paralellized seq.error and dist.shared added some error checks to libshuff and dist...

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index ad9698b695815cc77459cc85d2cca1ec7cd24f67..a4697ca3fded8c34ec5320630a588e243601373d 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -25,7 +25,8 @@ vector<string> GetSeqsCommand::setParameters(){
                CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-               
+               CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos2);
+
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
                return myArray;
@@ -232,6 +233,11 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                        if (qualfile == "not open") { abort = true; }
                        else if (qualfile == "not found") {  qualfile = "";  }
                        
+                       accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
+                       if (accnosfile2 == "not open") { abort = true; }
+                       else if (accnosfile2 == "not found") {  accnosfile2 = "";  }
+                       
+                       
                        string usedDups = "true";
                        string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "true"; usedDups = ""; }
                        dups = m->isTrue(temp);
@@ -824,7 +830,15 @@ int GetSeqsCommand::compareAccnos(){
                        in >> name;
                        
                        if (namesAccnos.count(name) == 0){ //name unique to accnos2
-                               namesAccnos2.insert(name);
+                               int pos = name.find_last_of('_');
+                               string tempName = name;
+                               if (pos != string::npos) {  tempName = tempName.substr(pos+1); cout << tempName << endl; }
+                               if (namesAccnos.count(tempName) == 0){
+                                       namesAccnos2.insert(name);
+                               }else { //you are in both so erase
+                                       namesAccnos.erase(name);
+                                       namesDups.insert(name);
+                               }
                        }else { //you are in both so erase
                                namesAccnos.erase(name);
                                namesDups.insert(name);