added shhh.seqs command

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 66409e88f9013abd8deb9fd2ba78f6bfdf249a38..3562dcc3e88265a93c23af38fa69b3b2c776e4c1 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -316,7 +316,7 @@ int SffInfoCommand::extractSffInfo(string input, string accnos){
                if (sfftxt) { m->openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint);  outputNames.push_back(sfftxtFileName);  outputTypes["sfftxt"].push_back(sfftxtFileName); }
                if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
                if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qual"].push_back(outQualFileName);  }
-               if (flow)       { m->openOutputFile(outFlowFileName, outFlow);          outputNames.push_back(outFlowFileName);  outputTypes["flow"].push_back(outFlowFileName);  }
+               if (flow)       { m->openOutputFile(outFlowFileName, outFlow);          outputNames.push_back(outFlowFileName);  outFlow.setf(ios::fixed, ios::floatfield); outFlow.setf(ios::showpoint); outputTypes["flow"].push_back(outFlowFileName);  }
                
                ifstream in;
                in.open(input.c_str(), ios::binary);
@@ -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()) {
                        
@@ -778,10 +779,16 @@ int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& heade
 //**********************************************************************************************************************
 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
        try {
+               if(header.clipQualRight > header.clipQualLeft){
+                       
+                       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;
+               }
                
-               out << ">" << header.name << " xy=" << header.xy << endl;
-               for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
-               out << endl;
                
                return 0;
        }