X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=ba368fc8569fdfde5d3587ffc5a1e65240e8acdf;hb=9b53f130ac9af5e95444ce2e817fce25ed19ff03;hp=29b8733721a2b710468f960ac474c99734a181df;hpb=ea4f373c28543cd1002b0dd7dc6e55c526647d59;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 29b8733..ba368fc 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -114,7 +114,7 @@ string TrimSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
             else if (type == "fasta")            {   outputFileName =  "fasta";   }
             else if (type == "group")            {   outputFileName =  "groups";   }
             else if (type == "name")            {   outputFileName =  "names";   }
-            else if (type == "count")            {   outputFileName =  "count.table";   }
+            else if (type == "count")            {   outputFileName =  "count_table";   }
             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
         }
         return outputFileName;
@@ -660,7 +660,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 		
 		int count = 0;
 		bool moreSeqs = 1;
-		TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, rbarcodes, revPrimer, linker, spacer);
+		TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
 	
 		while (moreSeqs) {
 				
@@ -704,12 +704,6 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 					if(success > bdiffs)		{	trashCode += 'b';	}
 					else{ currentSeqsDiffs += success;  }
 				}
-                
-                if(rbarcodes.size() != 0){
-					success = trimOligos.stripRBarcode(currSeq, currQual, barcodeIndex);
-					if(success > bdiffs)		{	trashCode += 'b';	}
-					else{ currentSeqsDiffs += success;  }
-				}
 				
                 if(numSpacers != 0){
 					success = trimOligos.stripSpacer(currSeq, currQual);
@@ -1042,10 +1036,10 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
 		HANDLE  hThreadArray[processors-1]; 
 		
 		//Create processor worker threads.
-		for( int i=0; i<processors-1; i++){
+		for( int h=0; h<processors-1; h++){
 			
             string extension = "";
-			if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
+			if (h != 0) { extension = toString(h) + ".temp"; processIDS.push_back(h); }
             vector<vector<string> > tempFASTAFileNames = fastaFileNames;
             vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
             vector<vector<string> > tempNameFileNames = nameFileNames;
@@ -1087,14 +1081,14 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                               tempFASTAFileNames,
                                               tempPrimerQualFileNames,
                                               tempNameFileNames,
-                                              lines[i].start, lines[i].end, qLines[i].start, qLines[i].end, m,
-                                              pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, rbarcodes, revPrimer, linker, spacer, 
+                                              lines[h].start, lines[h].end, qLines[h].start, qLines[h].end, m,
+                                              pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, revPrimer, linker, spacer, 
                                              primerNameVector, barcodeNameVector, createGroup, allFiles, keepforward, keepFirst, removeLast,
                                               qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage,
                                              minLength, maxAmbig, maxHomoP, maxLength, flip, nameMap, nameCount);
 			pDataArray.push_back(tempTrim);
             
-			hThreadArray[i] = CreateThread(NULL, 0, MyTrimThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);   
+			hThreadArray[h] = CreateThread(NULL, 0, MyTrimThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]);   
 		}
         
         //parent do my part
@@ -1109,8 +1103,32 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
 			m->openOutputFile(trimNameFileName, temp);		temp.close();
 			m->openOutputFile(scrapNameFileName, temp);		temp.close();
 		}
+        vector<vector<string> > tempFASTAFileNames = fastaFileNames;
+        vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
+        vector<vector<string> > tempNameFileNames = nameFileNames;
+        if(allFiles){
+            ofstream temp;
+            string extension = toString(processors-1) + ".temp";
+            for(int i=0;i<tempFASTAFileNames.size();i++){
+                for(int j=0;j<tempFASTAFileNames[i].size();j++){
+                    if (tempFASTAFileNames[i][j] != "") {
+                        tempFASTAFileNames[i][j] += extension;
+                        m->openOutputFile(tempFASTAFileNames[i][j], temp);			temp.close();
+                        
+                        if(qFileName != ""){
+                            tempPrimerQualFileNames[i][j] += extension;
+                            m->openOutputFile(tempPrimerQualFileNames[i][j], temp);		temp.close();
+                        }
+                        if(nameFile != ""){
+                            tempNameFileNames[i][j] += extension;
+                            m->openOutputFile(tempNameFileNames[i][j], temp);		temp.close();
+                        }
+                    }
+                }
+            }
+        }
         
-		driverCreateTrim(filename, qFileName, (trimFASTAFileName + toString(processors-1) + ".temp"), (scrapFASTAFileName + toString(processors-1) + ".temp"), (trimQualFileName + toString(processors-1) + ".temp"), (scrapQualFileName + toString(processors-1) + ".temp"), (trimNameFileName + toString(processors-1) + ".temp"), (scrapNameFileName + toString(processors-1) + ".temp"), (trimCountFileName + toString(processors-1) + ".temp"), (scrapCountFileName + toString(processors-1) + ".temp"), (groupFile + toString(processors-1) + ".temp"), fastaFileNames, qualFileNames, nameFileNames, lines[processors-1], qLines[processors-1]);
+		driverCreateTrim(filename, qFileName, (trimFASTAFileName + toString(processors-1) + ".temp"), (scrapFASTAFileName + toString(processors-1) + ".temp"), (trimQualFileName + toString(processors-1) + ".temp"), (scrapQualFileName + toString(processors-1) + ".temp"), (trimNameFileName + toString(processors-1) + ".temp"), (scrapNameFileName + toString(processors-1) + ".temp"), (trimCountFileName + toString(processors-1) + ".temp"), (scrapCountFileName + toString(processors-1) + ".temp"), (groupFile + toString(processors-1) + ".temp"), tempFASTAFileNames, tempPrimerQualFileNames, tempNameFileNames, lines[processors-1], qLines[processors-1]);
         processIDS.push_back(processors-1);
 
         
@@ -1435,40 +1453,11 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
 				}
 				else if(type == "BARCODE"){
 					inOligos >> group;
-                    
-                    //barcode lines can look like   BARCODE   atgcatgc   groupName  - for 454 seqs
-                    //or                            BARCODE   atgcatgc   atgcatgc    groupName  - for illumina data that has forward and reverse info
-					string temp = "";
-                    while (!inOligos.eof())	{	
-						char c = inOligos.get(); 
-						if (c == 10 || c == 13){	break;	}
-						else if (c == 32 || c == 9){;} //space or tab
-						else { 	temp += c;  }
-					} 
 					
-                    //then this is illumina data with 4 columns
-                    if (temp != "") {  
-                        
-                        for(int i=0;i<group.length();i++){
-                            group[i] = toupper(group[i]);
-                            if(group[i] == 'U')	{	group[i] = 'T';	}
-                        }
-                        
-                        if (m->debug) { m->mothurOut("[DEBUG]: reading reverse " + group + ", and group = " + temp + ".\n"); }
-                        
-                        string reverseBarcode = reverseOligo(group); //reverse barcode
-                        //check for repeat barcodes
-                        map<string, int>::iterator itBar = rbarcodes.find(reverseBarcode);
-                        if (itBar != rbarcodes.end()) { m->mothurOut("reverse barcode " + group + " is in your oligos file already."); m->mothurOutEndLine();  }
-                        
-                        group = temp;
-                        rbarcodes[reverseBarcode]=indexBarcode; 
-                    }else { if (m->debug) { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); } }
-                        
 					//check for repeat barcodes
 					map<string, int>::iterator itBar = barcodes.find(oligo);
 					if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
-						
+                    
 					barcodes[oligo]=indexBarcode; indexBarcode++;
 					barcodeNameVector.push_back(group);
 				}else if(type == "LINKER"){