fixed problem with sffinfo that caused a file mismatch when the trimming trimmed...

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 2caad96df797bc2d5dca067a4ae2b3f4a4ebed5c..f9f6db6cead382e12e85068ac66d56b4b7c7d148 100644 (file)
--- 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)){