changes while testing

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index 25a68be75c950de1ebad3afe6955cf308ad0ce0b..005a89f2ebbee9e1b4c37567b6ce382979c90226 100644 (file)
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -318,7 +318,7 @@ GetLineageCommand::GetLineageCommand(string option)  {
             
             if ((sharedfile != "") || (listfile != "")) {
                 label = validParameter.validFile(parameters, "label", false);
-                if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }
+                if (label == "not found") { label = ""; m->mothurOut("[WARNING]: You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); }
             }
             
             if (countfile == "") {

diff --git a/makefile b/makefile
index 3ce1686327126b12c45afb51599b2e5a066e19aa..de21717ce03df122f7df9ddc014cc49900768250 100644 (file)
--- a/makefile
+++ b/makefile
@@ -15,8 +15,8 @@ USEREADLINE ?= yes
 CYGWIN_BUILD ?= no
 USECOMPRESSION ?= no
 MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"2/12/2013\""
-VERSION = "\"1.29.2\""
+RELEASE_DATE = "\"5/24/2013\""
+VERSION = "\"1.31.0\""
 FORTAN_COMPILER = gfortran
 FORTRAN_FLAGS = 
 

diff --git a/makelookupcommand.cpp b/makelookupcommand.cpp
index dd5bacfbc12aed0444fce46e3e836e4c2aea22d8..5b280f54fa297dd8401c964df08d7673cce0c6d9 100644 (file)
--- a/makelookupcommand.cpp
+++ b/makelookupcommand.cpp
@@ -197,7 +197,7 @@ int MakeLookupCommand::execute(){
         
         double gapOpening = 10;
         int maxHomoP = 101;
-        vector<vector<double> > penaltyMatrix(maxHomoP);
+        vector<vector<double> > penaltyMatrix; penaltyMatrix.resize(maxHomoP);
         for(int i=0;i<maxHomoP;i++){
             penaltyMatrix[i].resize(maxHomoP, 5);
             penaltyMatrix[i][i] = 0;
@@ -210,26 +210,31 @@ int MakeLookupCommand::execute(){
         
         while(!refFASTA.eof()){
             if (m->control_pressed) { refFASTA.close(); return 0; }
+            
             Sequence seq(refFASTA);  m->gobble(refFASTA);
             
+            if (m->debug) { m->mothurOut("[DEBUG]: seq = " + seq.getName() + ".\n"); }
+            
             string fullSequence = keySequence + barcodeSequence + seq.getAligned(); //  *   concatenate the keySequence, barcodeSequence, and
             //      referenceSequences
             refFlowgrams[seq.getName()] = convertSeqToFlow(fullSequence, flowOrder); //  *   translate concatenated sequences into flowgram
         }
         refFASTA.close();
         
-        vector<vector<double> > lookupTable(1000);
+        vector<vector<double> > lookupTable; lookupTable.resize(1000);
         for(int i=0;i<1000;i++){
             lookupTable[i].resize(11, 0);
         }
         
-        
+        if (m->debug) { m->mothurOut("[DEBUG]: here .\n"); }
         //Loop through each sequence in the flow file and the error summary file.
         ifstream flowFile;
         m->openInputFile(flowFileName, flowFile);
         int numFlows;
         flowFile >> numFlows;
         
+        if (m->debug) { m->mothurOut("[DEBUG]: numflows = " + toString(numFlows) +  ".\n"); }
+        
         ifstream errorFile;
         m->openInputFile(errorFileName, errorFile);
         m->getline(errorFile); //grab headers
@@ -238,7 +243,7 @@ int MakeLookupCommand::execute(){
         string chimera;
         float intensity;
         
-        vector<double> std(11, 0);
+        vector<double> std;  std.resize(11, 0);
         
         while(errorFile && flowFile){
             
@@ -260,26 +265,37 @@ int MakeLookupCommand::execute(){
                 flowFile >> flowQuery >> dummy;
                 if(flowQuery != errorQuery){    cout << flowQuery << " != " << errorQuery << endl;  }
                 
