fixed problem with trim.seqs writing over files if barcodes belonged to the same...

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index fab1b645c0934de1bebadcfa26b5876d874cb275..287086a28a3b0b1ecc18b3988f68ef41ec1909dc 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -146,7 +146,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
 void SplitAbundCommand::help(){
        try {
                m->mothurOut("The split.abund command reads a fasta file and a list or a names file splits the sequences into rare and abundant groups. \n");
-               m->mothurOut("The split.abund command parameters are list, name, cutoff, group, label, groups and accnos.\n");
+               m->mothurOut("The split.abund command parameters are fasta, list, name, cutoff, group, label, groups, cutoff and accnos.\n");
                m->mothurOut("The fasta and a list or name parameter are required, and you must provide a cutoff value.\n");
                m->mothurOut("The cutoff parameter is used to qualify what is abundant and rare.\n");
                m->mothurOut("The group parameter allows you to parse a group file into rare and abundant groups.\n");
@@ -155,8 +155,8 @@ void SplitAbundCommand::help(){
                m->mothurOut("The groups parameter allows you to parse the files into rare and abundant files by group.  \n");
                m->mothurOut("For example if you set groups=A-B-C, you will get a .A.abund, .A.rare, .B.abund, .B.rare, .C.abund, .C.rare files.  \n");
                m->mothurOut("If you want .abund and .rare files for all groups, set groups=all.  \n");
-               m->mothurOut("The split.abund command should be used in the following format: split.abund(list=yourListFile, group=yourGroupFile, label=yourLabels, cutoff=yourCutoff).\n");
-               m->mothurOut("Example: split.abundt(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, cutoff=2).\n");
+               m->mothurOut("The split.abund command should be used in the following format: split.abund(fasta=yourFasta, list=yourListFile, group=yourGroupFile, label=yourLabels, cutoff=yourCutoff).\n");
+               m->mothurOut("Example: split.abund(fasta=abrecovery.fasta, list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, cutoff=2).\n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
 
        }

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 580fc22c978e0105b464e214593599fe15970f1d..4947b38ec8acb49ac0925f8b277133cc18196519 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -283,10 +283,13 @@ int TrimSeqsCommand::execute(){
                for(int i=0;i<fastaFileNames.size();i++){
                        ifstream inFASTA;
                        string seqName;
-                       openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
+                       //openInputFile(getRootName(fastaFile) +  groupVector[i] + ".fasta", inFASTA);
+                       openInputFile(fastaFileNames[i], inFASTA);
                        ofstream outGroups;
-                       openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups);
-                       outputNames.push_back(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups");
+                       string outGroupFilename = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "groups";
+                       openOutputFile(outGroupFilename, outGroups);
+                       //openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups);
+                       outputNames.push_back(outGroupFilename);
                        
                        while(!inFASTA.eof()){
                                if(inFASTA.get() == '>'){
@@ -353,15 +356,8 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                for(int i=0;i<line->num;i++){
                                
                        if (m->control_pressed) { 
-                               inFASTA.close(); 
-                               outFASTA.close();
-                               scrapFASTA.close();
-                               if (oligoFile != "") {   outGroups.close();   }
-                               if(qFileName != "")     {       qFile.close();  }
-                               for(int i=0;i<fastaFileNames.size();i++){
-                                       fastaFileNames[i]->close();
-                                       delete fastaFileNames[i];
-                               }       
+                               inFASTA.close(); outFASTA.close(); scrapFASTA.close(); if (oligoFile != "") {    outGroups.close();   } if(qFileName != "")     {       qFile.close();  }
+                               for(int i=0;i<fastaFileNames.size();i++){  fastaFileNames[i]->close(); delete fastaFileNames[i];  }     
                                for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
                                return 0;
                        }
@@ -587,13 +583,13 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*
                                }
                                else if(type == "barcode"){
                                        inOligos >> group;
-                                       barcodes[oligo]=index++;
+                                       barcodes[oligo]=index; index++;
                                        groupVector.push_back(group);
                                        
                                        if(allFiles){
                                                //outFASTAVec.push_back(new ofstream((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta").c_str(), ios::ate));
-                                               outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
-                                               outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
+                                               outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
+                                               outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
                                        }
                                }
                        }