changed sffinfo flow default to true. fixed bug in trim.seqs and filter.seqs related...

diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp
index fa9f7231228d92585edabe144d9434b04b5be058..b67c6ea02c5b71befcd467127b0db554f124cb4b 100644 (file)
--- a/cooccurrencecommand.cpp
+++ b/cooccurrencecommand.cpp
@@ -33,8 +33,16 @@ vector<string> CooccurrenceCommand::setParameters() {
 //**********************************************************************************************************************
 string CooccurrenceCommand::getHelpString(){   
        try {
-               string helpString = "help!";
-
+               string helpString = "The cooccurrence command calculates four metrics and tests their significance to assess whether presence-absence patterns are different than what one would expect by chance.";
+        helpString += "The cooccurrence command parameters are shared, metric, matrixmodel, iters, label and groups.";
+        helpString += "The matrixmodel parameter options are sim1, sim2, sim3, sim4, sim5, sim6, sim7, sim8 and sim9. Default=sim2";
+        helpString += "The metric parameter options are cscore, checker, combo and vratio. Default=cscore";
+        helpString += "The label parameter is used to analyze specific labels in your input.\n";
+               helpString += "The groups parameter allows you to specify which of the groups you would like analyzed.\n";
+        helpString += "The cooccurrence command should be in the following format: \n";
+               helpString += "cooccurrence(shared=yourSharedFile) \n";
+               helpString += "Example cooccurrence(shared=final.an.shared).\n";
+               helpString += "Note: No spaces between parameter labels (i.e. shared), '=' and parameters (i.e.yourShared).\n";
                return helpString;
        }
        catch(exception& e) {

diff --git a/cooccurrencecommand.h b/cooccurrencecommand.h
index da7cde84a5372acb083e509b0fb0a997039ad835..8f60e08330ced9099c8b3b777e618a94ca2f9ed1 100644 (file)
--- a/cooccurrencecommand.h
+++ b/cooccurrencecommand.h
@@ -30,7 +30,7 @@ public:
        string getCommandCategory()             { return "Hypothesis Testing";  }
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Cooccurrence"; }
-       string getDescription()         { return "Cooccurrence"; }
+       string getDescription()         { return "calculates four metrics and tests their significance to assess whether presence-absence patterns are different than what one would expect by chance."; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 806ca0d69cabd6056de8ce1870c628e40916e080..9096bb671c830a7f5b0b3638ef0ef0a1d0a5f65d 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -420,7 +420,19 @@ int FilterSeqsCommand::filterSequences() {
                                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
                                
 #else
-                       vector<unsigned long long> positions = savedPositions[s];
+            
+            vector<unsigned long long> positions;
+            if (savedPositions.size() != 0) { positions = savedPositions[s]; }
+            else {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                               positions = m->divideFile(fastafileNames[s], processors);
+#else
+                if(processors != 1){
+                    int numFastaSeqs = 0;
+                    positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs); 
+                }
+#endif
+            }
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                        //vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
                        

diff --git a/linearalgebra.cpp b/linearalgebra.cpp
index 0269fc49d3ddbf5c661fc99d21e2ef5ac4e5a1f3..2e0321e53bb8f601fcaff916db5534cc217709be 100644 (file)
--- a/linearalgebra.cpp
+++ b/linearalgebra.cpp
@@ -9,6 +9,7 @@
 
 #include "linearalgebra.h"
 
+// This class references functions used from "Numerical Recipes in C++" //
 /*********************************************************************************************************************************/
 
 inline double SIGN(const double a, const double b)

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 4965cfd75e06c9f8ba8157056922514581e3e10e..e008ce47d2153530af1c0ab09a585a94d4963662 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -16,7 +16,7 @@ vector<string> SffInfoCommand::setParameters(){
                CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
                CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
                CommandParameter psfftxt("sfftxt", "String", "", "", "", "", "",false,false); parameters.push_back(psfftxt);
-               CommandParameter pflow("flow", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflow);
+               CommandParameter pflow("flow", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pflow);
                CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(ptrim);
                CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pfasta);
                CommandParameter pqfile("name", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pqfile);
@@ -41,7 +41,7 @@ string SffInfoCommand::getHelpString(){
                helpString += "The sff parameter allows you to enter the sff file you would like to extract data from.  You may enter multiple files by separating them by -'s.\n";
                helpString += "The fasta parameter allows you to indicate if you would like a fasta formatted file generated.  Default=True. \n";
                helpString += "The qfile parameter allows you to indicate if you would like a quality file generated.  Default=True. \n";
-               helpString += "The flow parameter allows you to indicate if you would like a flowgram file generated.  Default=False. \n";
+               helpString += "The flow parameter allows you to indicate if you would like a flowgram file generated.  Default=True. \n";
                helpString += "The sfftxt parameter allows you to indicate if you would like a sff.txt file generated.  Default=False. \n";
                helpString += "If you want to parse an existing sfftxt file into flow, fasta and quality file, enter the file name using the sfftxt parameter. \n";
                helpString += "The trim parameter allows you to indicate if you would like a sequences and quality scores trimmed to the clipQualLeft and clipQualRight values.  Default=True. \n";
@@ -256,7 +256,7 @@ SffInfoCommand::SffInfoCommand(string option)  {
                        temp = validParameter.validFile(parameters, "fasta", false);                            if (temp == "not found"){       temp = "T";                             }
                        fasta = m->isTrue(temp); 
                        
