {
@@ -357,11 +361,18 @@ ShhherCommand::ShhherCommand(string option) {
                        temp = validParameter.validFile(parameters, "sigma", false);if (temp == "not found")    {       temp = "60";            }
                        m->mothurConvert(temp, sigma); 
                        
-                       flowOrder = validParameter.validFile(parameters, "order", false);
-                       if (flowOrder == "not found"){ flowOrder = "TACG";              }
-                       else if(flowOrder.length() != 4){
-                               m->mothurOut("The value of the order option must be four bases long\n");
-                       }
+                       temp = validParameter.validFile(parameters, "order", false);  if (temp == "not found"){         temp = "A";     }
+            if (temp.length() > 1) {  m->mothurOut("[ERROR]: " + temp + " is not a valid option for order. order options are A or B. A = TACG and B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC.\n");  abort=true;
+            }
+            else {
+                if (toupper(temp[0]) == 'A') {  flowOrder = "TACG";   }
+                else if(toupper(temp[0]) == 'B'){ 
+                    flowOrder = "TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC";   }
+                else {
+                    m->mothurOut("[ERROR]: " + temp + " is not a valid option for order. order options are A or B. A = TACG and B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC.\n");  abort=true;
+                }
+            }
+
                        
                }
 #ifdef USE_MPI
@@ -1777,7 +1788,7 @@ void ShhherCommand::writeSequences(vector<int> otuCounts){
                 
                 for(int j=0;j<numFlowCells;j++){
                     
-                    char base = flowOrder[j % 4];
+                    char base = flowOrder[j % flowOrder.length()];
                     for(int k=0;k<uniqueFlowgrams[index * numFlowCells + j];k++){
                         newSeq += base;
                     }
@@ -1895,7 +1906,7 @@ void ShhherCommand::writeClusters(vector<int> otuCounts){
                 
                 otuCountsFile << "ideal\t";
                 for(int j=8;j<numFlowCells;j++){
-                    char base = bases[j % 4];
+                    char base = bases[j % bases.length()];
                     for(int s=0;s<uniqueFlowgrams[index * numFlowCells + j];s++){
                         otuCountsFile << base;
                     }
@@ -1909,7 +1920,7 @@ void ShhherCommand::writeClusters(vector<int> otuCounts){
                     string newSeq = "";
                     
                     for(int k=0;k<lengths[sequence];k++){
-                        char base = bases[k % 4];
+                        char base = bases[k % bases.length()];
                         int freq = int(0.01 * (double)flowDataIntI[sequence * numFlowCells + k] + 0.5);
                         
                         for(int s=0;s<freq;s++){
@@ -1947,10 +1958,10 @@ int ShhherCommand::execute(){
         if (numFiles < processors) { processors = numFiles; }
         
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-        if (processors == 1) { driver(flowFileVector, compositeFASTAFileName, compositeNamesFileName, 0, flowFileVector.size()); }
+        if (processors == 1) { driver(flowFileVector, compositeFASTAFileName, compositeNamesFileName); }
         else { createProcesses(flowFileVector); } //each processor processes one file
 #else
-        driver(flowFileVector, compositeFASTAFileName, compositeNamesFileName, 0, flowFileVector.size());
+        driver(flowFileVector, compositeFASTAFileName, compositeNamesFileName);
 #endif
         
                if(compositeFASTAFileName != ""){
@@ -1971,6 +1982,40 @@ int ShhherCommand::execute(){
        }
 }
 #endif
+//********************************************************************************************************************
+//sorts biggest to smallest
+inline bool compareFileSizes(string left, string right){
+    
+    FILE * pFile;
+    long leftsize = 0;
+    
+    //get num bytes in file
+    string filename = left;
+    pFile = fopen (filename.c_str(),"rb");
+    string error = "Error opening " + filename;
+    if (pFile==NULL) perror (error.c_str());
+    else{
+        fseek (pFile, 0, SEEK_END);
+        leftsize=ftell (pFile);
+        fclose (pFile);
+    }
+    
+    FILE * pFile2;
+    long rightsize = 0;
+    
+    //get num bytes in file
+    filename = right;
+    pFile2 = fopen (filename.c_str(),"rb");
+    error = "Error opening " + filename;
+    if (pFile2==NULL) perror (error.c_str());
+    else{
+        fseek (pFile2, 0, SEEK_END);
+        rightsize=ftell (pFile2);
+        fclose (pFile2);
+    }
+    
+    return (leftsize > rightsize);     
+} 
 /**************************************************************************************************/
 
