added end of file character to some type type reads. fixes while testing.

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 3c14d55163ab260db87b7a35c271e664b7584945..ce07a034d64154d2d77fcf7cab64f922bec56231 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -2353,7 +2353,6 @@
                                GCC_OPTIMIZATION_LEVEL = 3;
                                "INSTALL_PATH[sdk=*]" = TARGET_BUILD_DIR;
                                PRODUCT_NAME = mothur;
                                GCC_OPTIMIZATION_LEVEL = 3;
                                "INSTALL_PATH[sdk=*]" = TARGET_BUILD_DIR;
                                PRODUCT_NAME = mothur;

-                               SDKROOT = macosx;

                                SDKROOT = macosx10.8;
                                SKIP_INSTALL = NO;
                        };
                                SDKROOT = macosx10.8;
                                SKIP_INSTALL = NO;
                        };


@@ -2423,8 +2422,8 @@
                                GCC_MODEL_TUNING = "";
                                GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                GCC_MODEL_TUNING = "";
                                GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (

-                                       "VERSION=\"\\\"1.29.2\\\"\"",
-                                       "RELEASE_DATE=\"\\\"2/12/2013\\\"\"",
+                                       "VERSION=\"\\\"1.30.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"4/01/2013\\\"\"",

                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index 842a65ee22fd54c730143cbed94f91688dba8006..f7dc597cf8ca514712bf06f29f2010982d6c03c9 100644 (file)
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -469,10 +469,7 @@ ChimeraPerseusCommand::ChimeraPerseusCommand(string option)  {
                        m->mothurConvert(temp, beta);
             
                        temp = validParameter.validFile(parameters, "dereplicate", false);      
                        m->mothurConvert(temp, beta);
             
                        temp = validParameter.validFile(parameters, "dereplicate", false);      

-                       if (temp == "not found") { 
-                               if (groupfile != "")    {  temp = "false";                                      }
-                               else                    {  temp = "true";       }
-                       }
+                       if (temp == "not found") { temp = "false";                      }

                        dups = m->isTrue(temp);
                }
        }
                        dups = m->isTrue(temp);
                }
        }

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index fceef2180163f60e3c33cfecb7e861839c4bd1c7..d16843c8d612fac2bde8c03db8e45ce68e869412 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -603,10 +603,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        m->mothurConvert(temp, numwanted);
             
                        temp = validParameter.validFile(parameters, "dereplicate", false);      
                        m->mothurConvert(temp, numwanted);
             
                        temp = validParameter.validFile(parameters, "dereplicate", false);      

-                       if (temp == "not found") { 
-                               if (groupfile != "")    {  temp = "false";                                      }
-                               else                    {  temp = "true";       }
-                       }
+                       if (temp == "not found") { temp = "false";                      }

                        dups = m->isTrue(temp);
                        
                        blastlocation = validParameter.validFile(parameters, "blastlocation", false);   
                        dups = m->isTrue(temp);
                        
                        blastlocation = validParameter.validFile(parameters, "blastlocation", false);   


@@ -1631,7 +1628,7 @@ int ChimeraSlayerCommand::createProcessesGroups(string outputFName, string accno
                //Create processor worker threads.
                for(int i=1; i<processors; i++ ){
                        string extension = toString(i) + ".temp";
                //Create processor worker threads.
                for(int i=1; i<processors; i++ ){
                        string extension = toString(i) + ".temp";

-                       slayerData* tempslayer = new slayerData(group2NameMap, hasCount, dups, (accnos + extension+".byCount"), (outputFName + extension), (fasta + extension), (accnos + extension), templatefile, search, blastlocation, trimera, trim, realign, m, breakUp[i], fileGroup, ksize, match, mismatch, window, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, divR, priority, i);
+                       slayerData* tempslayer = new slayerData(group2NameMap, hasCount, dups, (accnos + toString(i) +".byCount"), (outputFName + extension), (fasta + extension), (accnos + extension), templatefile, search, blastlocation, trimera, trim, realign, m, breakUp[i], fileGroup, ksize, match, mismatch, window, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, divR, priority, i);

