mods to trim.seqs

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 2ad4f0607a24c23506109745553d608544a43d6c..7f82366331830baf3ca6640b2af83073662ec9f6 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -14,7 +14,7 @@
 
 vector<string> TrimSeqsCommand::getValidParameters(){  
        try {
-               string Array[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "group","minlength", "maxlength", "qfile", 
+               string Array[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop","minlength", "maxlength", "qfile", 
                                                                        "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage",
                                                                        "keepfirst", "removelast",
                                                                        "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
@@ -35,7 +35,6 @@ TrimSeqsCommand::TrimSeqsCommand(){
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
                outputTypes["qual"] = tempOutNames;
-               outputTypes["group"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
@@ -83,7 +82,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string AlignArray[] =  {        "fasta", "flip", "oligos", "maxambig", "maxhomop", "group","minlength", "maxlength", "qfile", 
+                       string AlignArray[] =  {        "fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile", 
                                                                "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage",
                                                                "keepfirst", "removelast",
                                                                "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
@@ -105,7 +104,6 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        vector<string> tempOutNames;
                        outputTypes["fasta"] = tempOutNames;
                        outputTypes["qual"] = tempOutNames;
-                       outputTypes["group"] = tempOutNames;
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
@@ -136,13 +134,6 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                                        if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
                                }
                                
-                               it = parameters.find("group");
-                               //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["group"] = inputDir + it->second;            }
-                               }
                        }
 
                        
@@ -170,10 +161,6 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        else if(temp == "not open"){    abort = true;   } 
                        else                                    {       oligoFile = temp;               }
                        
-                       temp = validParameter.validFile(parameters, "group", true);
-                       if (temp == "not found"){       groupfile = "";         }
-                       else if(temp == "not open"){    abort = true;   } 
-                       else                                    {       groupfile = temp;               }
                        
                        temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
                        convert(temp, maxAmbig);  
@@ -268,9 +255,8 @@ void TrimSeqsCommand::help(){
        try {
                m->mothurOut("The trim.seqs command reads a fastaFile and creates 2 new fasta files, .trim.fasta and scrap.fasta, as well as group files if you provide and oligos file.\n");
                m->mothurOut("The .trim.fasta contains sequences that meet your requirements, and the .scrap.fasta contains those which don't.\n");
-               m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, group, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast and allfiles.\n");
+               m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast and allfiles.\n");
                m->mothurOut("The fasta parameter is required.\n");
-               m->mothurOut("The group parameter allows you to enter a group file for your fasta file.\n");
                m->mothurOut("The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n");
                m->mothurOut("The oligos parameter allows you to provide an oligos file.\n");
                m->mothurOut("The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n");