From 01b7dae5525a480d31a1de5bc273692726da8570 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Wed, 30 Mar 2011 13:33:57 +0000
Subject: [PATCH] fixed problem with sffinfo that caused a file mismatch when
 the trimming trimmed the entire sequence.  in trim.seqs checked for blank
 primer name to remove extra .

---
 sffinfocommand.cpp  | 5 ++++-
 sffinfocommand.h    | 1 +
 trimseqscommand.cpp | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 2caad96..f9f6db6 100644
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -356,8 +356,9 @@ int SffInfoCommand::extractSffInfo(string input, string accnos){
 		
 		CommonHeader header; 
 		readCommonHeader(in, header);
-		
+	
 		int count = 0;
+		mycount = 0;
 		
 		//check magic number and version
 		if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); return count; }
@@ -392,6 +393,7 @@ int SffInfoCommand::extractSffInfo(string input, string accnos){
 			}
 			
 			count++;
+			mycount++;
 		
 			//report progress
 			if((count+1) % 10000 == 0){	m->mothurOut(toString(count+1)); m->mothurOutEndLine();		}
@@ -788,6 +790,7 @@ int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& heade
 		
 		if (trim) {
 			if(header.clipQualRight < header.clipQualLeft){
+				out << ">" << header.name << " xy=" << header.xy << endl;
 				out << "0\t0\t0\t0";
 			}
 			else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
diff --git a/sffinfocommand.h b/sffinfocommand.h
index d98edbd..0fdf6fc 100644
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -76,6 +76,7 @@ private:
 	string sffFilename, sfftxtFilename, outputDir, accnosName;
 	vector<string> filenames, outputNames, accnosFileNames;
 	bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
+	int mycount;
 	set<string> seqNames;
 	map<string, vector<string> > outputTypes;
 	
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 0734a88..6924ffc 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -597,7 +597,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 					
 					if(barcodes.size() != 0){
 						string thisGroup = barcodeNameVector[barcodeIndex];
-						if (primers.size() != 0) { thisGroup += "." + primerNameVector[primerIndex]; }
+						if (primers.size() != 0) {  if (primerNameVector[primerIndex] != "") { thisGroup += "." + primerNameVector[primerIndex]; } }
 						
 						outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
 						
-- 
2.39.2