                        pDataArray.push_back(tempslayer);
                        processIDS.push_back(i);
                        
                        pDataArray.push_back(tempslayer);
                        processIDS.push_back(i);
                        

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index e82dc1bc8dce5ffd0887025d5816b5eec8d0eab9..3d23a7693818f329ff6ac53cca560998c8a9fc95 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -564,10 +564,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
             
             
                        temp = validParameter.validFile(parameters, "dereplicate", false);      
             
             
                        temp = validParameter.validFile(parameters, "dereplicate", false);      

-                       if (temp == "not found") { 
-                               if (groupfile != "")    {  temp = "false";                                      }
-                               else                    {  temp = "true";       }
-                       }
+                       if (temp == "not found") { temp = "false";                      }

                        dups = m->isTrue(temp);
 
                        
                        dups = m->isTrue(temp);
 
                        

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 480bde3222c9057aafecacc208d84eac24573b72..287f5a6acdc08a9c40b6e2e12b159a2f83fc9636 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -501,7 +501,7 @@ int GetSeqsCommand::readQual(){
                                saveName = name.substr(1);
                                while (!in.eof())       {       
                                        char c = in.get(); 
                                saveName = name.substr(1);
                                while (!in.eof())       {       
                                        char c = in.get(); 

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

                                        else { name += c; }     
                                } 
                                m->gobble(in);
                                        else { name += c; }     
                                } 
                                m->gobble(in);

diff --git a/makecontigscommand.cpp b/makecontigscommand.cpp
index c8f20f10eed04c59df0aa27c136029e43713579e..85b6a8fdcbacf1ca1ee5b471b2142480ecf5da48 100644 (file)
--- a/makecontigscommand.cpp
+++ b/makecontigscommand.cpp
@@ -1681,7 +1681,7 @@ bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, stri
                                        // get rest of line in case there is a primer name
                                        while (!in.eof())       {       
                                                char c = in.get(); 
                                        // 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;  }
                                        } 
                                                else if (c == 32 || c == 9){;} //space or tab
                                                else {  group += c;  }
                                        } 


@@ -1713,7 +1713,7 @@ bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, stri
                     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;  }
                                        } 

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index fbc7c6003989044eba397ba7d8d6d58fa37c768a..16117053fc7c0a8147c7f00fcdd935324ff66edb 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -17,7 +17,8 @@
 vector<string> PhylotypeCommand::setParameters(){      
        try {
                CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","list-rabund-sabund",false,true,true); parameters.push_back(ptaxonomy);
 vector<string> PhylotypeCommand::setParameters(){      
        try {
                CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","list-rabund-sabund",false,true,true); parameters.push_back(ptaxonomy);

-               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pname);
+               CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","rabund-sabund",false,false,true); parameters.push_back(pname);
+               CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pcount);

                CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pcutoff);
                CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
                CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pcutoff);
                CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);


@@ -37,7 +38,7 @@ string PhylotypeCommand::getHelpString(){
        try {
                string helpString = "";
                helpString += "The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n";
        try {
                string helpString = "";
                helpString += "The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n";

-               helpString += "The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n";
+               helpString += "The phylotype command parameter options are taxonomy, name, count, cutoff and label. The taxonomy parameter is required.\n";

                helpString += "The cutoff parameter allows you to specify the level you want to stop at.  The default is the highest level in your taxonomy file. \n";
                helpString += "For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n";
                helpString += "For the cutoff parameter levels count up from the root of the phylotree. This enables you to look at the grouping down to a specific resolution, say the genus level.\n";
                helpString += "The cutoff parameter allows you to specify the level you want to stop at.  The default is the highest level in your taxonomy file. \n";
                helpString += "For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n";
                helpString += "For the cutoff parameter levels count up from the root of the phylotree. This enables you to look at the grouping down to a specific resolution, say the genus level.\n";


@@ -58,9 +59,9 @@ string PhylotypeCommand::getOutputPattern(string type) {
     try {
         string pattern = "";
         
     try {
         string pattern = "";
         

