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

[mothur.git] / sffinfocommand.cpp

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";                             }