 int ShhherCommand::createProcesses(vector<string> filenames){
@@ -1981,9 +2026,31 @@ int ShhherCommand::createProcesses(vector<string> filenames){
                
                //sanity check
                if (filenames.size() < processors) { processors = filenames.size(); }
-               
+        
+        //sort file names by size to divide load better
+        sort(filenames.begin(), filenames.end(), compareFileSizes);
+        
+        vector < vector <string> > dividedFiles; //dividedFiles[1] = vector of filenames for process 1...
+        dividedFiles.resize(processors);
+        
+        //for each file, figure out which process will complete it
+        //want to divide the load intelligently so the big files are spread between processes
+        for (int i = 0; i < filenames.size(); i++) { 
+            int processToAssign = (i+1) % processors; 
+            if (processToAssign == 0) { processToAssign = processors; }
+            
+            dividedFiles[(processToAssign-1)].push_back(filenames[i]);
+        }
+        
+        //now lets reverse the order of ever other process, so we balance big files running with little ones
+        for (int i = 0; i < processors; i++) {
+            int remainder = ((i+1) % processors);
+            if (remainder) {  reverse(dividedFiles[i].begin(), dividedFiles[i].end());  }
+        }
+        
+                       
                //divide the groups between the processors
-               vector<linePair> lines;
+               /*vector<linePair> lines;
         vector<int> numFilesToComplete;
                int numFilesPerProcessor = filenames.size() / processors;
                for (int i = 0; i < processors; i++) {
@@ -1992,7 +2059,7 @@ int ShhherCommand::createProcesses(vector<string> filenames){
                        if(i == (processors - 1)){      endIndex = filenames.size();    }
                        lines.push_back(linePair(startIndex, endIndex));
             numFilesToComplete.push_back((endIndex-startIndex));
-               }
+               }*/
                
         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)         
                
@@ -2004,7 +2071,7 @@ int ShhherCommand::createProcesses(vector<string> filenames){
                                processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
                                process++;
                        }else if (pid == 0){
-                               num = driver(filenames, compositeFASTAFileName + toString(getpid()) + ".temp", compositeNamesFileName  + toString(getpid()) + ".temp", lines[process].start, lines[process].end);
+                               num = driver(dividedFiles[process], compositeFASTAFileName + toString(getpid()) + ".temp", compositeNamesFileName  + toString(getpid()) + ".temp");
                 
                 //pass numSeqs to parent
                                ofstream out;
@@ -2022,7 +2089,7 @@ int ShhherCommand::createProcesses(vector<string> filenames){
                }
                
                //do my part
-               driver(filenames, compositeFASTAFileName, compositeNamesFileName, lines[0].start, lines[0].end);
+               driver(dividedFiles[0], compositeFASTAFileName, compositeNamesFileName);
                
                //force parent to wait until all the processes are done
                for (int i=0;i<processIDS.size();i++) { 
@@ -2081,8 +2148,8 @@ int ShhherCommand::createProcesses(vector<string> filenames){
                        if (!in.eof()) { 
                 int tempNum = 0; 
                 in >> tempNum; 
-                if (tempNum != numFilesToComplete[i+1]) {
-                    m->mothurOut("[ERROR]: main process expected " + toString(processIDS[i]) + " to complete " + toString(numFilesToComplete[i+1]) + " files, and it only reported completing " + toString(tempNum) + ". This will cause file mismatches.  The flow files may be too large to process with multiple processors. \n");
+                if (tempNum != dividedFiles[i+1].size()) {
+                    m->mothurOut("[ERROR]: main process expected " + toString(processIDS[i]) + " to complete " + toString(dividedFiles[i+1].size()) + " files, and it only reported completing " + toString(tempNum) + ". This will cause file mismatches.  The flow files may be too large to process with multiple processors. \n");
                 }
             }
                        in.close(); m->mothurRemove(tempFile);
@@ -2152,12 +2219,12 @@ vector<string> ShhherCommand::parseFlowFiles(string filename){
 }
 /**************************************************************************************************/
 