-        if (type == "list") {  pattern = "[filename],[tag],list"; } 
-        else if (type == "rabund") {  pattern = "[filename],[tag],rabund"; } 
-        else if (type == "sabund") {  pattern = "[filename],[tag],sabund"; }
+        if (type == "list") {  pattern = "[filename],[clustertag],list-[filename],[clustertag],[tag2],list"; }
+        else if (type == "rabund") {  pattern = "[filename],[clustertag],rabund"; }
+        else if (type == "sabund") {  pattern = "[filename],[clustertag],sabund"; }

         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;


@@ -134,6 +135,14 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["name"] = inputDir + it->second;             }
                                }
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["name"] = inputDir + it->second;             }
                                }

+                
+                it = parameters.find("count");
+                               //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["count"] = inputDir + it->second;            }
+                               }

                        }
 
                        taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
                        }
 
                        taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);


@@ -150,7 +159,12 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { namefile = ""; abort = true; }
                        else if (namefile == "not found") { namefile = ""; }
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { namefile = ""; abort = true; }
                        else if (namefile == "not found") { namefile = ""; }

-                       else { readNamesFile(); m->setNameFile(namefile); }     
+                       else { readNamesFile(); m->setNameFile(namefile); }
+            
+            countfile = validParameter.validFile(parameters, "count", true);
+                       if (countfile == "not open") { abort = true; countfile = ""; }
+                       else if (countfile == "not found") { countfile = ""; }
+                       else { m->setCountTableFile(countfile); }

                        
                        //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"){  
                        
                        //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"){  


@@ -158,6 +172,8 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                                outputDir += m->hasPath(taxonomyFileName); //if user entered a file with a path then preserve it        
                        }
                        
                                outputDir += m->hasPath(taxonomyFileName); //if user entered a file with a path then preserve it        
                        }
                        

+            if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
+            

                        string temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "-1"; }
                        m->mothurConvert(temp, cutoff); 
                        string temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "-1"; }
                        m->mothurConvert(temp, cutoff); 


@@ -169,11 +185,12 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                                else { allLines = 1;  }
                        }
                        
                                else { allLines = 1;  }
                        }
                        

-                       if (namefile == "") {
-                               vector<string> files; files.push_back(taxonomyFileName);
-                               parser.getNameFile(files);
+            if (countfile == "") {
+                if (namefile == "") {
+                    vector<string> files; files.push_back(taxonomyFileName);
+                    parser.getNameFile(files);
+                }

                        }
                        }

-                       

                }
        }
        catch(exception& e) {
                }
        }
        catch(exception& e) {


@@ -211,24 +228,27 @@ int PhylotypeCommand::execute(){
                
                if (m->control_pressed) { delete tree; return 0; }
                
                
                if (m->control_pressed) { delete tree; return 0; }
                

-               string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
-               map<string, string> variables; 
+               ofstream outList, outRabund, outSabund;
+        map<string, string> variables;
+        string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));

         variables["[filename]"] = fileroot;
         variables["[filename]"] = fileroot;

-        variables["[tag]"] = "tx";
-        ofstream outList;
-               string outputListFile = getOutputFileName("list",variables);
-               m->openOutputFile(outputListFile, outList);
-               ofstream outSabund;
-               string outputSabundFile = getOutputFileName("sabund",variables);
-               m->openOutputFile(outputSabundFile, outSabund);
-               ofstream outRabund;
-               string outputRabundFile = getOutputFileName("rabund",variables);
-               m->openOutputFile(outputRabundFile, outRabund);
-               
-               outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
-               outputNames.push_back(outputSabundFile); outputTypes["sabund"].push_back(outputSabundFile);
-               outputNames.push_back(outputRabundFile); outputTypes["rabund"].push_back(outputRabundFile);
-               
+        variables["[clustertag]"] = "tx";
+        string sabundFileName = getOutputFileName("sabund", variables);
+        string rabundFileName = getOutputFileName("rabund", variables);
+        if (countfile != "") { variables["[tag2]"] = "unique_list"; }
+        string listFileName = getOutputFileName("list", variables);
+        
+        if (countfile == "") {
+            m->openOutputFile(sabundFileName,  outSabund);
+            m->openOutputFile(rabundFileName,  outRabund);
+            outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
+            outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+            
+        }
+               m->openOutputFile(listFileName, outList);
+        outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
+
+        

