added binary file operations to mothurout class. added comment to sequence class...

[mothur.git] / makecontigscommand.cpp

diff --git a/makecontigscommand.cpp b/makecontigscommand.cpp
index 32e2d68a3d1ebe51e0acc8fa64b7a499324fd60f..bf27d264ec5f06f15a3d25b7ac8c5952cd03e17a 100644 (file)
--- a/makecontigscommand.cpp
+++ b/makecontigscommand.cpp
@@ -15,24 +15,27 @@ vector<string> MakeContigsCommand::setParameters(){
         CommandParameter prfastq("rfastq", "InputTypes", "", "", "none", "none", "fastqGroup","fasta-qfile",false,false,true); parameters.push_back(prfastq);
         CommandParameter pfasta("ffasta", "InputTypes", "", "", "FastaFastqFile", "FastaFastqFile", "fastaGroup","fasta",false,false,true); parameters.push_back(pfasta);
         CommandParameter prfasta("rfasta", "InputTypes", "", "", "none", "none", "none","fastaGroup",false,false,true); parameters.push_back(prfasta);
         CommandParameter prfastq("rfastq", "InputTypes", "", "", "none", "none", "fastqGroup","fasta-qfile",false,false,true); parameters.push_back(prfastq);
         CommandParameter pfasta("ffasta", "InputTypes", "", "", "FastaFastqFile", "FastaFastqFile", "fastaGroup","fasta",false,false,true); parameters.push_back(pfasta);
         CommandParameter prfasta("rfasta", "InputTypes", "", "", "none", "none", "none","fastaGroup",false,false,true); parameters.push_back(prfasta);

-        CommandParameter pfqual("fqfile", "InputTypes", "", "", "none", "none", "qfileGroup","qfile",false,false,true); parameters.push_back(pfqual);
-        CommandParameter prqual("rqfile", "InputTypes", "", "", "none", "none", "qfileGroup","qfile",false,false,true); parameters.push_back(prqual);
+        CommandParameter pfqual("fqfile", "InputTypes", "", "", "none", "none", "qfileGroup","",false,false,true); parameters.push_back(pfqual);
+        CommandParameter prqual("rqfile", "InputTypes", "", "", "none", "none", "qfileGroup","",false,false,true); parameters.push_back(prqual);

         CommandParameter pfile("file", "InputTypes", "", "", "FastaFastqFile", "FastaFastqFile", "none","fasta-qfile",false,false,true); parameters.push_back(pfile);
         CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","group",false,false,true); parameters.push_back(poligos);
         CommandParameter pfile("file", "InputTypes", "", "", "FastaFastqFile", "FastaFastqFile", "none","fasta-qfile",false,false,true); parameters.push_back(pfile);
         CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","group",false,false,true); parameters.push_back(poligos);

+        CommandParameter pfindex("findex", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pfindex);
+        CommandParameter prindex("rindex", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(prindex);

                CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
                CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs);
                CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
                CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs);

-//        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 palign("align", "Multiple", "needleman-gotoh", "needleman", "", "", "","",false,false); parameters.push_back(palign);
         CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pallfiles);
         CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
 
         CommandParameter palign("align", "Multiple", "needleman-gotoh", "needleman", "", "", "","",false,false); parameters.push_back(palign);
         CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pallfiles);

+        CommandParameter ptrimoverlap("trimoverlap", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptrimoverlap);

                CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
                CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
                CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
                CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
                CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
                CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
                CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
                CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);

-        CommandParameter pthreshold("threshold", "Number", "", "40", "", "", "","",false,false); parameters.push_back(pthreshold);
+        CommandParameter pthreshold("insert", "Number", "", "20", "", "", "","",false,false); parameters.push_back(pthreshold);
+        CommandParameter pdeltaq("deltaq", "Number", "", "6", "", "", "","",false,false); parameters.push_back(pdeltaq);

                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);

+        CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa-illumina1.8+", "illumina1.8+", "", "", "","",false,false,true); parameters.push_back(pformat);

                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                


@@ -49,27 +52,33 @@ vector<string> MakeContigsCommand::setParameters(){
 string MakeContigsCommand::getHelpString(){    
        try {
                string helpString = "";
 string MakeContigsCommand::getHelpString(){    
        try {
                string helpString = "";

-               helpString += "The make.contigs command reads a file, forward fastq file and a reverse fastq file or forward fasta and reverse fasta files and outputs new fasta.  It will also provide new quality files if the fastq or file parameter is used.\n";
+               helpString += "The make.contigs command reads a file, forward fastq file and a reverse fastq file or forward fasta and reverse fasta files and outputs new fasta. \n";

         helpString += "If an oligos file is provided barcodes and primers will be trimmed, and a group file will be created.\n";
         helpString += "If an oligos file is provided barcodes and primers will be trimmed, and a group file will be created.\n";

-               helpString += "The make.contigs command parameters are ffastq, rfastq, oligos, tdiffs, bdiffs, ldiffs, sdiffs, pdiffs, align, match, mismatch, gapopen, gapextend, allfiles and processors.\n";
+        helpString += "If a forward index or reverse index file is provided barcodes be trimmed, and a group file will be created. The oligos parameter is required if an index file is given.\n";
+               helpString += "The make.contigs command parameters are file, ffastq, rfastq, ffasta, rfasta, fqfile, rqfile, oligos, findex, rindex, format, tdiffs, bdiffs, pdiffs, align, match, mismatch, gapopen, gapextend, insert, deltaq, allfiles and processors.\n";

                helpString += "The ffastq and rfastq, file, or ffasta and rfasta parameters are required.\n";
                helpString += "The ffastq and rfastq, file, or ffasta and rfasta parameters are required.\n";

-        helpString += "The file parameter is 2 column file containing the forward fastq files in the first column and their matching reverse fastq files in the second column.  Mothur will process each pair and create a combined fasta and qual file with all the sequences.\n";
+        helpString += "The file parameter is 2, 3 or 4 column file containing the forward fastq files in the first column and their matching reverse fastq files in the second column, or a groupName then forward fastq file and reverse fastq file, or forward fastq file then reverse fastq then forward index and reverse index file.  If you only have one index file add 'none' for the other one.  Mothur will process each pair and create a combined fasta and report file with all the sequences.\n";

         helpString += "The ffastq and rfastq parameters are used to provide a forward fastq and reverse fastq file to process.  If you provide one, you must provide the other.\n";
         helpString += "The ffasta and rfasta parameters are used to provide a forward fasta and reverse fasta file to process.  If you provide one, you must provide the other.\n";
         helpString += "The fqfile and rqfile parameters are used to provide a forward quality and reverse quality files to process with the ffasta and rfasta parameters.  If you provide one, you must provide the other.\n";
         helpString += "The ffastq and rfastq parameters are used to provide a forward fastq and reverse fastq file to process.  If you provide one, you must provide the other.\n";
         helpString += "The ffasta and rfasta parameters are used to provide a forward fasta and reverse fasta file to process.  If you provide one, you must provide the other.\n";
         helpString += "The fqfile and rqfile parameters are used to provide a forward quality and reverse quality files to process with the ffasta and rfasta parameters.  If you provide one, you must provide the other.\n";

-               helpString += "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh and needleman. The default is needleman.\n";
+               helpString += "The format parameter is used to indicate whether your sequences are sanger, solexa, illumina1.8+ or illumina, default=illumina1.8+.\n";
+        helpString += "The findex and rindex parameters are used to provide a forward index and reverse index files to process.  \n";
+        helpString += "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh and needleman. The default is needleman.\n";

         helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs + sdiffs + ldiffs.\n";
                helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
                helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
         helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs + sdiffs + ldiffs.\n";
                helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
                helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";

-        helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
-               helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
+        //helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
+               //helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";

                helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
                helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n";
                helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
                helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n";

+        helpString += "The deltaq parameter allows you to specify the delta allowed between quality scores of a mismatched base.  For example in the overlap, if deltaq=5 and in the alignment seqA, pos 200 has a quality score of 30 and the same position in seqB has a quality score of 20, you take the base from seqA (30-20 >= 5).  If the quality score in seqB is 28 then the base in the consensus will be an N (30-28<5) The default is 6.\n";

                helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
                helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n";
                helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
                helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n";

-        helpString += "The threshold parameter allows you to set a quality scores threshold. In the case where we are trying to decide whether to keep a base or remove it because the base is compared to a gap in the other fragment, if the base has a quality score below the threshold we eliminate it. Default=40.\n";
+        helpString += "The insert parameter allows you to set a quality scores threshold. In the case where we are trying to decide whether to keep a base or remove it because the base is compared to a gap in the other fragment, if the base has a quality score equal to or below the threshold we eliminate it. Default=20.\n";

         helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
         helpString += "The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n";
         helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
         helpString += "The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n";

+
+        helpString += "The trimoverlap parameter allows you to trim the sequences to only the overlapping section. The default is F.\n";

         helpString += "The make.contigs command should be in the following format: \n";
                helpString += "make.contigs(ffastq=yourForwardFastqFile, rfastq=yourReverseFastqFile, align=yourAlignmentMethod) \n";
                helpString += "Note: No spaces between parameter labels (i.e. ffastq), '=' and parameters (i.e.yourForwardFastqFile).\n";
         helpString += "The make.contigs command should be in the following format: \n";
                helpString += "make.contigs(ffastq=yourForwardFastqFile, rfastq=yourReverseFastqFile, align=yourAlignmentMethod) \n";
                helpString += "Note: No spaces between parameter labels (i.e. ffastq), '=' and parameters (i.e.yourForwardFastqFile).\n";


@@ -86,9 +95,8 @@ string MakeContigsCommand::getOutputPattern(string type) {
         string pattern = "";
         
         if (type == "fasta") {  pattern = "[filename],[tag],contigs.fasta"; } 
         string pattern = "";
         
         if (type == "fasta") {  pattern = "[filename],[tag],contigs.fasta"; } 

-        else if (type == "qfile") {  pattern = "[filename],[tag],contigs.qual"; } 

         else if (type == "group") {  pattern = "[filename],[tag],contigs.groups"; }
         else if (type == "group") {  pattern = "[filename],[tag],contigs.groups"; }

-        else if (type == "mismatch") {  pattern = "[filename],[tag],contigs.mismatch"; }
+        else if (type == "report") {  pattern = "[filename],[tag],contigs.report"; }

         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
         
         return pattern;
         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
         
         return pattern;


@@ -105,10 +113,9 @@ MakeContigsCommand::MakeContigsCommand(){
                setParameters();
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
                setParameters();
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;

-               outputTypes["qfile"] = tempOutNames;

         outputTypes["group"] = tempOutNames;
         outputTypes["group"] = tempOutNames;

-        outputTypes["mismatch"] = tempOutNames;
-       }
+        outputTypes["report"] = tempOutNames;
+    }

        catch(exception& e) {
                m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
                exit(1);
        catch(exception& e) {
                m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
                exit(1);


@@ -117,7 +124,8 @@ MakeContigsCommand::MakeContigsCommand(){
 //**********************************************************************************************************************
 MakeContigsCommand::MakeContigsCommand(string option)  {
        try {
 //**********************************************************************************************************************
 MakeContigsCommand::MakeContigsCommand(string option)  {
        try {

-               abort = false; calledHelp = false;   
+               abort = false; calledHelp = false;
+        createFileGroup = false; createOligosGroup = false;

         
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
         
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }


@@ -140,8 +148,7 @@ MakeContigsCommand::MakeContigsCommand(string option)  {
                        //initialize outputTypes
                        vector<string> tempOutNames;
                        outputTypes["fasta"] = tempOutNames;
                        //initialize outputTypes
                        vector<string> tempOutNames;
                        outputTypes["fasta"] = tempOutNames;

-                       outputTypes["qfile"] = tempOutNames;
-            outputTypes["mismatch"] = tempOutNames;
+            outputTypes["report"] = tempOutNames;

             outputTypes["group"] = tempOutNames;
                        
             
             outputTypes["group"] = tempOutNames;
                        
             


@@ -213,6 +220,22 @@ MakeContigsCommand::MakeContigsCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
                                }
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
                                }

+                
+                it = parameters.find("findex");
+                               //user has given a template file
+                               if(it != parameters.end()){
+                                       path = m->hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["findex"] = inputDir + it->second;           }
+                               }
+                
+                it = parameters.find("rindex");
+                               //user has given a template file
+                               if(it != parameters.end()){
+                                       path = m->hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["rindex"] = inputDir + it->second;           }
+                               }

             }
             
             ffastqfile = validParameter.validFile(parameters, "ffastq", true);
             }
             
             ffastqfile = validParameter.validFile(parameters, "ffastq", true);


