working on sffinfo

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 049cea982864ad78ee11b5fdb7cfafc82780ffc7..86635e42481a68a6ec715c005adff14a77ebaad7 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -183,95 +183,95 @@ int SffInfoCommand::extractSffInfo(string input, string output){
        }
 }
 //**********************************************************************************************************************
-int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader*& header){
+int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader* header){
        try {
 
                if (!in.eof()) {
                
                        //read magic number
-                       char* buffer = new char(sizeof(header->magicNumber));
+                       char buffer[sizeof(header->magicNumber)];
                        in.read(buffer, sizeof(header->magicNumber));
-                       header->magicNumber = be_int4(*(unsigned int *)(buffer));
-                       delete[] buffer;
-       //cout << "here " << header->magicNumber << '\t' << in.tellg() << endl;                 
+                       header->magicNumber = be_int4(*(unsigned int *)(&buffer));
+                       //delete[] buffer;
+       cout << "here " << header->magicNumber << '\t' << in.tellg() << endl;                   
                        //read version
                        header->version = new char(4);
                        in.read(header->version, 4);
                        string tempBuf0 = header->version;  //this is in here because the read sometimes tacks on extra chars, not sure why?
                        if (tempBuf0.length() > 4) { tempBuf0 = tempBuf0.substr(0, 4);  strcpy(header->version, tempBuf0.c_str());  }
                        //memcpy(header->version, buffer+4, 4);
-       //cout << "here " << header->version  << '\t' << in.tellg() << endl;    
+       cout << "here " << header->version  << '\t' << in.tellg() << endl;      
                        //read offset
-                       buffer = new char(sizeof(header->indexOffset));
-                       in.read(buffer, sizeof(header->indexOffset));
-                       header->indexOffset =  be_int8(*(unsigned long int *)(buffer));
-                       delete[] buffer;
-       //cout << "here " << header->indexOffset  << '\t' << in.tellg() << endl;                
+                       char buffer2 [sizeof(header->indexOffset)];
+                       in.read(buffer2, sizeof(header->indexOffset));
+                       header->indexOffset =  be_int8(*(unsigned long int *)(&buffer2));
+                       //delete[] buffer;
+       cout << "here " << header->indexOffset  << '\t' << in.tellg() << endl;          
                        //read index length
-                       buffer = new char(sizeof(header->indexLength));
-                       in.read(buffer, sizeof(header->indexLength));
-                       header->indexLength =  be_int4(*(unsigned int *)(buffer));
-                       delete[] buffer;
-       //cout << "here " << header->indexLength << '\t' << in.tellg() << endl;                 
+                       char buffer3 [sizeof(header->indexLength)];
+                       in.read(buffer3, sizeof(header->indexLength));
+                       header->indexLength =  be_int4(*(unsigned int *)(&buffer3));
+                       //delete[] buffer;
+       cout << "here " << header->indexLength << '\t' << in.tellg() << endl;                   
                        //read num reads
-                       buffer = new char(sizeof(header->numReads));
-                       in.read(buffer, sizeof(header->numReads));
-                       header->numReads =  be_int4(*(unsigned int *)(buffer));
-                       delete[] buffer;        
-       //cout << "here " << header->numReads << '\t' << in.tellg() << endl;                    
+                       char buffer4 [sizeof(header->numReads)];
+                       in.read(buffer4, sizeof(header->numReads));
+                       header->numReads =  be_int4(*(unsigned int *)(&buffer4));
+                       //delete[] buffer;      
+       cout << "here " << header->numReads << '\t' << in.tellg() << endl;                      
                        //read header length
-                       buffer = new char(sizeof(header->headerLength));
-                       in.read(buffer, sizeof(header->headerLength));
-                       header->headerLength =  be_int2(*(unsigned short *)(buffer));
-                       delete[] buffer;
-       //cout << "here " << header->headerLength << '\t' << in.tellg() << endl;                        
+                       char buffer5 [sizeof(header->headerLength)];
+                       in.read(buffer5, sizeof(header->headerLength));
+                       header->headerLength =  be_int2(*(unsigned short *)(&buffer5));
+                       //delete[] buffer;
+       cout << "here " << header->headerLength << '\t' << in.tellg() << endl;                  
                        //read key length
-                       buffer = new char(sizeof(header->keyLength));
-                       in.read(buffer, sizeof(header->keyLength));
-                       header->keyLength = be_int2(*(unsigned short *)(buffer));
-                       delete[] buffer;
+                       char buffer6 [sizeof(header->keyLength)];
+                       in.read(buffer6, sizeof(header->keyLength));
+                       header->keyLength = be_int2(*(unsigned short *)(&buffer6));
+                       //delete[] buffer;
        
