}
}
//**********************************************************************************************************************
-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();
}
}
//**********************************************************************************************************************
-int SffInfoCommand::readHeader(ifstream& in, Header*& header){
+int SffInfoCommand::readHeader(ifstream& in, Header* header){
try {
if (!in.eof()) {
}
}
//**********************************************************************************************************************
-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()) {
//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
projects / mothur.git / blobdiff