@@ -261,6 +284,29 @@ MakeContigsCommand::MakeContigsCommand(string option)  {
                        else if(oligosfile == "not open")   {   abort = true;       } 
                        else {   m->setOligosFile(oligosfile);          }
             
                        else if(oligosfile == "not open")   {   abort = true;       } 
                        else {   m->setOligosFile(oligosfile);          }
             

+            findexfile = validParameter.validFile(parameters, "findex", true);
+                       if (findexfile == "not found")      {   findexfile = "";        }
+                       else if(findexfile == "not open")   {   abort = true;       }
+            
+            rindexfile = validParameter.validFile(parameters, "rindex", true);
+                       if (rindexfile == "not found")      {   rindexfile = "";        }
+                       else if(rindexfile == "not open")   {   abort = true;       }
+        
+            if ((rindexfile != "") || (findexfile != "")) {
+                               if (oligosfile == ""){
+                                       oligosfile = m->getOligosFile();
+                                       if (oligosfile != "") {  m->mothurOut("Using " + oligosfile + " as input file for the oligos parameter.\n");  }
+                                       else {
+                        m->mothurOut("You need to provide an oligos file if you are going to use an index file.\n"); abort = true;
+                                       }
+                               }
+                
+                //can only use an index file with the fastq parameters not fasta and qual
+                if ((ffastafile != "") || (rfastafile != "")) {
+                    m->mothurOut("[ERROR]: You can only use an index file with the fastq parameters or the file option.\n"); abort = true;
+                }
+                       }
+            

             //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
                  outputDir = ""; 
             //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
                  outputDir = ""; 


@@ -285,10 +331,13 @@ MakeContigsCommand::MakeContigsCommand(string option)  {
                        m->mothurConvert(temp, gapExtend); 
             if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
                        
                        m->mothurConvert(temp, gapExtend); 
             if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
                        

-            temp = validParameter.validFile(parameters, "threshold", false);   if (temp == "not found"){       temp = "40";                    }
-                       m->mothurConvert(temp, threshold); 
-            if ((threshold < 0) || (threshold > 40)) { m->mothurOut("[ERROR]: threshold must be between 0 and 40.\n"); abort=true; }
+            temp = validParameter.validFile(parameters, "insert", false);      if (temp == "not found"){       temp = "20";                    }
+                       m->mothurConvert(temp, insert); 
+            if ((insert < 0) || (insert > 40)) { m->mothurOut("[ERROR]: insert must be between 0 and 40.\n"); abort=true; }

 
 

+            temp = validParameter.validFile(parameters, "deltaq", false);      if (temp == "not found"){       temp = "6";                     }
+                       m->mothurConvert(temp, deltaq);
+            

                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
                        m->mothurConvert(temp, processors);
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
                        m->mothurConvert(temp, processors);


@@ -314,9 +363,26 @@ MakeContigsCommand::MakeContigsCommand(string option)  {
 
             temp = validParameter.validFile(parameters, "allfiles", false);            if (temp == "not found") { temp = "F"; }
                        allFiles = m->isTrue(temp);
 
             temp = validParameter.validFile(parameters, "allfiles", false);            if (temp == "not found") { temp = "F"; }
                        allFiles = m->isTrue(temp);

+            
+            
+            temp = validParameter.validFile(parameters, "trimoverlap", false);         if (temp == "not found") { temp = "F"; }
+                       trimOverlap = m->isTrue(temp);

                        
                        align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
                        if ((align != "needleman") && (align != "gotoh")) { m->mothurOut(align + " is not a valid alignment method. Options are needleman or gotoh. I will use needleman."); m->mothurOutEndLine(); align = "needleman"; }
                        
                        align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
                        if ((align != "needleman") && (align != "gotoh")) { m->mothurOut(align + " is not a valid alignment method. Options are needleman or gotoh. I will use needleman."); m->mothurOutEndLine(); align = "needleman"; }

+            
+            format = validParameter.validFile(parameters, "format", false);            if (format == "not found"){     format = "illumina1.8+";        }
+            
+            if ((format != "sanger") && (format != "illumina") && (format != "illumina1.8+") && (format != "solexa"))  { 
+                               m->mothurOut(format + " is not a valid format. Your format choices are sanger, solexa, illumina1.8+ and illumina, aborting." ); m->mothurOutEndLine();
+                               abort=true;
+                       }
+            
+            //fill convert table - goes from solexa to sanger. Used fq_all2std.pl as a reference.
+            for (int i = -64; i < 65; i++) { 
+                char temp = (char) ((int)(33 + 10*log(1+pow(10,(i/10.0)))/log(10)+0.499));
+                convertTable.push_back(temp);
+            }

         }
                
        }
         }
                
        }


@@ -350,67 +416,54 @@ int MakeContigsCommand::execute(){
         string compositeGroupFile = getOutputFileName("group",cvars);
         cvars["[tag]"] = "trim";
         string compositeFastaFile = getOutputFileName("fasta",cvars);
         string compositeGroupFile = getOutputFileName("group",cvars);
         cvars["[tag]"] = "trim";
         string compositeFastaFile = getOutputFileName("fasta",cvars);

-        string compositeQualFile = getOutputFileName("qfile",cvars);

         cvars["[tag]"] = "scrap";
         string compositeScrapFastaFile = getOutputFileName("fasta",cvars);
         cvars["[tag]"] = "scrap";
         string compositeScrapFastaFile = getOutputFileName("fasta",cvars);

-        string compositeScrapQualFile = getOutputFileName("qfile",cvars);

         cvars["[tag]"] = "";
         cvars["[tag]"] = "";

-        string compositeMisMatchFile = getOutputFileName("mismatch",cvars);
+        string compositeMisMatchFile = getOutputFileName("report",cvars);

         
         if (filesToProcess.size() > 1) { //clear files for append below
             ofstream outCTFasta, outCTQual, outCSFasta, outCSQual, outCMisMatch;
             m->openOutputFile(compositeFastaFile, outCTFasta); outCTFasta.close();
             m->openOutputFile(compositeScrapFastaFile, outCSFasta); outCSFasta.close();
             m->openOutputFile(compositeMisMatchFile, outCMisMatch); outCMisMatch.close();
         
         if (filesToProcess.size() > 1) { //clear files for append below
             ofstream outCTFasta, outCTQual, outCSFasta, outCSQual, outCMisMatch;
             m->openOutputFile(compositeFastaFile, outCTFasta); outCTFasta.close();
             m->openOutputFile(compositeScrapFastaFile, outCSFasta); outCSFasta.close();
             m->openOutputFile(compositeMisMatchFile, outCMisMatch); outCMisMatch.close();

-            m->openOutputFile(compositeQualFile, outCTQual); outCTQual.close();
-            m->openOutputFile(compositeScrapQualFile, outCSQual); outCSQual.close();

             outputNames.push_back(compositeFastaFile); outputTypes["fasta"].push_back(compositeFastaFile);
             outputNames.push_back(compositeFastaFile); outputTypes["fasta"].push_back(compositeFastaFile);

-            outputNames.push_back(compositeQualFile); outputTypes["qfile"].push_back(compositeQualFile);
-            outputNames.push_back(compositeMisMatchFile); outputTypes["mismatch"].push_back(compositeMisMatchFile);
+            outputNames.push_back(compositeMisMatchFile); outputTypes["report"].push_back(compositeMisMatchFile);

             outputNames.push_back(compositeScrapFastaFile); outputTypes["fasta"].push_back(compositeScrapFastaFile);
             outputNames.push_back(compositeScrapFastaFile); outputTypes["fasta"].push_back(compositeScrapFastaFile);

-            outputNames.push_back(compositeScrapQualFile); outputTypes["qfile"].push_back(compositeScrapQualFile);

         }
         
         }
         

+        map<string, int> totalGroupCounts;
+        

         for (int l = 0; l < filesToProcess.size(); l++) {
             
             m->mothurOut("\n>>>>>\tProcessing " + filesToProcess[l][0][0] + " (file " + toString(l+1) + " of " + toString(filesToProcess.size()) + ")\t<<<<<\n");
             
         for (int l = 0; l < filesToProcess.size(); l++) {
             
             m->mothurOut("\n>>>>>\tProcessing " + filesToProcess[l][0][0] + " (file " + toString(l+1) + " of " + toString(filesToProcess.size()) + ")\t<<<<<\n");
             

+            groupCounts.clear();
+            groupMap.clear();

             vector<vector<string> > fastaFileNames;
             vector<vector<string> > fastaFileNames;

-            vector<vector<string> > qualFileNames;
-            createGroup = false;
+            createOligosGroup = false;

             string outputGroupFileName;
             map<string, string> variables; 
             string thisOutputDir = outputDir;
             if (outputDir == "") {  thisOutputDir = m->hasPath(filesToProcess[l][0][0]); }
             variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(filesToProcess[l][0][0]));
             variables["[tag]"] = "";
             string outputGroupFileName;
             map<string, string> variables; 
             string thisOutputDir = outputDir;
             if (outputDir == "") {  thisOutputDir = m->hasPath(filesToProcess[l][0][0]); }
             variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(filesToProcess[l][0][0]));
             variables["[tag]"] = "";

-            if(oligosfile != ""){
-                createGroup = getOligos(fastaFileNames, qualFileNames, variables["[filename]"]);
-                if (createGroup) { 
-                    outputGroupFileName = getOutputFileName("group",variables);
-                    outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
-                }
+            if(oligosfile != ""){  createOligosGroup = getOligos(fastaFileNames, variables["[filename]"]);  }
+            if (createOligosGroup || createFileGroup) {
+                outputGroupFileName = getOutputFileName("group",variables);

             }
             
             }
             

+            //give group in file file precedence
+            if (createFileGroup) {  createOligosGroup = false; }
+            

             variables["[tag]"] = "trim";
             string outFastaFile = getOutputFileName("fasta",variables);
             variables["[tag]"] = "trim";
             string outFastaFile = getOutputFileName("fasta",variables);

-            string outQualFile = getOutputFileName("qfile",variables);

             variables["[tag]"] = "scrap";
             string outScrapFastaFile = getOutputFileName("fasta",variables);
             variables["[tag]"] = "scrap";
             string outScrapFastaFile = getOutputFileName("fasta",variables);

-            string outScrapQualFile = getOutputFileName("qfile",variables);

             variables["[tag]"] = "";
             variables["[tag]"] = "";

-            string outMisMatchFile = getOutputFileName("mismatch",variables);
-            outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
-            outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile);
-            if (filesToProcess[l][0][1] != "") {
-                outputNames.push_back(outQualFile); outputTypes["qfile"].push_back(outQualFile);
-                outputNames.push_back(outScrapQualFile); outputTypes["qfile"].push_back(outScrapQualFile);
-            }
-            outputNames.push_back(outMisMatchFile); outputTypes["mismatch"].push_back(outMisMatchFile);
-            
+            string outMisMatchFile = getOutputFileName("report",variables);
+                        

             m->mothurOut("Making contigs...\n"); 
             m->mothurOut("Making contigs...\n"); 

-            createProcesses(filesToProcess[l], outFastaFile, outQualFile, outScrapFastaFile, outScrapQualFile, outMisMatchFile, fastaFileNames, qualFileNames);
-            m->mothurOut("Done.\n");
+            createProcesses(filesToProcess[l], outFastaFile, outScrapFastaFile, outMisMatchFile, fastaFileNames, l);

             
             //remove temp fasta and qual files
             for (int i = 0; i < processors; i++) { for(int j = 0; j < filesToProcess[l][i].size(); j++) { m->mothurRemove(filesToProcess[l][i][j]); }  }
             
             //remove temp fasta and qual files
             for (int i = 0; i < processors; i++) { for(int j = 0; j < filesToProcess[l][i].size(); j++) { m->mothurRemove(filesToProcess[l][i][j]); }  }


@@ -428,11 +481,6 @@ int MakeContigsCommand::execute(){
                                 if(m->isBlank(fastaFileNames[i][j])){
                                     m->mothurRemove(fastaFileNames[i][j]);
                                     namesToRemove.insert(fastaFileNames[i][j]);
                                 if(m->isBlank(fastaFileNames[i][j])){
                                     m->mothurRemove(fastaFileNames[i][j]);
                                     namesToRemove.insert(fastaFileNames[i][j]);

-                                    
-                                    if (filesToProcess[l][0][1] != "") {
-                                        m->mothurRemove(qualFileNames[i][j]);
-                                        namesToRemove.insert(qualFileNames[i][j]);
-                                    }

                                 }else{ 
                                     it = uniqueFastaNames.find(fastaFileNames[i][j]);
                                     if (it == uniqueFastaNames.end()) {        
                                 }else{ 
                                     it = uniqueFastaNames.find(fastaFileNames[i][j]);
                                     if (it == uniqueFastaNames.end()) {        


