X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.cpp;h=f9f6db6cead382e12e85068ac66d56b4b7c7d148;hb=01b7dae5525a480d31a1de5bc273692726da8570;hp=2caad96df797bc2d5dca067a4ae2b3f4a4ebed5c;hpb=d0954e27635712cdbd8b86e3c4510670803a2665;p=mothur.git

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)){