-int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFileName, string thisCompositeNamesFileName, int start, int end){
+int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFileName, string thisCompositeNamesFileName){
     try {
         
         int numCompleted = 0;
         
-        for(int i=start;i<end;i++){
+        for(int i=0;i<filenames.size();i++){
                        
                        if (m->control_pressed) { break; }
                        
@@ -3307,7 +3374,7 @@ void ShhherCommand::writeSequences(string thisCompositeFASTAFileName, int numOTU
                                
                                for(int j=0;j<numFlowCells;j++){
                                        
-                                       char base = flowOrder[j % 4];
+                                       char base = flowOrder[j % flowOrder.length()];
                                        for(int k=0;k<uniqueFlowgrams[index * numFlowCells + j];k++){
                                                newSeq += base;
                                        }
@@ -3408,7 +3475,7 @@ void ShhherCommand::writeClusters(string otuCountsFileName, int numOTUs, int num
                                
                                otuCountsFile << "ideal\t";
                                for(int j=8;j<numFlowCells;j++){
-                                       char base = bases[j % 4];
+                                       char base = bases[j % bases.length()];
                                        for(int s=0;s<uniqueFlowgrams[index * numFlowCells + j];s++){
                                                otuCountsFile << base;
                                        }
@@ -3422,7 +3489,7 @@ void ShhherCommand::writeClusters(string otuCountsFileName, int numOTUs, int num
                                        string newSeq = "";
                                        
                                        for(int k=0;k<lengths[sequence];k++){
-                                               char base = bases[k % 4];
+                                               char base = bases[k % bases.length()];
                                                int freq = int(0.01 * (double)flowDataIntI[sequence * numFlowCells + k] + 0.5);
                         
                                                for(int s=0;s<freq;s++){

diff --git a/shhhercommand.h b/shhhercommand.h
index 3b757241eacee655570ef823bfed96bfd39abe64..c787fe41d5c0f2a30975feb9461bdaa3194aae18 100644 (file)
--- a/shhhercommand.h
+++ b/shhhercommand.h
@@ -70,7 +70,7 @@ private:
     vector<string> flowFileVector;
        
     vector<string> parseFlowFiles(string);
-    int driver(vector<string>, string, string, int, int);
+    int driver(vector<string>, string, string);
     int createProcesses(vector<string>);
     int getFlowData(string, vector<string>&, vector<int>&, vector<short>&, map<string, int>&, int&);
     int getUniques(int, int, vector<short>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<double>&, vector<short>&);

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 0df53d5649881c924be60140338e5fff7c2bc840..b793dc885ef9213f290f118be55066a0e2837086 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -644,6 +644,7 @@ int TreeGroupCommand::makeSimsShared() {
             }else {
                 m->clearGroups();
                 Groups.clear();
+                m->Treenames.clear();
                 vector<SharedRAbundVector*> temp;
                 for (int i = 0; i < lookup.size(); i++) {
                     if (lookup[i]->getNumSeqs() < subsampleSize) { 
@@ -652,6 +653,7 @@ int TreeGroupCommand::makeSimsShared() {
                     }else { 
                         Groups.push_back(lookup[i]->getGroup()); 
                         temp.push_back(lookup[i]);
+                        m->Treenames.push_back(lookup[i]->getGroup());
                     }
                 } 
                 lookup = temp;
@@ -917,11 +919,15 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 for (int i = 0; i < calcDists.size(); i++) {  calcDists[i].clear(); }
             }
                }
-               
+        
+               if (m->debug) {  m->mothurOut("[DEBUG]: done with iters.\n"); }
+            
         if (iters != 1) {
             //we need to find the average distance and standard deviation for each groups distance
             vector< vector<seqDist>  > calcAverages = m->getAverages(calcDistsTotals);  
             