@@ -455,21 +503,21 @@ int MakeContigsCommand::execute(){
                     
                     ofstream out;
                     string thisGroupName = thisOutputDir + m->getRootName(m->getSimpleName(it->first));
                     
                     ofstream out;
                     string thisGroupName = thisOutputDir + m->getRootName(m->getSimpleName(it->first));

-                    thisGroupName += getOutputFileName("group",variables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName); 
+                    thisGroupName += getOutputFileName("group",variables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);

                     m->openOutputFile(thisGroupName, out);
                     
                     while (!in.eof()){
                         if (m->control_pressed) { break; }
                         
                         Sequence currSeq(in); m->gobble(in);
                     m->openOutputFile(thisGroupName, out);
                     
                     while (!in.eof()){
                         if (m->control_pressed) { break; }
                         
                         Sequence currSeq(in); m->gobble(in);

-                        out << currSeq.getName() << '\t' << it->second << endl;  
+                        out << currSeq.getName() << '\t' << it->second << endl;

                     }
                     }

-                    in.close();

                     out.close();
                     out.close();

+                    in.close();

                 }
             }
             
                 }
             }
             

-            if (createGroup) {
+            if (createFileGroup || createOligosGroup) {

                 ofstream outGroup;
                 m->openOutputFile(outputGroupFileName, outGroup);
                 for (map<string, string>::iterator itGroup = groupMap.begin(); itGroup != groupMap.end(); itGroup++) {
                 ofstream outGroup;
                 m->openOutputFile(outputGroupFileName, outGroup);
                 for (map<string, string>::iterator itGroup = groupMap.begin(); itGroup != groupMap.end(); itGroup++) {


@@ -479,21 +527,47 @@ int MakeContigsCommand::execute(){
             }
             
             if (filesToProcess.size() > 1) { //merge into large combo files
             }
             
             if (filesToProcess.size() > 1) { //merge into large combo files

-                if (createGroup) {  
-                    if (l == 0) { 
+                if (createFileGroup || createOligosGroup) {
+                    if (l == 0) {

                         ofstream outCGroup;
                         m->openOutputFile(compositeGroupFile, outCGroup); outCGroup.close();
                         outputNames.push_back(compositeGroupFile); outputTypes["group"].push_back(compositeGroupFile);
                     }
                         ofstream outCGroup;
                         m->openOutputFile(compositeGroupFile, outCGroup); outCGroup.close();
                         outputNames.push_back(compositeGroupFile); outputTypes["group"].push_back(compositeGroupFile);
                     }

-                    m->appendFiles(outputGroupFileName, compositeGroupFile);  
+                    m->appendFiles(outputGroupFileName, compositeGroupFile);
+                    if (!allFiles) { m->mothurRemove(outputGroupFileName);  }
+                    else { outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName); }
+                    
+                    for (map<string, int>::iterator itGroups = groupCounts.begin(); itGroups != groupCounts.end(); itGroups++) {
+                        map<string, int>::iterator itTemp = totalGroupCounts.find(itGroups->first);
+                        if (itTemp == totalGroupCounts.end()) { totalGroupCounts[itGroups->first] = itGroups->second; } //new group create it in totalGroups
+                        else { itTemp->second += itGroups->second; } //existing group, update total
+                    }

                 }
                 }

-                m->appendFiles(outMisMatchFile, compositeMisMatchFile);
+                if (l == 0) {  m->appendFiles(outMisMatchFile, compositeMisMatchFile);  }
+                else {  m->appendFilesWithoutHeaders(outMisMatchFile, compositeMisMatchFile);  }

                 m->appendFiles(outFastaFile, compositeFastaFile);
                 m->appendFiles(outFastaFile, compositeFastaFile);

-                m->appendFiles(outQualFile, compositeQualFile);

                 m->appendFiles(outScrapFastaFile, compositeScrapFastaFile);
                 m->appendFiles(outScrapFastaFile, compositeScrapFastaFile);

-                m->appendFiles(outScrapQualFile, compositeScrapQualFile);
+                if (!allFiles) {
+                    m->mothurRemove(outMisMatchFile);
+                    m->mothurRemove(outFastaFile);
+                    m->mothurRemove(outScrapFastaFile);
+                }else {
+                    outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
+                    outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile);
+                    outputNames.push_back(outMisMatchFile); outputTypes["report"].push_back(outMisMatchFile);
+                }
+            }else {
+                totalGroupCounts = groupCounts;
+                outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
+                outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile);
+                outputNames.push_back(outMisMatchFile); outputTypes["report"].push_back(outMisMatchFile);
+                if (createFileGroup || createOligosGroup) {
+                     outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName); 
+                }

             }
             }

+            m->mothurOut("Done.\n");

         }
         }

+        

         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n");
         
         if (m->control_pressed) {      for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n");
         
         if (m->control_pressed) {      for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }


@@ -501,8 +575,8 @@ int MakeContigsCommand::execute(){
                //output group counts
                m->mothurOutEndLine();
                int total = 0;
                //output group counts
                m->mothurOutEndLine();
                int total = 0;

-               if (groupCounts.size() != 0) {  m->mothurOut("Group count: \n");  }
-               for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
+               if (totalGroupCounts.size() != 0) {  m->mothurOut("Group count: \n");  }
+               for (map<string, int>::iterator it = totalGroupCounts.begin(); it != totalGroupCounts.end(); it++) {

             total += it->second; m->mothurOut(it->first + "\t" + toString(it->second)); m->mothurOutEndLine(); 
                }
                if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
             total += it->second; m->mothurOut(it->first + "\t" + toString(it->second)); m->mothurOutEndLine(); 
                }
                if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }


@@ -515,12 +589,6 @@ int MakeContigsCommand::execute(){
                        if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
                }
         
                        if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
                }
         

-        string currentQual = "";
-               itTypes = outputTypes.find("qfile");
-               if (itTypes != outputTypes.end()) {
-                       if ((itTypes->second).size() != 0) { currentQual = (itTypes->second)[0]; m->setQualFile(currentQual); }
-               }
-        

         string currentGroup = "";
                itTypes = outputTypes.find("group");
                if (itTypes != outputTypes.end()) {
         string currentGroup = "";
                itTypes = outputTypes.find("group");
                if (itTypes != outputTypes.end()) {


@@ -546,7 +614,7 @@ vector< vector< vector<string> > > MakeContigsCommand::preProcessData(unsigned l
         vector< vector< vector<string> > > filesToProcess;
         
         if (ffastqfile != "") { //reading one file
         vector< vector< vector<string> > > filesToProcess;
         
         if (ffastqfile != "") { //reading one file

-            vector< vector<string> > files = readFastqFiles(numReads, ffastqfile, rfastqfile); 
+            vector< vector<string> > files = readFastqFiles(numReads, ffastqfile, rfastqfile, findexfile, rindexfile);

             //adjust for really large processors or really small files
             if (numReads == 0) {  m->mothurOut("[ERROR]: no good reads.\n"); m->control_pressed = true; }
             if (numReads < processors) { 
             //adjust for really large processors or really small files
             if (numReads == 0) {  m->mothurOut("[ERROR]: no good reads.\n"); m->control_pressed = true; }
             if (numReads < processors) { 


@@ -567,12 +635,20 @@ vector< vector< vector<string> > > MakeContigsCommand::preProcessData(unsigned l
                     if (m->control_pressed) { for (int l = 0; l < filesToProcess.size(); l++) { for (int k = 0; k < filesToProcess[l].size(); k++) { for(int j = 0; j < filesToProcess[l][k].size(); j++) { m->mothurRemove(filesToProcess[l][k][j]); } filesToProcess[l][k].clear(); } return filesToProcess; } }
                     
                     unsigned long int thisFilesReads;
                     if (m->control_pressed) { for (int l = 0; l < filesToProcess.size(); l++) { for (int k = 0; k < filesToProcess[l].size(); k++) { for(int j = 0; j < filesToProcess[l][k].size(); j++) { m->mothurRemove(filesToProcess[l][k][j]); } filesToProcess[l][k].clear(); } return filesToProcess; } }
                     
                     unsigned long int thisFilesReads;

-                    vector< vector<string> > files = readFastqFiles(thisFilesReads, filePairsToProcess[i][0], filePairsToProcess[i][1]); 
+                    vector< vector<string> > files = readFastqFiles(thisFilesReads, filePairsToProcess[i][0], filePairsToProcess[i][1], filePairsToProcess[i][2], filePairsToProcess[i][3]);

                     
                     //adjust for really large processors or really small files
                     if (thisFilesReads < processors) { 
                         m->mothurOut("[ERROR]: " + filePairsToProcess[i][0] + " has less than " + toString(processors) + " good reads, skipping\n"); 
                         for (int k = 0; k < files.size(); k++) { for(int j = 0; j < files[k].size(); j++) { m->mothurRemove(files[k][j]); } files[k].clear(); }
                     
                     //adjust for really large processors or really small files
                     if (thisFilesReads < processors) { 
                         m->mothurOut("[ERROR]: " + filePairsToProcess[i][0] + " has less than " + toString(processors) + " good reads, skipping\n"); 
                         for (int k = 0; k < files.size(); k++) { for(int j = 0; j < files[k].size(); j++) { m->mothurRemove(files[k][j]); } files[k].clear(); }

+                        //remove from file2Group if necassary
+                        map<int, string> cFile2Group;
+                        for (map<int, string>::iterator it = file2Group.begin(); it != file2Group.end(); it++) {
+                            if ((it->first) < i) { cFile2Group[it->first] = it->second; }
+                            else if ((it->first) == i) { } //do nothing, we removed files for i
+                            else { cFile2Group[(it->first-1)] = it->second; } //adjust files because i was removed
+                        }
+                        file2Group = cFile2Group;

                     }else {
                         filesToProcess.push_back(files);
                         numReads += thisFilesReads;
                     }else {
                         filesToProcess.push_back(files);
                         numReads += thisFilesReads;


@@ -601,10 +677,14 @@ vector< vector< vector<string> > > MakeContigsCommand::preProcessData(unsigned l
        }
 }
 //**********************************************************************************************************************
        }
 }
 //**********************************************************************************************************************

-int MakeContigsCommand::createProcesses(vector< vector<string> > files, string outputFasta, string outputQual, string outputScrapFasta, string outputScrapQual, string outputMisMatches, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames) {
+int MakeContigsCommand::createProcesses(vector< vector<string> > files, string outputFasta, string outputScrapFasta, string outputMisMatches, vector<vector<string> > fastaFileNames, int index) {

        try {
                int num = 0;
                vector<int> processIDS;
        try {
                int num = 0;
                vector<int> processIDS;

+        string group = "";
+        map<int, string>::iterator it = file2Group.find(index);
+        if (it != file2Group.end()) { group = it->second; }
+        

 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                int process = 0;
                
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                int process = 0;
                


@@ -617,7 +697,6 @@ int MakeContigsCommand::createProcesses(vector< vector<string> > files, string o
                                process++;
                        }else if (pid == 0){
                 vector<vector<string> > tempFASTAFileNames = fastaFileNames;
                                process++;
                        }else if (pid == 0){
                 vector<vector<string> > tempFASTAFileNames = fastaFileNames;

-                               vector<vector<string> > tempPrimerQualFileNames = qualFileNames;

                 
                                if(allFiles){
                                        ofstream temp;
                 
                                if(allFiles){
                                        ofstream temp;


@@ -627,31 +706,23 @@ int MakeContigsCommand::createProcesses(vector< vector<string> > files, string o
                                                        if (tempFASTAFileNames[i][j] != "") {
                                                                tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
                                                                m->openOutputFile(tempFASTAFileNames[i][j], temp);                      temp.close();
                                                        if (tempFASTAFileNames[i][j] != "") {
                                                                tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
                                                                m->openOutputFile(tempFASTAFileNames[i][j], temp);                      temp.close();

-                                
-                                if (files[processors-1][1] != "") {
-                                    tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp";
-                                    m->openOutputFile(tempPrimerQualFileNames[i][j], temp);            temp.close();
-                                }

                                                        }
                                                }
                                        }
                                }
                                                        }
                                                }
                                        }
                                }

-
+                

                                num = driver(files[process], 
                              outputFasta + toString(getpid()) + ".temp", 
                                num = driver(files[process], 
                              outputFasta + toString(getpid()) + ".temp", 

-                             outputQual + toString(getpid()) + ".temp", 

                              outputScrapFasta + toString(getpid()) + ".temp", 
                              outputScrapFasta + toString(getpid()) + ".temp", 

-                             outputScrapQual + toString(getpid()) + ".temp",

                              outputMisMatches + toString(getpid()) + ".temp",
                              outputMisMatches + toString(getpid()) + ".temp",

-                             tempFASTAFileNames,
-                             tempPrimerQualFileNames);
+                             tempFASTAFileNames, process, group);

