trim.seqs couts

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 944e2cdc0a110828157301f14f2470a06ac3e052..71cf7143c55392208523c390cfb3924304eeede9 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -377,7 +377,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                        int success = 1;
                        
                        Sequence currSeq(inFASTA);
-
+       cout << i << '\t' << currSeq.getName() << endl;
                        string origSeq = currSeq.getUnaligned();
                        if (origSeq != "") {
                                int groupBar, groupPrime;
@@ -583,11 +583,14 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*
                
                while(!inOligos.eof()){
                        inOligos >> type;
-                       
+                                       
                        if(type[0] == '#'){
                                while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
                        }
                        else{
+                               //make type case insensitive
+                               for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
+                               
                                inOligos >> oligo;
                                
                                for(int i=0;i<oligo.length();i++){
@@ -595,7 +598,7 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*
                                        if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
                                }
                                
-                               if(type == "forward"){
+                               if(type == "FORWARD"){
                                        group = "";
                                        
                                        // get rest of line in case there is a primer name
@@ -619,13 +622,14 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*
                                                        outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(index) + "." + group + ".fasta"));
                                                }
                                        }
+
                                }
-                               else if(type == "reverse"){
+                               else if(type == "REVERSE"){
                                        Sequence oligoRC("reverse", oligo);
                                        oligoRC.reverseComplement();
                                        revPrimer.push_back(oligoRC.getUnaligned());
                                }
-                               else if(type == "barcode"){
+                               else if(type == "BARCODE"){
                                        inOligos >> group;
                                        
                                        //check for repeat barcodes