                int count = 1;          
                //start at leaves of tree and work towards root, processing the labels the user wants
                while((!done) && ((allLines == 1) || (labels.size() != 0))) {
                int count = 1;          
                //start at leaves of tree and work towards root, processing the labels the user wants
                while((!done) && ((allLines == 1) || (labels.size() != 0))) {


@@ -237,7 +257,7 @@ int PhylotypeCommand::execute(){
                        count++;
                        
                        if (m->control_pressed) { 
                        count++;
                        
                        if (m->control_pressed) { 

-                               outRabund.close(); outSabund.close(); outList.close();
+                               if (countfile == "") { outRabund.close(); outSabund.close(); } outList.close();

                                for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
                                delete tree; return 0; 
                        }
                                for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
                                delete tree; return 0; 
                        }


@@ -284,11 +304,12 @@ int PhylotypeCommand::execute(){
                                
                                //print listvector
                                list.print(outList);
                                
                                //print listvector
                                list.print(outList);

-                               //print rabund
-                               list.getRAbundVector().print(outRabund);
-                               //print sabund
-                               list.getSAbundVector().print(outSabund);
-                       
+                if (countfile == "") {
+                    //print rabund
+                    list.getRAbundVector().print(outRabund);
+                    //print sabund
+                    list.getSAbundVector().print(outSabund);
+                }

                                labels.erase(level);
                                
                        }else {
                                labels.erase(level);
                                
                        }else {


@@ -309,8 +330,10 @@ int PhylotypeCommand::execute(){
                }
                        
                outList.close();
                }
                        
                outList.close();

-               outSabund.close();
-               outRabund.close();      
+        if (countfile == "") {
+            outSabund.close();
+            outRabund.close();
+        }

                
                delete tree;
                
                
                delete tree;
                

diff --git a/phylotypecommand.h b/phylotypecommand.h
index 534dc8eefcc643bda6f71d23291462b01c4d3940..ef8b8f17e37051be4951d6dd662d0db1beb1dbaa 100644 (file)
--- a/phylotypecommand.h
+++ b/phylotypecommand.h
@@ -37,7 +37,7 @@ public:
        
 private:
        bool abort, allLines;
        
 private:
        bool abort, allLines;

-       string taxonomyFileName, label, outputDir, namefile;
+       string taxonomyFileName, label, outputDir, namefile, countfile;

        set<string> labels; //holds labels to be used
        int cutoff;
        map<string, string> namemap;
        set<string> labels; //holds labels to be used
        int cutoff;
        map<string, string> namemap;

diff --git a/prcseqscommand.cpp b/prcseqscommand.cpp
index 5fa71bef6b3474cc516491044c41729a318d449f..cf93cb796104aa90428e5466546c9839789216f7 100644 (file)
--- a/prcseqscommand.cpp
+++ b/prcseqscommand.cpp
@@ -804,7 +804,7 @@ bool PcrSeqsCommand::readOligos(){
                                        // get rest of line in case there is a primer name
                                        while (!inOligos.eof()) {       
                         char c = inOligos.get(); 
                                        // get rest of line in case there is a primer name
                                        while (!inOligos.eof()) {       
                         char c = inOligos.get(); 

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

                         else if (c == 32 || c == 9){;} //space or tab
                                        } 
                                        primers[oligo] = primerCount; primerCount++;
                         else if (c == 32 || c == 9){;} //space or tab
                                        } 
                                        primers[oligo] = primerCount; primerCount++;

