worked on trim.seqs - added in the groupfiles for allfiles=t, cleaned up the outputNa...

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index abfe15a17a18d9e203be7bc4bfaac0fd0e6b4a0f..6aea7d827b5a3acab51a330958fb62bacaaa16d0 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -352,7 +352,6 @@ int TrimSeqsCommand::execute(){
                if (m->control_pressed) {  return 0; }                  
                        
                if(allFiles){
-                       //clear out all old group files
                        map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
                        map<string, string>::iterator it;
                        set<string> namesToRemove;

diff --git a/trimseqscommand.h b/trimseqscommand.h
index d43eaa484aad5be4403d7967a6abda1e066a127c..c5cbd3da1b0044467e8558a5619dc651434bcffe 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -69,6 +69,7 @@ private:
        map<string, int> groupToIndex;
        vector<string> primerNameVector;        //needed here?
        vector<string> barcodeNameVector;       //needed here?
+       vector<int> groupCounts;  //same order as barcodeNameVector
 
        vector<int> processIDS;   //processid
        vector<linePair*> lines;