-                vector<double> refFlow = refFlowgrams[referenceName];       //  * compare sequence to its closest reference
-                
-                vector<double> flowgram(numFlows);
-                
-                for(int i=0;i<numFlows;i++){
-                    flowFile >> intensity;
-                    flowgram[i] = intensity;// (int)round(100 * intensity);
-                }
-                m->gobble(flowFile);
-                
-                alignFlowGrams(flowgram, refFlow, gapOpening, penaltyMatrix, flowOrder);
-                
-                if (m->control_pressed) { errorFile.close(); flowFile.close(); return 0; }
-                
-                for(int i=0;i<flowgram.size();i++){
-                    int count = (int)round(100*flowgram[i]);
-                    if(count > 1000){count = 999;}
-                    if(abs(flowgram[i]-refFlow[i])<=0.50){
-                        lookupTable[count][int(refFlow[i])]++;               //  * build table
-                        std[int(refFlow[i])] += (100*refFlow[i]-count)*(100*refFlow[i]-count);
+                map<string, vector<double> >::iterator it = refFlowgrams.find(referenceName);       //  * compare sequence to its closest reference
+                if (it == refFlowgrams.end()) {
+                    m->mothurOut("[WARNING]: missing reference flow " + referenceName + ", ignoring flow " + flowQuery + ".\n");
+                    m->getline(flowFile); m->gobble(flowFile);
+                }else {
+                    vector<double> refFlow = it->second;
+                    vector<double> flowgram; flowgram.resize(numFlows);
+                    
+                    if (m->debug) { m->mothurOut("[DEBUG]: flowQuery = " + flowQuery +  ".\t" + "refName " + referenceName+  ".\n"); }
+                    
+                    for(int i=0;i<numFlows;i++){
+                        flowFile >> intensity;
+                        flowgram[i] = intensity;// (int)round(100 * intensity);
+                    }
+                    m->gobble(flowFile);
+                    
+                    if (m->debug) { m->mothurOut("[DEBUG]: before align.\n"); }
+                    
+                    alignFlowGrams(flowgram, refFlow, gapOpening, penaltyMatrix, flowOrder);
+                    
+                    if (m->debug) { m->mothurOut("[DEBUG]: after align.\n"); }
+                    
+                    if (m->control_pressed) { errorFile.close(); flowFile.close(); return 0; }
+                    
+                    for(int i=0;i<flowgram.size();i++){
+                        int count = (int)round(100*flowgram[i]);
+                        if(count > 1000){count = 999;}
+                        if(abs(flowgram[i]-refFlow[i])<=0.50){
+                            lookupTable[count][int(refFlow[i])]++;               //  * build table
+                            std[int(refFlow[i])] += (100*refFlow[i]-count)*(100*refFlow[i]-count);
+                        }
                     }
                 }
                 
@@ -289,8 +305,9 @@ int MakeLookupCommand::execute(){
         }
         errorFile.close(); flowFile.close();
         
+        
         //get probabilities
-        vector<int> counts(11, 0);
+        vector<int> counts; counts.resize(11, 0);
         int totalCount = 0;
         for(int i=0;i<1000;i++){
             for(int j=0;j<11;j++){
@@ -337,7 +354,7 @@ int MakeLookupCommand::execute(){
         
         
         //calculate the probability of each homopolymer length
-        vector<double> negLogHomoProb(11, 0.00);  //bring back
+        vector<double> negLogHomoProb; negLogHomoProb.resize(11, 0.00);  //bring back
         for(int i=0;i<N;i++){
             negLogHomoProb[i] = -log(counts[i] / (double)totalCount);
         }
@@ -438,8 +455,8 @@ int MakeLookupCommand::alignFlowGrams(vector<double>& flowgram, vector<double>&
         
             //cout << numQueryFlows << '\t' << numRefFlows << endl;
         
-        vector<vector<double> > scoreMatrix(numQueryFlows+1);
-        vector<vector<char> > directMatrix(numQueryFlows+1);
+        vector<vector<double> > scoreMatrix; scoreMatrix.resize(numQueryFlows+1);
+        vector<vector<char> > directMatrix; directMatrix.resize(numQueryFlows+1);
         
         for(int i=0;i<=numQueryFlows;i++){
             if (m->control_pressed) { return 0; }
@@ -458,6 +475,7 @@ int MakeLookupCommand::alignFlowGrams(vector<double>& flowgram, vector<double>&
             directMatrix[0][i] = 'l';
         }
         