                                
                                //pass groupCounts to parent
                 ofstream out;
                 string tempFile = toString(getpid()) + ".num.temp";
                 m->openOutputFile(tempFile, out);
                 out << num << endl;
                                
                                //pass groupCounts to parent
                 ofstream out;
                 string tempFile = toString(getpid()) + ".num.temp";
                 m->openOutputFile(tempFile, out);
                 out << num << endl;

-                               if(createGroup){
+                               if (createFileGroup || createOligosGroup) {

                                        out << groupCounts.size() << endl;
                                        
                                        for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
                                        out << groupCounts.size() << endl;
                                        
                                        for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {


@@ -676,13 +747,9 @@ int MakeContigsCommand::createProcesses(vector< vector<string> > files, string o
         ofstream temp;
                m->openOutputFile(outputFasta, temp);           temp.close();
         m->openOutputFile(outputScrapFasta, temp);             temp.close();
         ofstream temp;
                m->openOutputFile(outputFasta, temp);           temp.close();
         m->openOutputFile(outputScrapFasta, temp);             temp.close();

-        if (files[processors-1][1] != "") {
-            m->openOutputFile(outputScrapQual, temp);          temp.close();
-            m->openOutputFile(outputQual, temp);       temp.close();
-        }
-        
+                

                //do my part
                //do my part

-               num = driver(files[processors-1], outputFasta, outputQual, outputScrapFasta, outputScrapQual, outputMisMatches, fastaFileNames, qualFileNames);
+               num = driver(files[processors-1], outputFasta, outputScrapFasta,  outputMisMatches, fastaFileNames, processors-1, group);

                
                //force parent to wait until all the processes are done
                for (int i=0;i<processIDS.size();i++) { 
                
                //force parent to wait until all the processes are done
                for (int i=0;i<processIDS.size();i++) { 


@@ -697,7 +764,7 @@ int MakeContigsCommand::createProcesses(vector< vector<string> > files, string o
             int tempNum;
             in >> tempNum; num += tempNum; m->gobble(in);
             
             int tempNum;
             in >> tempNum; num += tempNum; m->gobble(in);
             

-                       if(createGroup){
+                       if (createFileGroup || createOligosGroup) {

                                string group;
                                in >> tempNum; m->gobble(in);
                                
                                string group;
                                in >> tempNum; m->gobble(in);
                                


@@ -741,8 +808,7 @@ int MakeContigsCommand::createProcesses(vector< vector<string> > files, string o
                        string extension = "";
                        if (h != 0) { extension = toString(h) + ".temp"; processIDS.push_back(h); }
             vector<vector<string> > tempFASTAFileNames = fastaFileNames;
                        string extension = "";
                        if (h != 0) { extension = toString(h) + ".temp"; processIDS.push_back(h); }
             vector<vector<string> > tempFASTAFileNames = fastaFileNames;

-            vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
-            
+                        

             if(allFiles){
                 ofstream temp;
                 
             if(allFiles){
                 ofstream temp;
                 


@@ -751,25 +817,18 @@ int MakeContigsCommand::createProcesses(vector< vector<string> > files, string o
                         if (tempFASTAFileNames[i][j] != "") {
                             tempFASTAFileNames[i][j] += extension;
                             m->openOutputFile(tempFASTAFileNames[i][j], temp);                 temp.close();
                         if (tempFASTAFileNames[i][j] != "") {
                             tempFASTAFileNames[i][j] += extension;
                             m->openOutputFile(tempFASTAFileNames[i][j], temp);                 temp.close();

-                            
-                            if (files[processors-1][1] != "") {
-                                tempPrimerQualFileNames[i][j] += extension;
-                                m->openOutputFile(tempPrimerQualFileNames[i][j], temp);                temp.close();
-                            }

                         }
                     }
                 }
             }
                         }
                     }
                 }
             }

-
-                                 
-                       contigsData* tempcontig = new contigsData(files[h], (outputFasta + extension), (outputQual + extension), (outputScrapFasta + extension), (outputScrapQual + extension),(outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, threshold, barcodes, primers, tempFASTAFileNames, tempPrimerQualFileNames, barcodeNameVector, primerNameVector, pdiffs, bdiffs, tdiffs, createGroup, allFiles, h);
+                                
+                       contigsData* tempcontig = new contigsData(group, files[h], (outputFasta + extension), (outputScrapFasta + extension), (outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, insert, deltaq, barcodes, primers, tempFASTAFileNames, barcodeNameVector, primerNameVector, pdiffs, bdiffs, tdiffs, createOligosGroup, createFileGroup, allFiles, trimOverlap, h);

                        pDataArray.push_back(tempcontig);
             
                        hThreadArray[h] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]);   
                }
         
         vector<vector<string> > tempFASTAFileNames = fastaFileNames;
                        pDataArray.push_back(tempcontig);
             
                        hThreadArray[h] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]);   
                }
         
         vector<vector<string> > tempFASTAFileNames = fastaFileNames;

-        vector<vector<string> > tempPrimerQualFileNames = qualFileNames;

 
         if(allFiles){
             ofstream temp;
 
         if(allFiles){
             ofstream temp;


@@ -780,11 +839,6 @@ int MakeContigsCommand::createProcesses(vector< vector<string> > files, string o
                     if (tempFASTAFileNames[i][j] != "") {
                         tempFASTAFileNames[i][j] += extension;
                         m->openOutputFile(tempFASTAFileNames[i][j], temp);                     temp.close();
                     if (tempFASTAFileNames[i][j] != "") {
                         tempFASTAFileNames[i][j] += extension;
                         m->openOutputFile(tempFASTAFileNames[i][j], temp);                     temp.close();

-                        
-                        if (files[processors-1][1] != "") {
-                            tempPrimerQualFileNames[i][j] += extension;
-                            m->openOutputFile(tempPrimerQualFileNames[i][j], temp);            temp.close();
-                        }

                     }
                 }
             }
                     }
                 }
             }


@@ -794,14 +848,10 @@ int MakeContigsCommand::createProcesses(vector< vector<string> > files, string o
                ofstream temp;
                m->openOutputFile(outputFasta, temp);           temp.close();
         m->openOutputFile(outputScrapFasta, temp);             temp.close();
                ofstream temp;
                m->openOutputFile(outputFasta, temp);           temp.close();
         m->openOutputFile(outputScrapFasta, temp);             temp.close();

-        if (files[processors-1][1] != "") {
-            m->openOutputFile(outputScrapQual, temp);          temp.close();
-            m->openOutputFile(outputQual, temp);       temp.close();
-               }

         
         //do my part
         processIDS.push_back(processors-1);
         
         //do my part
         processIDS.push_back(processors-1);

-               num = driver(files[processors-1], (outputFasta+ toString(processors-1) + ".temp"), (outputQual+ toString(processors-1) + ".temp"), (outputScrapFasta+ toString(processors-1) + ".temp"), (outputScrapQual+ toString(processors-1) + ".temp"), (outputMisMatches+ toString(processors-1) + ".temp"), tempFASTAFileNames, tempPrimerQualFileNames);       
+               num = driver(files[processors-1], (outputFasta+ toString(processors-1) + ".temp"),  (outputScrapFasta+ toString(processors-1) + ".temp"),  (outputMisMatches+ toString(processors-1) + ".temp"), tempFASTAFileNames, processors-1, group);

         
                //Wait until all threads have terminated.
                WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
         
                //Wait until all threads have terminated.
                WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);


@@ -809,6 +859,9 @@ int MakeContigsCommand::createProcesses(vector< vector<string> > files, string o
                //Close all thread handles and free memory allocations.
                for(int i=0; i < pDataArray.size(); i++){
                        num += pDataArray[i]->count;
                //Close all thread handles and free memory allocations.
                for(int i=0; i < pDataArray.size(); i++){
                        num += pDataArray[i]->count;

+            if (!pDataArray[i]->done) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }

             for (map<string, int>::iterator it = pDataArray[i]->groupCounts.begin(); it != pDataArray[i]->groupCounts.end(); it++) {
                 map<string, int>::iterator it2 = groupCounts.find(it->first);
                 if (it2 == groupCounts.end()) {        groupCounts[it->first] = it->second; }
             for (map<string, int>::iterator it = pDataArray[i]->groupCounts.begin(); it != pDataArray[i]->groupCounts.end(); it++) {
                 map<string, int>::iterator it2 = groupCounts.find(it->first);
                 if (it2 == groupCounts.end()) {        groupCounts[it->first] = it->second; }


@@ -831,16 +884,8 @@ int MakeContigsCommand::createProcesses(vector< vector<string> > files, string o
                        
                        m->appendFiles((outputScrapFasta + toString(processIDS[i]) + ".temp"), outputScrapFasta);
                        m->mothurRemove((outputScrapFasta + toString(processIDS[i]) + ".temp"));
                        
                        m->appendFiles((outputScrapFasta + toString(processIDS[i]) + ".temp"), outputScrapFasta);
                        m->mothurRemove((outputScrapFasta + toString(processIDS[i]) + ".temp"));

-                       
-            if (files[processors-1][1] != "") {
-                m->appendFiles((outputScrapQual + toString(processIDS[i]) + ".temp"), outputScrapQual);
-                m->mothurRemove((outputScrapQual + toString(processIDS[i]) + ".temp"));
-                
-                m->appendFiles((outputQual + toString(processIDS[i]) + ".temp"), outputQual);
-                m->mothurRemove((outputQual + toString(processIDS[i]) + ".temp"));
-            }

             
             

-            m->appendFiles((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches);
+            m->appendFilesWithoutHeaders((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches);

                        m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp"));
             
             if(allFiles){
                        m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp"));
             
             if(allFiles){


@@ -849,11 +894,6 @@ int MakeContigsCommand::createProcesses(vector< vector<string> > files, string o
                                                if (fastaFileNames[j][k] != "") {
                                                        m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
                                                        m->mothurRemove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"));
                                                if (fastaFileNames[j][k] != "") {
                                                        m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
                                                        m->mothurRemove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"));

-                                                       
-                            if (files[processors-1][1] != "") {
-                                m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]);
-                                m->mothurRemove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"));
-                            }

                                                }
                                        }
                                }
                                                }
                                        }
                                }


@@ -868,7 +908,7 @@ int MakeContigsCommand::createProcesses(vector< vector<string> > files, string o
        }
 }
 //**********************************************************************************************************************
        }
 }
 //**********************************************************************************************************************

-int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputQual, string outputScrapFasta, string outputScrapQual, string outputMisMatches, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames){
+int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputScrapFasta, string outputMisMatches, vector<vector<string> > fastaFileNames, int process, string group){

     try {
         
         Alignment* alignment;
     try {
         
         Alignment* alignment;


@@ -880,23 +920,27 @@ int MakeContigsCommand::driver(vector<string> files, string outputFasta, string
         string thisfqualfile = files[1];
         string thisrfastafile = files[2];
         string thisrqualfile = files[3];
         string thisfqualfile = files[1];
         string thisrfastafile = files[2];
         string thisrqualfile = files[3];

+        string thisfindexfile = files[4];
+        string thisrindexfile = files[5];

         
         

-        if (m->debug) {  m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
+        if (m->debug) {  m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n[DEBUG]: findex = " + thisfindexfile + ".\n[DEBUG]: rindex = " + thisrindexfile + ".\n"); }

         
         

-        ifstream inFFasta, inRFasta, inFQual, inRQual;
-        ofstream outFasta, outQual, outMisMatch, outScrapFasta, outScrapQual;
+        ifstream inFFasta, inRFasta, inFQual, inRQual, inFIndex, inRIndex;
+        ofstream outFasta, outMisMatch, outScrapFasta;

         m->openInputFile(thisffastafile, inFFasta);
         m->openInputFile(thisrfastafile, inRFasta);
         if (thisfqualfile != "") {
             m->openInputFile(thisfqualfile, inFQual);
             m->openInputFile(thisrqualfile, inRQual);
         m->openInputFile(thisffastafile, inFFasta);
         m->openInputFile(thisrfastafile, inRFasta);
         if (thisfqualfile != "") {
             m->openInputFile(thisfqualfile, inFQual);
             m->openInputFile(thisrqualfile, inRQual);

-            m->openOutputFile(outputScrapQual, outScrapQual);
-            m->openOutputFile(outputQual, outQual);

         }
         }

+        
+        if (thisfindexfile != "") { m->openInputFile(thisfindexfile, inFIndex);  }
+        if (thisrindexfile != "") { m->openInputFile(thisrindexfile, inRIndex);  }
+        

         m->openOutputFile(outputFasta, outFasta);
         m->openOutputFile(outputScrapFasta, outScrapFasta);
         m->openOutputFile(outputMisMatches, outMisMatch);
         m->openOutputFile(outputFasta, outFasta);
         m->openOutputFile(outputScrapFasta, outScrapFasta);
         m->openOutputFile(outputMisMatches, outMisMatch);

