sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / setcurrentcommand.cpp

diff --git a/setcurrentcommand.cpp b/setcurrentcommand.cpp
index 96735405c5e148159ab762a720a93f88ec2354ee..9d277f3e71ae3635d5f14cf468822fa3e1181e8c 100644 (file)
--- a/setcurrentcommand.cpp
+++ b/setcurrentcommand.cpp
@@ -13,31 +13,32 @@
 vector<string> SetCurrentCommand::setParameters(){     
        try {
                
-               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-               CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pflow);
-        CommandParameter pbiom("biom", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pbiom);
-               CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pphylip);
-               CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcolumn);
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pfasta);
-               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
-               CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
-               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
-               CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptaxonomy);
-               CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
-               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);            
-               CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prabund);
-               CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psabund);
-               CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pdesign);
-               CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(porder);
-               CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptree);
-               CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pshared);
-               CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
-               CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prelabund);
-               CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
-               CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
-               CommandParameter pclear("clear", "String", "", "", "", "", "",false,false); parameters.push_back(pclear);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+               CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pflow);
+        CommandParameter pbiom("biom", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pbiom);
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pphylip);
+               CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcolumn);
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pfasta);
+               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pname);
+               CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pgroup);
+               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(plist);
+               CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptaxonomy);
+               CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pqfile);
+               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);         
+               CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prabund);
+               CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psabund);
+               CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pdesign);
+               CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(porder);
+               CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptree);
+               CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pshared);
+               CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pordergroup);
+        CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcount);
+               CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prelabund);
+               CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psff);
+               CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(poligos);
+               CommandParameter pclear("clear", "String", "", "", "", "", "","",false,false); parameters.push_back(pclear);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -53,7 +54,7 @@ string SetCurrentCommand::getHelpString(){
        try {
                string helpString = "";
                helpString += "The set.current command allows you to set the current files saved by mothur.\n";
-               helpString += "The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, biom and taxonomy.\n";
+               helpString += "The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, biom, count and taxonomy.\n";
                helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
                helpString += "The set.current command should be in the following format: \n";
                helpString += "set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n";
@@ -210,6 +211,14 @@ SetCurrentCommand::SetCurrentCommand(string option)  {
                                        if (path == "") {       parameters["ordergroup"] = 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;            }
+                               }
+                
                                it = parameters.find("relabund");
                                //user has given a template file
                                if(it != parameters.end()){ 
@@ -318,6 +327,11 @@ SetCurrentCommand::SetCurrentCommand(string option)  {
                        if (groupfile == "not open") { m->mothurOut("Ignoring: " + parameters["group"]); m->mothurOutEndLine(); groupfile = ""; }
                        else if (groupfile == "not found") {  groupfile = "";  }
                        if (groupfile != "") { m->setGroupFile(groupfile); }
+            
+            countfile = validParameter.validFile(parameters, "count", true);
+                       if (countfile == "not open") { m->mothurOut("Ignoring: " + parameters["count"]); m->mothurOutEndLine(); countfile = ""; }
+                       else if (countfile == "not found") {  countfile = "";  }
+                       if (countfile != "") { m->setCountTableFile(countfile); }
                        
                        designfile = validParameter.validFile(parameters, "design", true);
                        if (designfile == "not open") { m->mothurOut("Ignoring: " + parameters["design"]); m->mothurOutEndLine(); designfile = ""; }
@@ -460,6 +474,8 @@ int SetCurrentCommand::execute(){
                                        m->setFlowFile("");
                 }else if (types[i] == "biom") {
                                        m->setBiomFile("");
+                }else if (types[i] == "count") {
+                                       m->setCountTableFile("");
                                }else if (types[i] == "processors") {
                                        m->setProcessors("1");
                                }else if (types[i] == "all") {