-                       temp = validParameter.validFile(parameters, "flow", false);                                     if (temp == "not found"){       temp = "F";                             }
+                       temp = validParameter.validFile(parameters, "flow", false);                                     if (temp == "not found"){       temp = "T";                             }
                        flow = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "trim", false);                                     if (temp == "not found"){       temp = "T";                             }

diff --git a/sortseqscommand.cpp b/sortseqscommand.cpp
index 2c9e85404c86380232e96d3fb0fa9387ffef6a86..0236a505d7dafb683ebe188bbad768a88ca5a5c3 100644 (file)
--- a/sortseqscommand.cpp
+++ b/sortseqscommand.cpp
@@ -232,7 +232,7 @@ int SortSeqsCommand::execute(){
                //read through the correct file and output lines you want to keep
         if (accnosfile != "")          {               readAccnos();   }
                if (fastafile != "")            {               readFasta();    }
-        if (flowfile != "")         {          readFlow();     }
+        if (flowfile != "")         {          readFlow();     }
         if (qualfile != "")                    {               readQual();             }
         if (namefile != "")                    {               readName();             }
                if (groupfile != "")            {               readGroup();    }

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index f55272e5b08a0b6e84a3052be2eabbcc22b170f3..9913727dcdc8257816e1f83fab2f8a4b903ff1cd 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -371,7 +371,7 @@ int TrimSeqsCommand::execute(){
                                outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
                        }
                }
-               
+       
         //fills lines and qlines
                setLines(fastaFile, qFileName);
                
@@ -1071,8 +1071,6 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
                //set file positions for fasta file
                fastaFilePos = m->divideFile(filename, processors);
                
-               if (qfilename == "") { return processors; }
-               
                //get name of first sequence in each chunk
                map<string, int> firstSeqNames;
                for (int i = 0; i < (fastaFilePos.size()-1); i++) {
@@ -1085,59 +1083,61 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
                
                        in.close();
                }
-                               
-               //seach for filePos of each first name in the qfile and save in qfileFilePos
-               ifstream inQual;
-               m->openInputFile(qfilename, inQual);
-               
-               string input;
-               while(!inQual.eof()){   
-                       input = m->getline(inQual);
-
-                       if (input.length() != 0) {
-                               if(input[0] == '>'){ //this is a sequence name line
-                                       istringstream nameStream(input);
-                                       
-                                       string sname = "";  nameStream >> sname;
-                                       sname = sname.substr(1);
-                                       
-                                       map<string, int>::iterator it = firstSeqNames.find(sname);
-                                       
-                                       if(it != firstSeqNames.end()) { //this is the start of a new chunk
-                                               unsigned long long pos = inQual.tellg(); 
-                                               qfileFilePos.push_back(pos - input.length() - 1);       
-                                               firstSeqNames.erase(it);
-                                       }
-                               }
-                       }
-                       
-                       if (firstSeqNames.size() == 0) { break; }
-               }
-               inQual.close();
-               
-               
-               if (firstSeqNames.size() != 0) { 
-                       for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
-                               m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
-                       }
-                       qFileName = "";
-                       return processors;
-               }
-
-               //get last file position of qfile
-               FILE * pFile;
-               unsigned long long size;
-               
-               //get num bytes in file
-               pFile = fopen (qfilename.c_str(),"rb");
-               if (pFile==NULL) perror ("Error opening file");
-               else{
-                       fseek (pFile, 0, SEEK_END);
-                       size=ftell (pFile);
-                       fclose (pFile);
-               }
                
-               qfileFilePos.push_back(size);
+               if(qfilename != "")     {
+            //seach for filePos of each first name in the qfile and save in qfileFilePos
+            ifstream inQual;
+            m->openInputFile(qfilename, inQual);
+            
+            string input;
+            while(!inQual.eof()){      
+                input = m->getline(inQual);
+                
+                if (input.length() != 0) {
+                    if(input[0] == '>'){ //this is a sequence name line
+                        istringstream nameStream(input);
+                        
+                        string sname = "";  nameStream >> sname;
+                        sname = sname.substr(1);
+                        
+                        map<string, int>::iterator it = firstSeqNames.find(sname);
+                        
+                        if(it != firstSeqNames.end()) { //this is the start of a new chunk
+                            unsigned long long pos = inQual.tellg(); 
+                            qfileFilePos.push_back(pos - input.length() - 1);  
+                            firstSeqNames.erase(it);
+                        }
+                    }
+                }
+                
+                if (firstSeqNames.size() == 0) { break; }
+            }
+            inQual.close();
+            
+            
+            if (firstSeqNames.size() != 0) { 
+                for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
+                    m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
+                }
+                qFileName = "";
+                return processors;
+            }
+            
+            //get last file position of qfile
+            FILE * pFile;
+            unsigned long long size;
+            
+            //get num bytes in file
+            pFile = fopen (qfilename.c_str(),"rb");
+            if (pFile==NULL) perror ("Error opening file");
+            else{
+                fseek (pFile, 0, SEEK_END);
+                size=ftell (pFile);
+                fclose (pFile);
+            }
+            
+            qfileFilePos.push_back(size);
+        }
         
         for (int i = 0; i < (fastaFilePos.size()-1); i++) {
                        lines.push_back(linePair(fastaFilePos[i], fastaFilePos[(i+1)]));