-        outMisMatch << "Name\tLength\tMisMatches\n";
+        outMisMatch << "Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns\n";  

         
         TrimOligos trimOligos(pdiffs, bdiffs, 0, 0, primers, barcodes);
         
         
         TrimOligos trimOligos(pdiffs, bdiffs, 0, 0, primers, barcodes);
         


@@ -916,13 +960,27 @@ int MakeContigsCommand::driver(vector<string> files, string outputFasta, string
                 fQual = new QualityScores(inFQual); m->gobble(inFQual);
                 rQual = new QualityScores(inRQual); m->gobble(inRQual);
             }
                 fQual = new QualityScores(inFQual); m->gobble(inFQual);
                 rQual = new QualityScores(inRQual); m->gobble(inRQual);
             }

+            Sequence findexBarcode("findex", "NONE");  Sequence rindexBarcode("rindex", "NONE");
+            if (thisfindexfile != "") {
+                Sequence temp(inFIndex); m->gobble(inFIndex);
+                findexBarcode.setAligned(temp.getAligned());
+            }
+            
+            if (thisrindexfile != "") {
+                Sequence temp(inRIndex); m->gobble(inRIndex);
+                rindexBarcode.setAligned(temp.getAligned());
+            }

             
             int barcodeIndex = 0;
             int primerIndex = 0;
             
             int barcodeIndex = 0;
             int primerIndex = 0;

-            
+                        

             if(barcodes.size() != 0){
                 if (thisfqualfile != "") {
             if(barcodes.size() != 0){
                 if (thisfqualfile != "") {

-                    success = trimOligos.stripBarcode(fSeq, rSeq, *fQual, *rQual, barcodeIndex);
+                    if ((thisfindexfile != "") || (thisrindexfile != "")) {
+                        success = trimOligos.stripBarcode(findexBarcode, rindexBarcode, *fQual, *rQual, barcodeIndex);
+                    }else {
+                        success = trimOligos.stripBarcode(fSeq, rSeq, *fQual, *rQual, barcodeIndex);
+                    }

                 }else {
                     success = trimOligos.stripBarcode(fSeq, rSeq, barcodeIndex);
                 }
                 }else {
                     success = trimOligos.stripBarcode(fSeq, rSeq, barcodeIndex);
                 }


@@ -956,7 +1014,6 @@ int MakeContigsCommand::driver(vector<string> files, string outputFasta, string
             
             //traverse alignments merging into one contiguous seq
             string contig = "";
             
             //traverse alignments merging into one contiguous seq
             string contig = "";

-            vector<int> contigScores; 

             int numMismatches = 0;
             string seq1 = fSeq.getAligned();
             string seq2 = rSeq.getAligned();
             int numMismatches = 0;
             string seq1 = fSeq.getAligned();
             string seq2 = rSeq.getAligned();


@@ -970,18 +1027,13 @@ int MakeContigsCommand::driver(vector<string> files, string outputFasta, string
             // if (num < 5) {  cout << fSeq.getStartPos() << '\t' << fSeq.getEndPos() << '\t' << rSeq.getStartPos() << '\t' << rSeq.getEndPos() << endl; }
             int overlapStart = fSeq.getStartPos();
             int seq2Start = rSeq.getStartPos();
             // if (num < 5) {  cout << fSeq.getStartPos() << '\t' << fSeq.getEndPos() << '\t' << rSeq.getStartPos() << '\t' << rSeq.getEndPos() << endl; }
             int overlapStart = fSeq.getStartPos();
             int seq2Start = rSeq.getStartPos();

+            

             //bigger of the 2 starting positions is the location of the overlapping start
             if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1
                 overlapStart = seq2Start; 
             //bigger of the 2 starting positions is the location of the overlapping start
             if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1
                 overlapStart = seq2Start; 

-                for (int i = 0; i < overlapStart; i++) {
-                    contig += seq1[i];
-                    if (thisfqualfile != "") { contigScores.push_back(scores1[ABaseMap[i]]); }
-                }
+                for (int i = 0; i < overlapStart; i++) { contig += seq1[i];  }

             }else { //seq1 starts later so take from 0 to overlapStart from seq2
             }else { //seq1 starts later so take from 0 to overlapStart from seq2

-                for (int i = 0; i < overlapStart; i++) {
-                    contig += seq2[i];
-                    if (thisfqualfile != "") { contigScores.push_back(scores2[BBaseMap[i]]); }
-                }
+                for (int i = 0; i < overlapStart; i++) {  contig += seq2[i]; }

             }
             
             int seq1End = fSeq.getEndPos();
             }
             
             int seq1End = fSeq.getEndPos();


@@ -989,61 +1041,53 @@ int MakeContigsCommand::driver(vector<string> files, string outputFasta, string
             int overlapEnd = seq1End;
             if (seq2End < overlapEnd) { overlapEnd = seq2End; }  //smallest end position is where overlapping ends
             
             int overlapEnd = seq1End;
             if (seq2End < overlapEnd) { overlapEnd = seq2End; }  //smallest end position is where overlapping ends
             

+            int oStart = contig.length();
+            //cout << fSeq.getAligned()  << endl; cout << rSeq.getAligned() << endl;

             for (int i = overlapStart; i < overlapEnd; i++) {
             for (int i = overlapStart; i < overlapEnd; i++) {

+                //cout << seq1[i] << ' ' << seq2[i] << ' ' << scores1[ABaseMap[i]] << ' ' << scores2[BBaseMap[i]] << endl;

                 if (seq1[i] == seq2[i]) { //match, add base and choose highest score
                     contig += seq1[i];
                 if (seq1[i] == seq2[i]) { //match, add base and choose highest score
                     contig += seq1[i];

-                    if (thisfqualfile != "") { 
-                        contigScores.push_back(scores1[ABaseMap[i]]); 
-                        if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; }
-                    }
-                }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below threshold. In that case eliminate base
+                }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below insert. In that case eliminate base

                     if (thisfqualfile != "") {
                     if (thisfqualfile != "") {

-                        if (scores2[BBaseMap[i]] < threshold) { } //
-                        else {
-                            contig += seq2[i];
-                            contigScores.push_back(scores2[BBaseMap[i]]);
-                        }
+                        if (scores2[BBaseMap[i]] <= insert) { } //
+                        else { contig += seq2[i];  }

                     }else { contig += seq2[i]; } //with no quality info, then we keep it?
                     }else { contig += seq2[i]; } //with no quality info, then we keep it?

-                }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1, unless quality score for base is below threshold. In that case eliminate base
+                }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1, unless quality score for base is below insert. In that case eliminate base

                     if (thisfqualfile != "") {
                     if (thisfqualfile != "") {

-                        if (scores1[ABaseMap[i]] < threshold) { } //
-                        else {
-                            contig += seq1[i];
-                            contigScores.push_back(scores1[ABaseMap[i]]);
-                        }
+                        if (scores1[ABaseMap[i]] <= insert) { } //
+                        else { contig += seq1[i];  }

                     }else { contig += seq1[i]; } //with no quality info, then we keep it?
                 }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
                     if (thisfqualfile != "") {
                     }else { contig += seq1[i]; } //with no quality info, then we keep it?
                 }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
                     if (thisfqualfile != "") {

-                        char c = seq1[i];
-                        contigScores.push_back(scores1[ABaseMap[i]]);
-                        if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; c = seq2[i]; }
-                        contig += c;
+                        if (abs(scores1[ABaseMap[i]] - scores2[BBaseMap[i]]) >= deltaq) { //is the difference in qual scores >= deltaq, if yes choose base with higher score
+                            char c = seq1[i];
+                            if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { c = seq2[i]; }
+                            contig += c;
+                        }else { //if no, base becomes n
+                            contig += 'N';
+                        }

                         numMismatches++;
                     }else { numMismatches++; } //cant decide, so eliminate and mark as mismatch
                 }else { //should never get here
                     m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
                 }
             }
                         numMismatches++;
                     }else { numMismatches++; } //cant decide, so eliminate and mark as mismatch
                 }else { //should never get here
                     m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
                 }
             }

-            
+            int oend = contig.length();

             if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2
             if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2

-                for (int i = overlapEnd; i < length; i++) {
-                    contig += seq2[i];
-                    if (thisfqualfile != "") { contigScores.push_back(scores2[BBaseMap[i]]); }
-                }
+                for (int i = overlapEnd; i < length; i++) { contig += seq2[i];  }

             }else { //seq2 ends before seq1 so take from overlap to length from seq1
             }else { //seq2 ends before seq1 so take from overlap to length from seq1

-                for (int i = overlapEnd; i < length; i++) {
-                    contig += seq1[i];
-                    if (thisfqualfile != "") { contigScores.push_back(scores1[ABaseMap[i]]); }
-                }
-                
+                for (int i = overlapEnd; i < length; i++) {  contig += seq1[i]; }

             }
             }

+            //cout << contig << endl;
+            //exit(1);
+            if (trimOverlap) { contig = contig.substr(overlapStart-1, oend-oStart);  if (contig.length() == 0) { trashCode += "l"; } }

             
             if(trashCode.length() == 0){
                 bool ignore = false;
                 
                 if (m->debug) { m->mothurOut(fSeq.getName()); }
                 
             
             if(trashCode.length() == 0){
                 bool ignore = false;
                 
                 if (m->debug) { m->mothurOut(fSeq.getName()); }
                 

-                if (createGroup) {
+                if (createOligosGroup) {

                     if(barcodes.size() != 0){
                         string thisGroup = barcodeNameVector[barcodeIndex];
                         if (primers.size() != 0) { 
                     if(barcodes.size() != 0){
                         string thisGroup = barcodeNameVector[barcodeIndex];
                         if (primers.size() != 0) { 


@@ -1068,6 +1112,15 @@ int MakeContigsCommand::driver(vector<string> files, string outputFasta, string
                         }else { ignore = true; }
                         
                     }
                         }else { ignore = true; }
                         
                     }

+                }else if (createFileGroup) {
+                    int pos = group.find("ignore");
+                    if (pos == string::npos) {
+                        groupMap[fSeq.getName()] = group;
+                        
+                        map<string, int>::iterator it = groupCounts.find(group);
+                        if (it == groupCounts.end()) { groupCounts[group] = 1; }
+                        else { groupCounts[it->first] ++; }
+                    }else { ignore = true; }

                 }
                 if (m->debug) { m->mothurOut("\n"); }
                 
                 }
                 if (m->debug) { m->mothurOut("\n"); }
                 


@@ -1076,32 +1129,16 @@ int MakeContigsCommand::driver(vector<string> files, string outputFasta, string
                     m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
                     output << ">" << fSeq.getName() << endl << contig << endl;
                     output.close();
                     m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
                     output << ">" << fSeq.getName() << endl << contig << endl;
                     output.close();

-                    
-                    if (thisfqualfile != "") {
-                        m->openOutputFileAppend(qualFileNames[barcodeIndex][primerIndex], output);
-                        output << ">" << fSeq.getName() << endl;
-                        for (int i = 0; i < contigScores.size(); i++) { output << contigScores[i] << ' '; }
-                        output << endl;
-                        output.close();        
-                    }

                 }
                 
                 //output
                 outFasta << ">" << fSeq.getName() << endl << contig << endl;
                 }
                 
                 //output
                 outFasta << ">" << fSeq.getName() << endl << contig << endl;

-                if (thisfqualfile != "") {
-                    outQual << ">" << fSeq.getName() << endl;
-                    for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
-                    outQual << endl;
-                }
-                outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
+                int numNs = 0;
+                for (int i = 0; i < contig.length(); i++) { if (contig[i] == 'N') { numNs++; }  }
+                outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << (oend-oStart) << '\t' << oStart << '\t' << oend << '\t' << numMismatches << '\t' << numNs << endl;

             }else {
                 //output
                 outScrapFasta << ">" << fSeq.getName() << " | " << trashCode << endl << contig << endl;
             }else {
                 //output
                 outScrapFasta << ">" << fSeq.getName() << " | " << trashCode << endl << contig << endl;

-                if (thisfqualfile != "") {
-                    outScrapQual << ">" << fSeq.getName() << " | " << trashCode << endl;
-                    for (int i = 0; i < contigScores.size(); i++) { outScrapQual << contigScores[i] << ' '; }
-                    outScrapQual << endl;
-                }

             }
             num++;
             
             }
             num++;
             


@@ -1120,12 +1157,10 @@ int MakeContigsCommand::driver(vector<string> files, string outputFasta, string
         if (thisfqualfile != "") {
             inFQual.close();
             inRQual.close();
         if (thisfqualfile != "") {
             inFQual.close();
             inRQual.close();

-            outQual.close();
-            outScrapQual.close();

         }
         delete alignment;
         
         }
         delete alignment;
         

