added shhh.seqs command

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 1a9b73f18c5abd36a0bb6ca98ce9658bda37665a..3562dcc3e88265a93c23af38fa69b3b2c776e4c1 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -331,8 +331,9 @@ int SffInfoCommand::extractSffInfo(string input, string accnos){
                if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); return count; }
        
                //print common header
-               if (sfftxt) { printCommonHeader(outSfftxt, header); }
-       
+               if (sfftxt) {   printCommonHeader(outSfftxt, header);           }
+               if (flow)       {       outFlow << header.numFlowsPerRead << endl;      }
+                       
                //read through the sff file
                while (!in.eof()) {
                        
@@ -779,8 +780,12 @@ int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& heade
 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
        try {
                if(header.clipQualRight > header.clipQualLeft){
-                       out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << " numflows=" << read.flowgram.size() << endl;
-                       for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << ' ';  }
+                       
+                       int rightIndex = 0;
+                       for (int i = 0; i < header.clipQualRight; i++) {  rightIndex +=  read.flowIndex[i];     }
+
+                       out << header.name << ' ' << rightIndex;
+                       for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100);  }
                        out << endl;
                }