-//cout << "here " << header->keyLength << '\t' << in.tellg() << endl;
+cout << "here " << header->keyLength << '\t' << in.tellg() << endl;
                        //read number of flow reads
-                       buffer = new char(sizeof(header->numFlowsPerRead));
-                       in.read(buffer, sizeof(header->numFlowsPerRead));
-                       header->numFlowsPerRead =  be_int2(*(unsigned short *)(buffer));
-                       delete[] buffer;
-               //cout << "here " << header->numFlowsPerRead << '\t' << in.tellg() << endl;             
+                       char buffer7 [sizeof(header->numFlowsPerRead)];
+                       in.read(buffer7, sizeof(header->numFlowsPerRead));
+                       header->numFlowsPerRead =  be_int2(*(unsigned short *)(&buffer7));
+                       //delete[] buffer;
+               cout << "here " << header->numFlowsPerRead << '\t' << in.tellg() << endl;               
                        //read format code
                        //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;   
+       cout << "here " << header->flogramFormatCode << '\t' << in.tellg() << endl;     
        
                        //read flow chars
                        //header->numFlowsPerRead = 800;
                        header->flowChars = new char(header->numFlowsPerRead);
-                       buffer = new char(header->numFlowsPerRead);
-       //cout << "here" << endl;
-                       //in.read(header->flowChars, header->numFlowsPerRead); 
+                       //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;
+                       //in.read(buffer, header->numFlowsPerRead); 
+                       //memcpy(header->flowChars, buffer, header->numFlowsPerRead);
+                       //delete[] buffer;
        //cout << "here" << endl;
                        //string tempBuf1 = header->flowChars;
        //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;
                        header->keySequence = new char(header->keyLength);
                        //char* myAlloc = new char(4);
-       //      cout << "here " << endl;                
+               cout << "here " << endl;                
                        in.read(header->keySequence, header->keyLength);
                        string tempBuf2 = header->keySequence;
                        if (tempBuf2.length() > header->keyLength) { tempBuf2 = tempBuf2.substr(0, header->keyLength);  strcpy(header->keySequence, tempBuf2.c_str()); }
-       //cout << "here " << header->keySequence << '\t' << in.tellg() << endl;
+       cout << "here " << header->keySequence << '\t' << in.tellg() << endl;
        
                        /* Pad to 8 chars */
                        int spotInFile = in.tellg();
@@ -294,7 +294,7 @@ int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader*& header){
        }
 }
 //**********************************************************************************************************************
-int SffInfoCommand::readHeader(ifstream& in, Header*& header){
+int SffInfoCommand::readHeader(ifstream& in, Header* header){
        try {
        
                if (!in.eof()) {
@@ -361,7 +361,7 @@ int SffInfoCommand::readHeader(ifstream& in, Header*& header){
        }
 }
 //**********************************************************************************************************************
-int SffInfoCommand::readSeqData(ifstream& in, seqRead*& read, int numFlowReads, int numBases){
+int SffInfoCommand::readSeqData(ifstream& in, seqRead* read, int numFlowReads, int numBases){
        try {
        
                if (!in.eof()) {
@@ -381,10 +381,11 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead*& read, int numFlowReads,
                        //read flowIndex
                        read->flowIndex.resize(numBases);
                        for (int i = 0; i < numBases; i++) {  
-                               buffer = new char(1);
-                               in.read(buffer, 1);
-                               read->flowgram[i] = be_int1(*(unsigned int *)(buffer));
-                               delete[] buffer;
+                               //buffer = new char(1);
+                               char temp;
+                               in.read(&temp, 1);
+                               read->flowgram[i] = be_int1(*(unsigned int *)(&temp));
+                               //delete[] buffer;
                        }
                
                        //read bases

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 6e9d87c30d0898e0b6027bb5d3e4a22bfaa388bd..e33bd59b8559bfda513c07d29f2356831e5cd4c8 100644 (file)
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -28,6 +28,9 @@ struct CommonHeader {
        char flogramFormatCode;
        char* flowChars; //length depends on number flow reads
        char* keySequence; //length depends on key length
+       
+       CommonHeader(){ magicNumber=0; version=NULL; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; flowChars=NULL; keySequence=NULL; }
+       ~CommonHeader() { if (version != NULL) { delete [] version; } if (flowChars != NULL) { delete [] flowChars; } if (keySequence != NULL) { delete [] keySequence; } }
 };
 /**********************************************************/
 struct Header {
@@ -39,6 +42,9 @@ struct Header {
        unsigned short clipAdapterLeft;
        unsigned short clipAdapterRight;
        char* name; //length depends on nameLength
+       
+       Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; name=NULL; }
+       ~Header() { if (name != NULL) { delete [] name; } }
 };
 /**********************************************************/
 struct seqRead {
@@ -46,6 +52,9 @@ struct seqRead {
        vector<unsigned int> flowIndex;
        char* bases;
        vector<unsigned int> qualScores;
+       
+       seqRead() { bases=NULL; }
+       ~seqRead() { if (bases != NULL) { delete [] bases; } }
 };
 /**********************************************************/
 
@@ -63,9 +72,9 @@ private:
        bool abort;
        
        int extractSffInfo(string, string);
-       int readCommonHeader(ifstream&, CommonHeader*&);
-       int readHeader(ifstream&, Header*&);
-       int readSeqData(ifstream&, seqRead*&, int, int);
+       int readCommonHeader(ifstream&, CommonHeader*);
+       int readHeader(ifstream&, Header*);
+       int readSeqData(ifstream&, seqRead*, int, int);
        
        int printCommonHeader(ofstream&, CommonHeader*, bool); //bool is debug mode
        int printHeader(ofstream&, Header*, bool);