working on sffinfo command.

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 66f65ac9f8422eb5a8b8877000228cdabc21b487..049cea982864ad78ee11b5fdb7cfafc82780ffc7 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -167,10 +167,11 @@ int SffInfoCommand::extractSffInfo(string input, string output){
                        
                        //print data
                        printSeqData(out, read, true);
-       
+                       
+                       delete readheader;
+                       delete read;
                }
                
-               
                in.close();
                out.close();
                
@@ -238,10 +239,10 @@ int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader*& header){
                        delete[] buffer;
                //cout << "here " << header->numFlowsPerRead << '\t' << in.tellg() << endl;             
                        //read format code
-                       buffer = new char(sizeof(header->flogramFormatCode));
-                       in.read(buffer, sizeof(header->flogramFormatCode));
-                       header->flogramFormatCode = be_int1(*(char *)(buffer));
-                       delete[] buffer;
+                       //buffer = new char(sizeof(header->flogramFormatCode));
+                       in.read(&header->flogramFormatCode, 1);
+                       header->flogramFormatCode = be_int1(*(char *)(&header->flogramFormatCode));
+                       //delete[] buffer;
        //cout << "here " << header->flogramFormatCode << '\t' << in.tellg() << endl;   
        
                        //read flow chars
@@ -250,6 +251,8 @@ int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader*& header){
                        buffer = new char(header->numFlowsPerRead);
        //cout << "here" << endl;
                        //in.read(header->flowChars, header->numFlowsPerRead); 
+                       //string tempBuf1 = header->flowChars + '\0';  //this is in here because the read sometimes tacks on extra chars, not sure why?
+                       //if (tempBuf0.length() > header->numFlowsPerRead) { tempBuf1 = tempBuf1.substr(0, header->numFlowsPerRead);  strcpy(header->flowChars, tempBuf1.c_str());  }
                        in.read(buffer, header->numFlowsPerRead); 
                        memcpy(header->flowChars, buffer, header->numFlowsPerRead);
                        delete[] buffer;
@@ -258,7 +261,7 @@ int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader*& header){
        //cout << "here " << in.tellg() << endl;
                        //if (tempBuf1.length() > header->numFlowsPerRead) { tempBuf1 = tempBuf1.substr(0, header->numFlowsPerRead);  strcpy(header->flowChars, tempBuf1.c_str()); }
                        
-       //      cout << "here " << header->flowChars << '\t' << in.tellg() << endl;     
+               //cout << "here " << header->flowChars << '\t' << in.tellg() << endl;   
                        //read key
                        //header->keyLength = 4;
        //char* myAlloc2 = new char(4); cout << "alloced" << endl;
@@ -374,8 +377,8 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead*& read, int numFlowReads,
                                read->flowgram[i] = be_int2(*(unsigned short *)(buffer));
                                delete[] buffer;
                        }
-                       
-                       //read flowgram
+       
+                       //read flowIndex
                        read->flowIndex.resize(numBases);
                        for (int i = 0; i < numBases; i++) {  
                                buffer = new char(1);
@@ -383,23 +386,21 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead*& read, int numFlowReads,
                                read->flowgram[i] = be_int1(*(unsigned int *)(buffer));
                                delete[] buffer;
                        }
-                       
+               
                        //read bases
                        read->bases = new char(numBases);
                        in.read(read->bases, numBases);
                        tempBuf = buffer;
                        if (tempBuf.length() > numBases) { tempBuf = tempBuf.substr(0, numBases); strcpy(read->bases, tempBuf.c_str());  }
-                       
 
                        //read flowgram
                        read->qualScores.resize(numBases);
                        for (int i = 0; i < numBases; i++) {  
-                               buffer = new char(1);
-                               in.read(buffer, 1);
-                               read->qualScores[i] = be_int1(*(unsigned int *)(buffer));
-                               delete[] buffer;
+                               char temp;
+                               in.read(&temp, 1);
+                               read->qualScores[i] = be_int1(*(unsigned int *)(&temp));
                        }
-                       
+               
                        /* Pad to 8 chars */
                        int spotInFile = in.tellg();
        cout << spotInFile << endl;