X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.cpp;h=00c4d94e1027c63d8a0c324167bb3d7ec8e4c570;hb=43ed0accfbc2852849e104ff7eccdd2c42acd4ec;hp=77dacfe711ea694d7d81cb7536fd15d14cb0ec97;hpb=0ca63a8165baa0afa459e644ebe140ba496d5ba0;p=mothur.git

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 77dacfe..00c4d94 100644
--- 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);
@@ -226,7 +235,7 @@ 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)]));
@@ -295,7 +304,7 @@ 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]);
 						}
@@ -309,7 +318,7 @@ 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();
 		}
@@ -381,9 +390,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
 		TrimOligos trimOligos(pdiffs, bdiffs, primers, barcodes, revPrimer);
 		
 		while(moreSeqs) {
-			//cout << "driver " << count << endl;
-			
-	
+				
 			if (m->control_pressed) { break; }
 			
 			int success = 1;
@@ -404,12 +411,26 @@ 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';	}
@@ -447,7 +468,7 @@ 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; }
@@ -534,6 +555,10 @@ 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();  
@@ -599,6 +624,8 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 		
 		numFPrimers = primers.size();
 		numRPrimers = revPrimer.size();
+        numLinkers = linker.size();
+        numSpacers = spacer.size();
 		
 	}
 	catch(exception& e) {
@@ -688,7 +715,7 @@ 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