-        if (m->control_pressed) {  m->mothurRemove(outputFasta); m->mothurRemove(outputScrapFasta);m->mothurRemove(outputMisMatches); if (thisfqualfile != "") { m->mothurRemove(outputQual); m->mothurRemove(outputScrapQual); } }
+        if (m->control_pressed) {  m->mothurRemove(outputFasta); m->mothurRemove(outputScrapFasta);m->mothurRemove(outputMisMatches);  }

     
         return num;
     }
     
         return num;
     }


@@ -1135,11 +1170,11 @@ int MakeContigsCommand::driver(vector<string> files, string outputFasta, string
        }
 }
 //**********************************************************************************************************************
        }
 }
 //**********************************************************************************************************************

-vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& count, string ffastq, string rfastq){
+vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& count, string ffastq, string rfastq, string findex, string rindex){

     try {
         vector< vector<string> > files;
         //maps processors number to file pointer
     try {
         vector< vector<string> > files;
         //maps processors number to file pointer

-        map<int, vector<ofstream*> > tempfiles;  //tempfiles[0] = forwardFasta, [1] = forwardQual, [2] = reverseFasta, [3] = reverseQual
+        map<int, vector<ofstream*> > tempfiles;  //tempfiles[0] = forwardFasta, [1] = forwardQual, [2] = reverseFasta, [3] = reverseQual, tempfiles[4] = forwardIndex, [4] = forwardReverse

         map<int, vector<ofstream*> >::iterator it;
         
         //create files to write to
         map<int, vector<ofstream*> >::iterator it;
         
         //create files to write to


@@ -1149,6 +1184,8 @@ vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& c
             ofstream* outFQ = new ofstream;     temp.push_back(outFQ);
             ofstream* outRF = new ofstream;     temp.push_back(outRF);
             ofstream* outRQ = new ofstream;     temp.push_back(outRQ);
             ofstream* outFQ = new ofstream;     temp.push_back(outFQ);
             ofstream* outRF = new ofstream;     temp.push_back(outRF);
             ofstream* outRQ = new ofstream;     temp.push_back(outRQ);

+            ofstream* outFI = new ofstream;     temp.push_back(outFI);  
+            ofstream* outRI = new ofstream;     temp.push_back(outRI);  

             tempfiles[i] = temp;
             
             vector<string> names;
             tempfiles[i] = temp;
             
             vector<string> names;


@@ -1158,8 +1195,13 @@ vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& c
             string rfastafilename = thisOutputDir + m->getRootName(m->getSimpleName(rfastq)) + toString(i) + "rfastatemp";
             string fqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(ffastq)) + toString(i) + "fqualtemp";
             string rqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(rfastq)) + toString(i) + "rqualtemp";
             string rfastafilename = thisOutputDir + m->getRootName(m->getSimpleName(rfastq)) + toString(i) + "rfastatemp";
             string fqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(ffastq)) + toString(i) + "fqualtemp";
             string rqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(rfastq)) + toString(i) + "rqualtemp";

+            string findexfilename = ""; string rindexfilename = "";
+            noneOk = false; //flag to oligos file read that its okay to allow for non paired barcodes
+            if (findex != "") {  findexfilename = thisOutputDir + m->getRootName(m->getSimpleName(findex)) + toString(i) + "findextemp"; m->openOutputFile(findexfilename, *outFI);  noneOk = true; }
+            if (rindex != "") {  rindexfilename = thisOutputDir + m->getRootName(m->getSimpleName(rindex)) + toString(i) + "rindextemp";  m->openOutputFile(rindexfilename, *outRI); noneOk = true; }

             names.push_back(ffastafilename); names.push_back(fqualfilename);
             names.push_back(rfastafilename); names.push_back(rqualfilename);
             names.push_back(ffastafilename); names.push_back(fqualfilename);
             names.push_back(rfastafilename); names.push_back(rqualfilename);

+            names.push_back(findexfilename); names.push_back(rindexfilename);

             files.push_back(names);
             
             m->openOutputFile(ffastafilename, *outFF);
             files.push_back(names);
             
             m->openOutputFile(ffastafilename, *outFF);


@@ -1173,7 +1215,7 @@ vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& c
             for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close();  delete (it->second)[i]; } }
             //remove files
             for (int i = 0; i < files.size(); i++) {  
             for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close();  delete (it->second)[i]; } }
             //remove files
             for (int i = 0; i < files.size(); i++) {  

-                for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }
+                for(int j = 0; j < files[i].size(); j++) { if (files[i][j] != "") {  m->mothurRemove(files[i][j]); }  }

             }
         }
         
             }
         }
         


@@ -1183,31 +1225,52 @@ vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& c
         ifstream inReverse;
         m->openInputFile(rfastq, inReverse);
         
         ifstream inReverse;
         m->openInputFile(rfastq, inReverse);
         

+        ifstream infIndex, inrIndex;
+        bool findexIsGood = false;
+        bool rindexIsGood = false;
+        if (findex != "") { m->openInputFile(findex, infIndex); findexIsGood = true; }
+        if (rindex != "") { m->openInputFile(rindex, inrIndex); rindexIsGood = true; }
+        

         count = 0;
         map<string, fastqRead> uniques;
         count = 0;
         map<string, fastqRead> uniques;

+        map<string, fastqRead> iUniques;
+        map<string, pairFastqRead> pairUniques;

         map<string, fastqRead>::iterator itUniques;
         map<string, fastqRead>::iterator itUniques;

-        while ((!inForward.eof()) || (!inReverse.eof())) {
+        while ((!inForward.eof()) || (!inReverse.eof()) || (findexIsGood) || (rindexIsGood)) {

             
             

-            if (m->control_pressed) { for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close();  delete (it->second)[i]; } } for (int i = 0; i < files.size(); i++) {  for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } } inForward.close(); inReverse.close(); return files; }
+            if (m->control_pressed) { for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close();  delete (it->second)[i]; } } for (int i = 0; i < files.size(); i++) {  for(int j = 0; j < files[i].size(); j++) { if (files[i][j] != "") { m->mothurRemove(files[i][j]); } } } inForward.close(); inReverse.close(); if (findex != "") { infIndex.close(); } if (findex != "") { inrIndex.close(); } return files; }

             
             //get a read from forward and reverse fastq files
             
             //get a read from forward and reverse fastq files

-            bool ignoref, ignorer;
-            fastqRead thisFread, thisRread;
+            bool ignoref, ignorer, ignorefi, ignoreri;
+            fastqRead thisFread, thisRread, thisFIread, thisRIread;

             if (!inForward.eof()) {  thisFread = readFastq(inForward, ignoref); }
             else { ignoref = true; }
             if (!inReverse.eof()) { thisRread = readFastq(inReverse, ignorer);  }
             else { ignorer = true; }
             if (!inForward.eof()) {  thisFread = readFastq(inForward, ignoref); }
             else { ignoref = true; }
             if (!inReverse.eof()) { thisRread = readFastq(inReverse, ignorer);  }
             else { ignorer = true; }

+            if (findexIsGood) { thisFIread = readFastq(infIndex, ignorefi); if (infIndex.eof()) { findexIsGood = false; } }
+            else { ignorefi = true; }
+            if (rindexIsGood) { thisRIread = readFastq(inrIndex, ignoreri);  if (inrIndex.eof()) { rindexIsGood = false; } }
+            else { ignoreri = true; }
+            
+            bool allowOne = false;
+            if ((findex == "") || (rindex == "")) { allowOne = true; }
+            vector<pairFastqRead> frReads = getReads(ignoref, ignorer, thisFread, thisRread, uniques, false);
+            vector<pairFastqRead> friReads = getReads(ignorefi, ignoreri, thisFIread, thisRIread, iUniques, allowOne);
+            
+            //add in index info if provided
+            vector<pairFastqRead> reads = frReads;
+            if ((findex != "") || (rindex != "")) {  reads = mergeReads(frReads, friReads, pairUniques); }

             
             

-            vector<pairFastqRead> reads = getReads(ignoref, ignorer, thisFread, thisRread, uniques);
-           

             for (int i = 0; i < reads.size(); i++) {
                 fastqRead fread = reads[i].forward;
                 fastqRead rread = reads[i].reverse;
             for (int i = 0; i < reads.size(); i++) {
                 fastqRead fread = reads[i].forward;
                 fastqRead rread = reads[i].reverse;

+                fastqRead firead = reads[i].findex;
+                fastqRead riread = reads[i].rindex;

                 
                 

-                if (m->debug) { m->mothurOut(toString(count) + '\t' + fread.name + '\t' + rread.name + '\n'); }
+                if (m->debug) { m->mothurOut(toString(count) + '\t' + fread.name + '\t' + rread.name + '\n'); if (findex != "") { m->mothurOut(toString(count) + '\t' + firead.name + '\n'); } if (rindex != "") { m->mothurOut(toString(count) + '\t' + riread.name + '\n'); } }

                
                

-                if (checkReads(fread, rread, ffastq, rfastq)) {
-                    if (m->control_pressed) { for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close();  delete (it->second)[i]; } } for (int i = 0; i < files.size(); i++) {  for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } } inForward.close(); inReverse.close(); return files; }
+                //if (checkReads(fread, rread, ffastq, rfastq)) {
+                    if (m->control_pressed) { for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close();  delete (it->second)[i]; } } for (int i = 0; i < files.size(); i++) {  for(int j = 0; j < files[i].size(); j++) { if (files[i][j] != "") { m->mothurRemove(files[i][j]); } } } inForward.close(); inReverse.close(); if (findex != "") { infIndex.close(); } if (findex != "") { inrIndex.close(); } return files; }

                     
                     //if the reads are okay write to output files
                     int process = count % processors;
                     
                     //if the reads are okay write to output files
                     int process = count % processors;


@@ -1220,12 +1283,14 @@ vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& c
                     *(tempfiles[process][3]) << ">" << rread.name << endl;
                     for (int i = 0; i < rread.scores.size(); i++) { *(tempfiles[process][3]) << rread.scores[i] << " "; }
                     *(tempfiles[process][3]) << endl;
                     *(tempfiles[process][3]) << ">" << rread.name << endl;
                     for (int i = 0; i < rread.scores.size(); i++) { *(tempfiles[process][3]) << rread.scores[i] << " "; }
                     *(tempfiles[process][3]) << endl;

-                    
+                    if (findex != "") {  *(tempfiles[process][4]) << ">" << firead.name << endl << firead.sequence << endl; }
+                    if (rindex != "") {  *(tempfiles[process][5]) << ">" << riread.name << endl << riread.sequence << endl; }
+                

                     count++;
                     
                     //report progress
                     if((count) % 10000 == 0){  m->mothurOut(toString(count)); m->mothurOutEndLine();           }
                     count++;
                     
                     //report progress
                     if((count) % 10000 == 0){  m->mothurOut(toString(count)); m->mothurOutEndLine();           }

-                }
+                //}

             }
                }
                //report progress
             }
                }
                //report progress


@@ -1233,8 +1298,13 @@ vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& c
         
         if (uniques.size() != 0) {
             for (itUniques = uniques.begin(); itUniques != uniques.end(); itUniques++) {
         
         if (uniques.size() != 0) {
             for (itUniques = uniques.begin(); itUniques != uniques.end(); itUniques++) {

+                if (m->control_pressed) { break; }

                 m->mothurOut("[WARNING]: did not find paired read for " + itUniques->first + ", ignoring.\n");
             }
                 m->mothurOut("[WARNING]: did not find paired read for " + itUniques->first + ", ignoring.\n");
             }

+            for (map<string, pairFastqRead>:: iterator it = pairUniques.begin(); it != pairUniques.end(); it++) {
+                if (m->control_pressed) { break; }
+                m->mothurOut("[WARNING]: did not find paired read for " + (it->first).substr(1) + ", ignoring.\n");
+            }

             m->mothurOutEndLine();
         }
         
             m->mothurOutEndLine();
         }
         


@@ -1242,7 +1312,9 @@ vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& c
         for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close();  delete (it->second)[i]; } }
         inForward.close();
         inReverse.close();
         for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close();  delete (it->second)[i]; } }
         inForward.close();
         inReverse.close();

-        
+        if (findex != "") { infIndex.close(); }
+        if (rindex != "") { inrIndex.close(); }
+       

         return files;
     }
     catch(exception& e) {
         return files;
     }
     catch(exception& e) {


@@ -1276,8 +1348,10 @@ vector< vector<string> > MakeContigsCommand::readFastaFiles(unsigned long int& c
             if (fqualfile != "") { fqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(fqualfile)) + toString(i) + "fqual.temp";  m->openOutputFile(fqualfilename, *outFQ); }
             string rqualfilename = "";
             if (rqualfile != "") { rqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(rqualfile)) + toString(i) + "rqual.temp"; m->openOutputFile(rqualfilename, *outRQ); }
             if (fqualfile != "") { fqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(fqualfile)) + toString(i) + "fqual.temp";  m->openOutputFile(fqualfilename, *outFQ); }
             string rqualfilename = "";
             if (rqualfile != "") { rqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(rqualfile)) + toString(i) + "rqual.temp"; m->openOutputFile(rqualfilename, *outRQ); }