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index b4fb467d6e395ce9b1655e043859cff0e2c77f67..c7af108325390221bd0313e4ad2a733dfd2e90d3 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -469,7 +469,7 @@ int RemoveSeqsCommand::readQual(){
                                saveName = name.substr(1);
                                while (!in.eof())       {       
                                        char c = in.get(); 
                                saveName = name.substr(1);
                                while (!in.eof())       {       
                                        char c = in.get(); 

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

                                        else { name += c; }     
                                } 
                                m->gobble(in);
                                        else { name += c; }     
                                } 
                                m->gobble(in);

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 29e541319081d5bbd2254923919a03b255a00ca7..033fbcad422abb62cd2470866bd4666db9e907bd 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -2301,7 +2301,7 @@ int ScreenSeqsCommand::screenQual(map<string, string> badSeqNames){
                                saveName = name.substr(1);
                                while (!in.eof())       {       
                                        char c = in.get(); 
                                saveName = name.substr(1);
                                while (!in.eof())       {       
                                        char c = in.get(); 

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

                                        else { name += c; }     
                                } 
                                m->gobble(in);
                                        else { name += c; }     
                                } 
                                m->gobble(in);

diff --git a/sequence.cpp b/sequence.cpp
index 4c631a23451d4d9723aec3a29bed423737b243ba..d1cf7299a46c522255eb725dccb058673f6b1c78 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -220,7 +220,7 @@ Sequence::Sequence(ifstream& fastaFile, string& extraInfo, bool getInfo){
                        //read info after sequence name
                        while (!fastaFile.eof())        {       
                 char c = fastaFile.get(); 
                        //read info after sequence name
                        while (!fastaFile.eof())        {       
                 char c = fastaFile.get(); 

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

                 extraInfo += c;
             } 
                        
                 extraInfo += c;
             } 
                        

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 0148ab19f407b91d293eebb547927d4c381fd6d0..911009982a3ed7a3e5da2845094a82b1338b74a3 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -1656,7 +1656,7 @@ bool SffInfoCommand::readOligos(string oligoFile){
                                        // get rest of line in case there is a primer name
                                        while (!inOligos.eof()) {       
                                                char c = inOligos.get(); 
                                        // get rest of line in case there is a primer name
                                        while (!inOligos.eof()) {       
                                                char c = inOligos.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;  }
                                        } 

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 1bab57f853a200d50aa4a62545f15a4697e167a8..2da240e21b5103d4d77b6eb24d0f0c335f3a7d3c 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -28,7 +28,7 @@ vector<string> TrimFlowsCommand::setParameters(){
                CommandParameter psignal("signal", "Number", "", "0.50", "", "", "","",false,false); parameters.push_back(psignal);
                CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "","",false,false); parameters.push_back(pnoise);
                CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(pallfiles);
                CommandParameter psignal("signal", "Number", "", "0.50", "", "", "","",false,false); parameters.push_back(psignal);
                CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "","",false,false); parameters.push_back(pnoise);
                CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(pallfiles);

-        CommandParameter porder("order", "Multiple", "A-B", "A", "", "", "","",false,false, true); parameters.push_back(porder);
+        CommandParameter porder("order", "Multiple", "A-B-I", "A", "", "", "","",false,false, true); parameters.push_back(porder);

                CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfasta);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfasta);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);


@@ -578,7 +578,7 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 
                                        while (!oligosFile.eof())       {       // get rest of line in case there is a primer name = will have the name of the primer
                                                char c = oligosFile.get(); 
 
                                        while (!oligosFile.eof())       {       // get rest of line in case there is a primer name = will have the name of the primer
                                                char c = oligosFile.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;  }
                                        } 

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index a103626f7dd9fbed1074f7132175651360bfe464..2c88bef2d036e798a0e84a85d0af1120c3fdd6df 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -1533,7 +1533,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                        // get rest of line in case there is a primer name
                                        while (!inOligos.eof()) {       
                                                char c = inOligos.get(); 
                                        // get rest of line in case there is a primer name
                                        while (!inOligos.eof()) {       
                                                char c = inOligos.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;  }
                                        }