+        
         for(int i=1;i<=numQueryFlows;i++){
             for(int j=1;j<=numRefFlows;j++){
                 if (m->control_pressed) { return 0; }
@@ -498,7 +516,7 @@ int MakeLookupCommand::alignFlowGrams(vector<double>& flowgram, vector<double>&
         
         int minColumnIndex = numRefFlows;
         double minColumnScore = scoreMatrix[numQueryFlows][numRefFlows];
-        for(int i=0;i<numQueryFlows;i++){
+        for(int i=0;i<numRefFlows;i++){
             if (m->control_pressed) { return 0; }
             if(scoreMatrix[numQueryFlows][i] < minColumnScore){
                 minColumnScore = scoreMatrix[numQueryFlows][i];
@@ -512,7 +530,7 @@ int MakeLookupCommand::alignFlowGrams(vector<double>& flowgram, vector<double>&
         
         vector<double> newFlowgram;
         vector<double> newRefFlowgram;
-        
+       
         while(i > 0 && j > 0){
             if (m->control_pressed) { return 0; }
             if(directMatrix[i][j] == 'd'){

diff --git a/setdircommand.cpp b/setdircommand.cpp
index dc4c9ac3baa8dcaafadc9e825ceb598ab4c1cabf..3e50f4a508d2608ef1b51b9445fd3a388d1f4dec 100644 (file)
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -37,7 +37,7 @@ string SetDirectoryCommand::getHelpString(){
                helpString += "The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n";
                helpString += "The set.dir command can also be used to override or set the default location mothur will look for files if it is unable to find them, the directory must exist.\n";
         helpString += "The set.dir command can also be used to run mothur in debug mode.\n";
-        helpString += "The set.dir command can also be used to set the modifynames parameter. Default=t, meaning if your sequence names contain ':' change them to '_' to aviod issues while making trees.  modifynames=F will leave sequence names as they are.\n";
+        helpString += "The set.dir command can also be used to set the modifynames parameter. Default=t, meaning if your sequence names contain ':' change them to '_' to avoid issues while making trees.  modifynames=F will leave sequence names as they are.\n";
                helpString += "The set.dir command parameters are input, output, tempdefault and debug and one is required.\n";
         helpString += "To run mothur in debug mode set debug=true. Default debug=false.\n";
                helpString += "To return the output to the same directory as the input files you may enter: output=clear.\n";

diff --git a/sffmultiplecommand.cpp b/sffmultiplecommand.cpp
index 41002e7754dd97c57e6ab075b5e7c26380a40104..00f23ed24cc83e8eddf66f328a1fe3ce765e122d 100644 (file)
--- a/sffmultiplecommand.cpp
+++ b/sffmultiplecommand.cpp
@@ -236,11 +236,11 @@ SffMultipleCommand::SffMultipleCommand(string option)  {
             if (temp.length() > 1) {  m->mothurOut("[ERROR]: " + temp + " is not a valid option for order. order options are A, B, or I. A = TACG, B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC, and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n");  abort=true;
             }
             else {
-                if (toupper(temp[0]) == 'A') {  flowOrder = "TACG";   }
+                if (toupper(temp[0]) == 'A') {  flowOrder = "A";   }
                 else if(toupper(temp[0]) == 'B'){
-                    flowOrder = "TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC";   }
+                    flowOrder = "B";   }
                 else if(toupper(temp[0]) == 'I'){
-                    flowOrder = "TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC";   }
+                    flowOrder = "I";   }
                 else {
                     m->mothurOut("[ERROR]: " + temp + " is not a valid option for order. order options are A, B, or I. A = TACG, B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC, and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n");  abort=true;
                 }
@@ -378,9 +378,9 @@ int SffMultipleCommand::execute(){
         string fileroot = outputDir + m->getRootName(m->getSimpleName(filename));
         map<string, string> variables; 
                variables["[filename]"] = fileroot;
-        string fasta = fileroot + getOutputFileName("fasta",variables);
-        string name = fileroot + getOutputFileName("name",variables);
-        string group = fileroot + getOutputFileName("group",variables);
+        string fasta = getOutputFileName("fasta",variables);
+        string name = getOutputFileName("name",variables);
+        string group = getOutputFileName("group",variables);
         
         if (m->control_pressed) { return 0; }