+            string findexfilename = ""; string rindexfilename = "";

             names.push_back(ffastafilename); names.push_back(fqualfilename);
             names.push_back(rfastafilename); names.push_back(rqualfilename);
             names.push_back(ffastafilename); names.push_back(fqualfilename);
             names.push_back(rfastafilename); names.push_back(rqualfilename);

+            names.push_back(findexfilename); names.push_back(rindexfilename);

             files.push_back(names);
             
             m->openOutputFile(ffastafilename, *outFF);
             files.push_back(names);
             
             m->openOutputFile(ffastafilename, *outFF);


@@ -1341,7 +1415,7 @@ vector< vector<string> > MakeContigsCommand::readFastaFiles(unsigned long int& c
                 }else { ignorer = true; }
             }
             
                 }else { ignorer = true; }
             }
             

-            vector<pairFastqRead> reads = getReads(ignoref, ignorer, thisFread, thisRread, uniques);
+            vector<pairFastqRead> reads = getReads(ignoref, ignorer, thisFread, thisRread, uniques, false);

             
             for (int i = 0; i < reads.size(); i++) {
                 fastqRead fread = reads[i].forward;
             
             for (int i = 0; i < reads.size(); i++) {
                 fastqRead fread = reads[i].forward;


@@ -1349,7 +1423,7 @@ vector< vector<string> > MakeContigsCommand::readFastaFiles(unsigned long int& c
                 
                 if (m->debug) { m->mothurOut(toString(count) + '\t' + fread.name + '\t' + rread.name + '\n'); }
                 
                 
                 if (m->debug) { m->mothurOut(toString(count) + '\t' + fread.name + '\t' + rread.name + '\n'); }
                 

-                if (checkReads(fread, rread, ffasta, rfasta)) {
+               // if (checkReads(fread, rread, ffasta, rfasta)) {

                     if (m->control_pressed) { for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close();  delete (it->second)[i]; } } for (int i = 0; i < files.size(); i++) {  for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } } inReverseFasta.close(); inForwardFasta.close(); if (fqualfile != "") { inReverseQual.close(); inReverseQual.close(); } return files; }
                     
                     //if the reads are okay write to output files
                     if (m->control_pressed) { for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close();  delete (it->second)[i]; } } for (int i = 0; i < files.size(); i++) {  for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } } inReverseFasta.close(); inForwardFasta.close(); if (fqualfile != "") { inReverseQual.close(); inReverseQual.close(); } return files; }
                     
                     //if the reads are okay write to output files


@@ -1369,7 +1443,7 @@ vector< vector<string> > MakeContigsCommand::readFastaFiles(unsigned long int& c
                     
                     //report progress
                     if((count) % 10000 == 0){  m->mothurOut(toString(count)); m->mothurOutEndLine();           }
                     
                     //report progress
                     if((count) % 10000 == 0){  m->mothurOut(toString(count)); m->mothurOutEndLine();           }

-                }
+                //}

             }
                }
                //report progress
             }
                }
                //report progress


@@ -1396,7 +1470,7 @@ vector< vector<string> > MakeContigsCommand::readFastaFiles(unsigned long int& c
     }
 }
 //**********************************************************************************************************************
     }
 }
 //**********************************************************************************************************************

-vector<pairFastqRead> MakeContigsCommand::getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map<string, fastqRead>& uniques){
+vector<pairFastqRead> MakeContigsCommand::getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map<string, fastqRead>& uniques, bool allowOne){

     try {
         vector<pairFastqRead> reads;
         map<string, fastqRead>::iterator itUniques;
     try {
         vector<pairFastqRead> reads;
         map<string, fastqRead>::iterator itUniques;


@@ -1444,25 +1518,36 @@ vector<pairFastqRead> MakeContigsCommand::getReads(bool ignoref, bool ignorer, f
                                 
             }
         }else if (!ignoref && ignorer) { //ignore reverse keep forward
                                 
             }
         }else if (!ignoref && ignorer) { //ignore reverse keep forward

-            //look for forward pair
-            itUniques = uniques.find(forward.name);
-            if (itUniques != uniques.end()) {  //we have the pair for this read
-                pairFastqRead temp(forward, itUniques->second);
+            if (allowOne) {
+                fastqRead dummy;
+                pairFastqRead temp(forward, dummy);

                 reads.push_back(temp);
                 reads.push_back(temp);

-                uniques.erase(itUniques);
-            }else { //save this read for later
-                uniques[forward.name] = forward;
+            }else {
+                //look for forward pair
+                itUniques = uniques.find(forward.name);
+                if (itUniques != uniques.end()) {  //we have the pair for this read
+                    pairFastqRead temp(forward, itUniques->second);
+                    reads.push_back(temp);
+                    uniques.erase(itUniques);
+                }else { //save this read for later
+                    uniques[forward.name] = forward;
+                }

             }
             }

-

         }else if (ignoref && !ignorer) { //ignore forward keep reverse
         }else if (ignoref && !ignorer) { //ignore forward keep reverse

-            //look for reverse pair
-            itUniques = uniques.find(reverse.name);
-            if (itUniques != uniques.end()) {  //we have the pair for this read
-                pairFastqRead temp(itUniques->second, reverse);
+            if (allowOne) {
+                fastqRead dummy;
+                pairFastqRead temp(dummy, reverse);

                 reads.push_back(temp);
                 reads.push_back(temp);

-                uniques.erase(itUniques);
-            }else { //save this read for later
-                uniques[reverse.name] = reverse;
+            }else {
+                //look for reverse pair
+                itUniques = uniques.find(reverse.name);
+                if (itUniques != uniques.end()) {  //we have the pair for this read
+                    pairFastqRead temp(itUniques->second, reverse);
+                    reads.push_back(temp);
+                    uniques.erase(itUniques);
+                }else { //save this read for later
+                    uniques[reverse.name] = reverse;
+                }

             }
         }//else ignore both and do nothing
         
             }
         }//else ignore both and do nothing
         


@@ -1474,6 +1559,73 @@ vector<pairFastqRead> MakeContigsCommand::getReads(bool ignoref, bool ignorer, f
     }
 }
 //**********************************************************************************************************************
     }
 }
 //**********************************************************************************************************************

+//look through the reads from the forward and reverse files and try to find matching reads from index files.
+vector<pairFastqRead> MakeContigsCommand::mergeReads(vector<pairFastqRead> thisReads, vector<pairFastqRead> indexes, map<string, pairFastqRead>& uniques){
+    try {
+        vector<pairFastqRead> reads;
+        map<string, pairFastqRead>::iterator itUniques;
+        
+        set<int> foundIndexes;
+        for (int i = 0; i < thisReads.size(); i++) {
+            bool found = false;
+            for (int j = 0; j < indexes.size(); j++) {
+                
+                //incase only one index
+                string indexName = indexes[j].forward.name;
+                if (indexName == "") { indexName = indexes[j].reverse.name; }
+                
+                if (thisReads[i].forward.name == indexName){
+                    thisReads[i].findex = indexes[j].forward;
+                    thisReads[i].rindex = indexes[j].reverse;
+                    reads.push_back(thisReads[i]);
+                    found = true;
+                    foundIndexes.insert(j);
+                }
+            }
+            
+            if (!found) {
+                //look for forward pair
+                itUniques = uniques.find('i'+thisReads[i].forward.name);
+                if (itUniques != uniques.end()) {  //we have the pair for this read
+                    thisReads[i].findex = itUniques->second.forward;
+                    thisReads[i].rindex = itUniques->second.reverse;
+                    reads.push_back(thisReads[i]);
+                    uniques.erase(itUniques);
+                }else { //save this read for later
+                    uniques['r'+thisReads[i].forward.name] = thisReads[i];
+                }
+            }
+        }
+        
+        if (foundIndexes.size() != indexes.size()) { //if we didnt match all the indexes look for them in uniques
+            for (int j = 0; j < indexes.size(); j++) {
+                if (foundIndexes.count(j) == 0) { //we didnt find this one
+                    //incase only one index
+                    string indexName = indexes[j].forward.name;
+                    if (indexName == "") { indexName = indexes[j].reverse.name; }
+                    
+                    //look for forward pair
+                    itUniques = uniques.find('r'+indexName);
+                    if (itUniques != uniques.end()) {  //we have the pair for this read
+                        pairFastqRead temp(itUniques->second.forward, itUniques->second.reverse, indexes[j].forward, indexes[j].reverse);
+                        reads.push_back(temp);
+                        uniques.erase(itUniques);
+                    }else { //save this read for later
+                        uniques['i'+indexName] = indexes[j];
+                    }
+                }
+            }
+        }
+       
+        
+        return reads;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "MakeContigsCommand", "mergeReads");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************

 fastqRead MakeContigsCommand::readFastq(ifstream& in, bool& ignore){
     try {
         fastqRead read;
 fastqRead MakeContigsCommand::readFastq(ifstream& in, bool& ignore){
     try {
         fastqRead read;


@@ -1508,18 +1660,14 @@ fastqRead MakeContigsCommand::readFastq(ifstream& in, bool& ignore){
         if (name2 != "") { if (name != name2) { m->mothurOut("[WARNING]: names do not match. read " + name + " for fasta and " + name2 + " for quality, ignoring."); ignore=true; } }
         if (quality.length() != sequence.length()) { m->mothurOut("[WARNING]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores, ignoring read."); ignore=true; }
         
         if (name2 != "") { if (name != name2) { m->mothurOut("[WARNING]: names do not match. read " + name + " for fasta and " + name2 + " for quality, ignoring."); ignore=true; } }
         if (quality.length() != sequence.length()) { m->mothurOut("[WARNING]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores, ignoring read."); ignore=true; }
         

-        vector<int> qualScores;
-               int controlChar = int('!');
-               for (int i = 0; i < quality.length(); i++) { 
-                       int temp = int(quality[i]);
-                       temp -= controlChar;
-                       
-                       qualScores.push_back(temp);
-               }
-    
+        vector<int> qualScores = convertQual(quality);
+        
+        m->checkName(name);

         read.name = name;
         read.sequence = sequence;
         read.scores = qualScores;
         read.name = name;
         read.sequence = sequence;
         read.scores = qualScores;

+        
+        if (m->debug) { m->mothurOut("[DEBUG]: " + read.name + " " + read.sequence + " " + quality + "\n"); }

 
         return read;
     }
 
         return read;
     }


@@ -1528,7 +1676,7 @@ fastqRead MakeContigsCommand::readFastq(ifstream& in, bool& ignore){
         exit(1);
     }
 }
         exit(1);
     }
 }

-//**********************************************************************************************************************
+/**********************************************************************************************************************

 bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse, string ffile, string rfile){
     try {
         bool good = true;
 bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse, string ffile, string rfile){
     try {
         bool good = true;


@@ -1551,12 +1699,18 @@ bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse, stri
         m->errorOut(e, "MakeContigsCommand", "checkReads");
         exit(1);
     }
         m->errorOut(e, "MakeContigsCommand", "checkReads");
         exit(1);
     }

-}
+}*/

 //***************************************************************************************************************
 //***************************************************************************************************************

+//lines can be 2, 3, or 4 columns
+// forward.fastq reverse.fastq -> 2 column
+// groupName forward.fastq reverse.fastq -> 3 column
+// forward.fastq reverse.fastq forward.index.fastq  reverse.index.fastq  -> 4 column
+// forward.fastq reverse.fastq none  reverse.index.fastq  -> 4 column
+// forward.fastq reverse.fastq forward.index.fastq  none  -> 4 column

 vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
        try {
         vector< vector<string> > files;
 vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
        try {
         vector< vector<string> > files;

-        string forward, reverse;
+        string forward, reverse, findex, rindex;

         
         ifstream in;
         m->openInputFile(filename, in);
         
         ifstream in;
         m->openInputFile(filename, in);