+            if (m->debug) {  m->mothurOut("[DEBUG]: found averages.\n"); }
+            
             //create average tree for each calc
             for (int i = 0; i < calcDists.size(); i++) {
                 vector< vector<double> > matrix; //square matrix to represent the distance
@@ -951,6 +957,8 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 if (newTree != NULL) { writeTree(outputFile, newTree); }                
             }
             
+            if (m->debug) {  m->mothurOut("[DEBUG]: done averages trees.\n"); }
+            
             //create all trees for each calc and find their consensus tree
             for (int i = 0; i < calcDists.size(); i++) {
                 if (m->control_pressed) { break; }
@@ -982,7 +990,7 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                         int row = calcDistsTotals[myIter][i][j].seq1;
                         int column = calcDistsTotals[myIter][i][j].seq2;
                         double dist = calcDistsTotals[myIter][i][j].dist;
-                        
+                       
                         matrix[row][column] = dist;
                         matrix[column][row] = dist;
                     }
@@ -997,11 +1005,15 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 outAll.close();
                 if (m->control_pressed) { for (int k = 0; k < trees.size(); k++) { delete trees[k]; } }
                 
+                if (m->debug) {  m->mothurOut("[DEBUG]: done all trees.\n"); }
+                
                 Consensus consensus;
                 //clear old tree names if any
                 m->Treenames.clear(); m->Treenames = m->getGroups(); //may have changed if subsample eliminated groups
                 Tree* conTree = consensus.getTree(trees);
                 
+                if (m->debug) {  m->mothurOut("[DEBUG]: done cons tree.\n"); }
+                
                 //create a new filename
                 variables["[tag]"] = "cons";
                 string conFile = getOutputFileName("tree",variables);                          

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index e9bd081605b4211a26084334122ee12da83b949b..61b19b8dbaa61546c0e984e444fa8ddda5b366f1 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -28,7 +28,7 @@ vector<string> TrimFlowsCommand::setParameters(){
                CommandParameter psignal("signal", "Number", "", "0.50", "", "", "","",false,false); parameters.push_back(psignal);
                CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "","",false,false); parameters.push_back(pnoise);
                CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(pallfiles);
-               CommandParameter porder("order", "String", "", "TACG", "", "", "","",false,false); parameters.push_back(porder);
+        CommandParameter porder("order", "Multiple", "A-B", "A", "", "", "","",false,false, true); parameters.push_back(porder);
                CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfasta);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
@@ -214,12 +214,18 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        m->setProcessors(temp);
                        m->mothurConvert(temp, processors);
        
-                       flowOrder = validParameter.validFile(parameters, "order", false);
-                       if (flowOrder == "not found"){ flowOrder = "TACG";              }
-                       else if(flowOrder.length() != 4){
-                               m->mothurOut("The value of the order option must be four bases long\n");
-                       }
-
+                       temp = validParameter.validFile(parameters, "order", false);  if (temp == "not found"){         temp = "A";     }
+            if (temp.length() > 1) {  m->mothurOut("[ERROR]: " + temp + " is not a valid option for order. order options are A or B. A = TACG and B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC.\n");  abort=true;
+            }
+            else {
+                if (toupper(temp[0]) == 'A') {  flowOrder = "TACG";   }
+                else if(toupper(temp[0]) == 'B'){ 
+                    flowOrder = "TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC";   }
+                else {
+                    m->mothurOut("[ERROR]: " + temp + " is not a valid option for order. order options are A or B. A = TACG and B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC.\n");  abort=true;
+                }
+            }
+            
                        if(oligoFileName == "") {       allFiles = 0;           }
                        else                                    {       allFiles = 1;           }
 
@@ -228,7 +234,6 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
             numLinkers = 0;
             numSpacers = 0;
                }
-               
        }
        catch(exception& e) {
                m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");