From: westcott <westcott>
Date: Fri, 4 Mar 2011 15:45:49 +0000 (+0000)
Subject: worked on trim.seqs - added in the groupfiles for allfiles=t, cleaned up the outputNa... 
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=df905918ace8537273616b4120d404ebd29dc9cc

worked on trim.seqs - added in the groupfiles for allfiles=t, cleaned up the outputNames, added sequence group counts
---

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index abfe15a..6aea7d8 100644
--- 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 d43eaa4..c5cbd3d 100644
--- 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;