sffinfo command is working

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index b4cdf615678e4de6cec3a9f9ffd3d30ae089314c..9c96491e4f970b7d681f79d6dee58b4c47fc39e0 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -146,6 +146,9 @@ int SffInfoCommand::extractSffInfo(string input, string output){
                CommonHeader header; 
                readCommonHeader(in, header);
                
+               //print common header
+               printCommonHeader(out, header);
+               
                int count = 0;
                
                //check magic number and version
@@ -154,9 +157,7 @@ int SffInfoCommand::extractSffInfo(string input, string output){
                
                //read through the sff file
                while (!in.eof()) {
-                       //print common header
-                       printCommonHeader(out, header);
-
+                       
                        //read header
                        Header readheader;
                        readHeader(in, readheader);
@@ -253,14 +254,14 @@ int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
                        if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead);  }
                        
                        //read key
-                       char myAlloc [header.keyLength];
-                       in.read(myAlloc, header.keyLength);
-                       header.keySequence = myAlloc;
+                       char tempBuffer2 [header.keyLength];
+                       in.read(tempBuffer2, header.keyLength);
+                       header.keySequence = tempBuffer2;
                        if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength);  }
                                
                        /* Pad to 8 chars */
                        int spotInFile = in.tellg();
-                       int spot = (spotInFile + 7)& ~7;
+                       int spot = (spotInFile + 7)& ~7;  // ~ inverts
                        in.seekg(spot);
                        
                }else{
@@ -416,9 +417,17 @@ int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {
 int SffInfoCommand::printHeader(ofstream& out, Header& header) {
        try {
                out << ">" << header.name << endl;
-               out << "Read Header Length: " << header.headerLength << endl;
+               out << "Run Prefix: " << endl;
+               out << "Region #:  " << endl;
+               out << "XY Location: " << endl << endl;
+               
+               out << "Run Name:  " << endl;
+               out << "Analysis Name:  " << endl;
+               out << "Full Path: " << endl << endl;
+               
+               out << "Read Header Len: " << header.headerLength << endl;
                out << "Name Length: " << header.nameLength << endl;
-               out << "Number of Bases: " << header.numBases << endl;
+               out << "# of Bases: " << header.numBases << endl;
                out << "Clip Qual Left: " << header.clipQualLeft << endl;
                out << "Clip Qual Right: " << header.clipQualRight << endl;
                out << "Clip Adap Left: " << header.clipAdapterLeft << endl;