@@ -1565,8 +1719,35 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
             
             if (m->control_pressed) { return files; }
             
             
             if (m->control_pressed) { return files; }
             

-            in >> forward; m->gobble(in);
-            in >> reverse; m->gobble(in);
+            string line = m->getline(in);  m->gobble(in);
+            vector<string> pieces = m->splitWhiteSpace(line);
+            
+            string group = "";
+            if (pieces.size() == 2) {
+                forward = pieces[0];
+                reverse = pieces[1];
+                group = "";
+                findex = "";
+                rindex = "";
+            }else if (pieces.size() == 3) {
+                group = pieces[0];
+                forward = pieces[1];
+                reverse = pieces[2];
+                findex = "";
+                rindex = "";
+                createFileGroup = true;
+            }else if (pieces.size() == 4) {
+                forward = pieces[0];
+                reverse = pieces[1];
+                findex = pieces[2];
+                rindex = pieces[3];
+                if ((findex == "none") || (findex == "NONE")){ findex = ""; }
+                if ((rindex == "none") || (rindex == "NONE")){ rindex = ""; }
+            }else {
+                m->mothurOut("[ERROR]: file lines can be 2, 3, or 4 columns. The forward fastq files in the first column and their matching reverse fastq files in the second column, or a groupName then forward fastq file and reverse fastq file, or forward fastq file then reverse fastq then forward index and reverse index file.  If you only have one index file add 'none' for the other one. \n"); m->control_pressed = true;
+            }
+            
+            if (m->debug) { m->mothurOut("[DEBUG]: group = " + group + ", forward = " + forward + ", reverse = " + reverse + ", forwardIndex = " + findex + ", reverseIndex = " + rindex + ".\n"); }

             
             //check to make sure both are able to be opened
             ifstream in2;
             
             //check to make sure both are able to be opened
             ifstream in2;


@@ -1631,20 +1812,92 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
                 m->mothurOut("[WARNING]: can't find " + reverse + ", ignoring pair.\n"); 
             }else{  in3.close();  }
             
                 m->mothurOut("[WARNING]: can't find " + reverse + ", ignoring pair.\n"); 
             }else{  in3.close();  }
             

-            if ((openForward != 1) && (openReverse != 1)) { //good pair
+            int openFindex = 0;
+            if (findex != "") {
+                ifstream in4;
+                openFindex = m->openInputFile(findex, in4, "noerror"); in4.close();
+                
+                //if you can't open it, try default location
+                if (openFindex == 1) {
+                    if (m->getDefaultPath() != "") { //default path is set
+                        string tryPath = m->getDefaultPath() + m->getSimpleName(findex);
+                        m->mothurOut("Unable to open " + findex + ". Trying default " + tryPath); m->mothurOutEndLine();
+                        ifstream in5;
+                        openFindex = m->openInputFile(tryPath, in5, "noerror");
+                        in5.close();
+                        findex = tryPath;
+                    }
+                }
+                
+                //if you can't open it, try output location
+                if (openFindex == 1) {
+                    if (m->getOutputDir() != "") { //default path is set
+                        string tryPath = m->getOutputDir() + m->getSimpleName(findex);
+                        m->mothurOut("Unable to open " + findex + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+                        ifstream in6;
+                        openFindex = m->openInputFile(tryPath, in6, "noerror");
+                        findex = tryPath;
+                        in6.close();
+                    }
+                }
+                
+                if (openFindex == 1) { //can't find it
+                    m->mothurOut("[WARNING]: can't find " + findex + ", ignoring pair.\n");
+                }
+            }
+            
+            int openRindex = 0;
+            if (rindex != "") {
+                ifstream in7;
+                openRindex = m->openInputFile(rindex, in7, "noerror"); in7.close();
+                
+                //if you can't open it, try default location
+                if (openRindex == 1) {
+                    if (m->getDefaultPath() != "") { //default path is set
+                        string tryPath = m->getDefaultPath() + m->getSimpleName(rindex);
+                        m->mothurOut("Unable to open " + rindex + ". Trying default " + tryPath); m->mothurOutEndLine();
+                        ifstream in8;
+                        openRindex = m->openInputFile(tryPath, in8, "noerror");
+                        in8.close();
+                        rindex = tryPath;
+                    }
+                }
+                
+                //if you can't open it, try output location
+                if (openRindex == 1) {
+                    if (m->getOutputDir() != "") { //default path is set
+                        string tryPath = m->getOutputDir() + m->getSimpleName(rindex);
+                        m->mothurOut("Unable to open " + rindex + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+                        ifstream in9;
+                        openRindex = m->openInputFile(tryPath, in9, "noerror");
+                        rindex = tryPath;
+                        in9.close();
+                    }
+                }
+                
+                if (openRindex == 1) { //can't find it
+                    m->mothurOut("[WARNING]: can't find " + rindex + ", ignoring pair.\n");
+                }
+            }
+
+            
+            if ((openForward != 1) && (openReverse != 1) && (openFindex != 1) && (openRindex != 1)) { //good pair
+                file2Group[files.size()] = group;

                 vector<string> pair;
                 pair.push_back(forward);
                 pair.push_back(reverse);
                 vector<string> pair;
                 pair.push_back(forward);
                 pair.push_back(reverse);

+                pair.push_back(findex);
+                pair.push_back(rindex);
+                if (((findex != "") || (rindex != "")) && (oligosfile == "")) { m->mothurOut("[ERROR]: You need to provide an oligos file if you are going to use an index file.\n"); m->control_pressed = true;  }

                 files.push_back(pair);
             }
                 files.push_back(pair);
             }

-            

         }
         in.close();
         
         return files;
     }
     catch(exception& e) {
         }
         in.close();
         
         return files;
     }
     catch(exception& e) {

-        m->errorOut(e, "MakeContigsCommand", "checkReads");
+        m->errorOut(e, "MakeContigsCommand", "readFileNames");

         exit(1);
     }
 }
         exit(1);
     }
 }


@@ -1653,7 +1906,7 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
 //BARCODE   atgcatgc   atgcatgc    groupName 
 //PRIMER   atgcatgc   atgcatgc    groupName  
 //PRIMER   atgcatgc   atgcatgc  
 //BARCODE   atgcatgc   atgcatgc    groupName 
 //PRIMER   atgcatgc   atgcatgc    groupName  
 //PRIMER   atgcatgc   atgcatgc  

-bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames, string rootname){
+bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, string rootname){

        try {
                ifstream in;
                m->openInputFile(oligosfile, in);
        try {
                ifstream in;
                m->openInputFile(oligosfile, in);


@@ -1670,7 +1923,7 @@ bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, vect
                while(!in.eof()){
             
                        in >> type; 
                while(!in.eof()){
             
                        in >> type; 

-            cout << type << endl;
+    

                        if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }      
             
                        if(type[0] == '#'){
                        if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }      
             
                        if(type[0] == '#'){


@@ -1691,7 +1944,7 @@ bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, vect
                                        if(foligo[i] == 'U')    {       foligo[i] = 'T';        }
                                }
                                
                                        if(foligo[i] == 'U')    {       foligo[i] = 'T';        }
                                }
                                

-                               if(type == "FORWARD"){
+                               if(type == "PRIMER"){

                                        m->gobble(in);
                                        
                     in >> roligo;
                                        m->gobble(in);
                                        
                     in >> roligo;


@@ -1702,18 +1955,22 @@ bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, vect
                     }
                     //roligo = reverseOligo(roligo);
                     
                     }
                     //roligo = reverseOligo(roligo);
                     

+                    if (m->debug) { m->mothurOut("[DEBUG]: reading - " + roligo + ".\n"); }
+                    

                     group = "";
                     
                                        // get rest of line in case there is a primer name
                                        while (!in.eof())       {       
                                                char c = in.get(); 
                     group = "";
                     
                                        // get rest of line in case there is a primer name
                                        while (!in.eof())       {       
                                                char c = in.get(); 

-                                               if (c == 10 || c == 13){        break;  }
+                                               if (c == 10 || c == 13 || c == -1){     break;  }

                                                else if (c == 32 || c == 9){;} //space or tab
                                                else {  group += c;  }
                                        } 
                     
                     oligosPair newPrimer(foligo, roligo);
                                                else if (c == 32 || c == 9){;} //space or tab
                                                else {  group += c;  }
                                        } 
                     
                     oligosPair newPrimer(foligo, roligo);

-                                       
+                    
+                    if (m->debug) { m->mothurOut("[DEBUG]: primer pair " + newPrimer.forward + " " + newPrimer.reverse + ", and group = " + group + ".\n"); }
+                    

                                        //check for repeat barcodes
                     string tempPair = foligo+roligo;
                     if (uniquePrimers.count(tempPair) != 0) { m->mothurOut("primer pair " + newPrimer.forward + " " + newPrimer.reverse + " is in your oligos file already."); m->mothurOutEndLine();  }
                                        //check for repeat barcodes
                     string tempPair = foligo+roligo;
                     if (uniquePrimers.count(tempPair) != 0) { m->mothurOut("primer pair " + newPrimer.forward + " " + newPrimer.reverse + " is in your oligos file already."); m->mothurOutEndLine();  }


@@ -1736,10 +1993,12 @@ bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, vect
                     
                     oligosPair newPair(foligo, roligo);
                     
                     
                     oligosPair newPair(foligo, roligo);
                     

+                    if ((foligo == "NONE") || (roligo == "NONE")) { if (!noneOk) { m->mothurOut("[ERROR]: barcodes must be paired unless you are using an index file.\n"); m->control_pressed = true; } }
+                    

                     group = "";
                     while (!in.eof())  {       
                                                char c = in.get(); 
                     group = "";
                     while (!in.eof())  {       
                                                char c = in.get(); 

-                                               if (c == 10 || c == 13){        break;  }
+                                               if (c == 10 || c == 13 || c == -1){     break;  }

                                                else if (c == 32 || c == 9){;} //space or tab
                                                else {  group += c;  }
                                        } 
                                                else if (c == 32 || c == 9){;} //space or tab
                                                else {  group += c;  }
                                        } 


@@ -1753,7 +2012,6 @@ bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, vect
                         
                     barcodes[indexBarcode]=newPair; indexBarcode++;
                                        barcodeNameVector.push_back(group);
                         
                     barcodes[indexBarcode]=newPair; indexBarcode++;
                                        barcodeNameVector.push_back(group);

-                    cout << group << endl;

                                }else if(type == "LINKER"){
                                        linker.push_back(foligo);
                     m->mothurOut("[WARNING]: make.contigs is not setup to remove linkers, ignoring.\n");
                                }else if(type == "LINKER"){
                                        linker.push_back(foligo);
                     m->mothurOut("[WARNING]: make.contigs is not setup to remove linkers, ignoring.\n");


@@ -1786,7 +2044,6 @@ bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, vect
                for(int i=0;i<fastaFileNames.size();i++){
                        fastaFileNames[i].assign(primerNameVector.size(), "");
                }
                for(int i=0;i<fastaFileNames.size();i++){
                        fastaFileNames[i].assign(primerNameVector.size(), "");
                }

-               qualFileNames = fastaFileNames; 

                
                if(allFiles){
                        set<string> uniqueNames; //used to cleanup outputFileNames
                
                if(allFiles){
                        set<string> uniqueNames; //used to cleanup outputFileNames


@@ -1827,17 +2084,6 @@ bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, vect
                         
                         fastaFileNames[itBar->first][itPrimer->first] = fastaFileName;
                         m->openOutputFile(fastaFileName, temp);                temp.close();
                         
                         fastaFileNames[itBar->first][itPrimer->first] = fastaFileName;
                         m->openOutputFile(fastaFileName, temp);                temp.close();

-                        
-                        if ((fqualfile != "") || (ffastqfile != "") || (file != "")) {
-                            qualFileName = rootname + ".qual";
-                            if (uniqueNames.count(qualFileName) == 0) {
-                                outputNames.push_back(qualFileName);
-                                outputTypes["qfile"].push_back(qualFileName);
-                            }
-                            
-                            qualFileNames[itBar->first][itPrimer->first] = qualFileName;
-                            m->openOutputFile(qualFileName, temp);             temp.close();
-                        }

                     }
                                }
                        }
                     }
                                }
                        }


@@ -1912,6 +2158,41 @@ string MakeContigsCommand::reverseOligo(string oligo){
        }
 }
 //**********************************************************************************************************************
        }
 }
 //**********************************************************************************************************************

+vector<int> MakeContigsCommand::convertQual(string qual) {
+       try {
+               vector<int> qualScores;
+        bool negativeScores = false;
+               
+               for (int i = 0; i < qual.length(); i++) { 
+            
+            int temp = 0;
+            temp = int(qual[i]);
+            if (format == "illumina") {
+                temp -= 64; //char '@'
+            }else if (format == "illumina1.8+") {
+                    temp -= int('!'); //char '!'
+            }else if (format == "solexa") {
+                temp = int(convertTable[temp]); //convert to sanger
+                temp -= int('!'); //char '!'
+            }else {
+                temp -= int('!'); //char '!'
+            }
+            
+            if (temp < -5) { negativeScores = true; }
+                       qualScores.push_back(temp);
+               }
+               
+        if (negativeScores) { m->mothurOut("[ERROR]: finding negative quality scores, do you have the right format selected? http://en.wikipedia.org/wiki/FASTQ_format#Encoding \n");  m->control_pressed = true;  }
+        
+               return qualScores;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MakeContigsCommand", "convertQual");
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************