Merge remote-tracking branch 'mothur/master'

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 6a26fac949a335999be1cf7c1355f9c5c4f7d48c..86de668b4f57596bf11efb80807b18f932136551 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -21,7 +21,9 @@ vector<string> TrimFlowsCommand::setParameters(){
                CommandParameter pminflows("minflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pminflows);
                CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
                CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
-               CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
+        CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
+               CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
+        CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
                CommandParameter psignal("signal", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(psignal);
                CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pnoise);
@@ -178,10 +180,17 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found"){       temp = "0";             }
                        m->mothurConvert(temp, pdiffs);
                        
-                       temp = validParameter.validFile(parameters, "tdiffs", false);
-                       if (temp == "not found"){ int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
+            temp = validParameter.validFile(parameters, "ldiffs", false);              if (temp == "not found") { temp = "0"; }
+                       m->mothurConvert(temp, ldiffs);
+            
+            temp = validParameter.validFile(parameters, "sdiffs", false);              if (temp == "not found") { temp = "0"; }
+                       m->mothurConvert(temp, sdiffs);
+                       
+                       temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs;  temp = toString(tempTotal); }
                        m->mothurConvert(temp, tdiffs);
-                       if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
+                       
+                       if(tdiffs == 0){        tdiffs = bdiffs + pdiffs + ldiffs + sdiffs;     }
+
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
@@ -228,7 +237,7 @@ int TrimFlowsCommand::execute(){
                }
                
                vector<unsigned long long> flowFilePos;
-       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                flowFilePos = getFlowFileBreaks();
                for (int i = 0; i < (flowFilePos.size()-1); i++) {
                        lines.push_back(new linePair(flowFilePos[i], flowFilePos[(i+1)]));
@@ -297,7 +306,7 @@ int TrimFlowsCommand::execute(){
                                                        m->mothurRemove(barcodePrimerComboFileNames[i][j]);
                                                }
                                                else{
-                                                       output << barcodePrimerComboFileNames[i][j] << endl;
+                                                       output << m->getFullPathName(barcodePrimerComboFileNames[i][j]) << endl;
                                                        outputNames.push_back(barcodePrimerComboFileNames[i][j]);
                                                        outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
                                                }
@@ -311,7 +320,7 @@ int TrimFlowsCommand::execute(){
                        flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
                        m->openOutputFile(flowFilesFileName, output);
                        
-                       output << trimFlowFileName << endl;
+                       output << m->getFullPathName(trimFlowFileName) << endl;
                        
                        output.close();
                }
@@ -380,7 +389,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                int count = 0;
                bool moreSeqs = 1;
                
-               TrimOligos trimOligos(pdiffs, bdiffs, primers, barcodes, revPrimer);
+               TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
                
                while(moreSeqs) {
                        //cout << "driver " << count << endl;
@@ -405,12 +414,26 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                        int primerIndex = 0;
                        int barcodeIndex = 0;
                        
+            if(numLinkers != 0){
+                success = trimOligos.stripLinker(currSeq);
+                if(success > ldiffs)           {       trashCode += 'k';       }
+                else{ currentSeqDiffs += success;  }
+                
+            }
+            
                        if(barcodes.size() != 0){
                                success = trimOligos.stripBarcode(currSeq, barcodeIndex);
                                if(success > bdiffs)            {       trashCode += 'b';       }
                                else{ currentSeqDiffs += success;  }
                        }
                        
+            if(numSpacers != 0){
+                success = trimOligos.stripSpacer(currSeq);
+                if(success > sdiffs)           {       trashCode += 's';       }
+                else{ currentSeqDiffs += success;  }
+                
+            }
+            
                        if(numFPrimers != 0){
                                success = trimOligos.stripForward(currSeq, primerIndex);
                                if(success > pdiffs)            {       trashCode += 'f';       }
@@ -448,7 +471,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                        //report progress
                        if((count) % 10000 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        unsigned long long pos = flowFile.tellg();
 
                        if ((pos == -1) || (pos >= line->end)) { break; }
@@ -522,9 +545,8 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 
                                }
                                else if(type == "REVERSE"){
-                                       Sequence oligoRC("reverse", oligo);
-                                       oligoRC.reverseComplement();
-                                       revPrimer.push_back(oligoRC.getUnaligned());
+                                       string oligoRC = reverseOligo(oligo);
+                                       revPrimer.push_back(oligoRC);
                                }
                                else if(type == "BARCODE"){
                                        oligosFile >> group;
@@ -535,6 +557,10 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 
                                        barcodes[oligo]=indexBarcode; indexBarcode++;
                                        barcodeNameVector.push_back(group);
+                               }else if(type == "LINKER"){
+                                       linker.push_back(oligo);
+                               }else if(type == "SPACER"){
+                                       spacer.push_back(oligo);
                                }
                                else{
                                        m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();  
@@ -600,6 +626,8 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
                
                numFPrimers = primers.size();
                numRPrimers = revPrimer.size();
+        numLinkers = linker.size();
+        numSpacers = spacer.size();
                
        }
        catch(exception& e) {
@@ -607,6 +635,47 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
                exit(1);
        }
 }
+//********************************************************************/
+string TrimFlowsCommand::reverseOligo(string oligo){
+       try {
+        string reverse = "";
+        
+        for(int i=oligo.length()-1;i>=0;i--){
+            
+            if(oligo[i] == 'A')                {       reverse += 'T'; }
+            else if(oligo[i] == 'T'){  reverse += 'A'; }
+            else if(oligo[i] == 'U'){  reverse += 'A'; }
+            
+            else if(oligo[i] == 'G'){  reverse += 'C'; }
+            else if(oligo[i] == 'C'){  reverse += 'G'; }
+            
+            else if(oligo[i] == 'R'){  reverse += 'Y'; }
+            else if(oligo[i] == 'Y'){  reverse += 'R'; }
+            
+            else if(oligo[i] == 'M'){  reverse += 'K'; }
+            else if(oligo[i] == 'K'){  reverse += 'M'; }
+            
+            else if(oligo[i] == 'W'){  reverse += 'W'; }
+            else if(oligo[i] == 'S'){  reverse += 'S'; }
+            
+            else if(oligo[i] == 'B'){  reverse += 'V'; }
+            else if(oligo[i] == 'V'){  reverse += 'B'; }
+            
+            else if(oligo[i] == 'D'){  reverse += 'H'; }
+            else if(oligo[i] == 'H'){  reverse += 'D'; }
+            
+            else                                               {       reverse += 'N'; }
+        }
+        
+        
+        return reverse;
+    }
+       catch(exception& e) {
+               m->errorOut(e, "TrimFlowsCommand", "reverseOligo");
+               exit(1);
+       }
+}
+
 /**************************************************************************************************/
 vector<unsigned long long> TrimFlowsCommand::getFlowFileBreaks() {
 
@@ -689,7 +758,7 @@ int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trim
                processIDS.clear();
                int exitCommand = 1;
                
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                int process = 1;
                
                //loop through and create all the processes you want