ifstream in;
in.open(input.c_str(), ios::binary);
- CommonHeader* header = readCommonHeader(in);
+ CommonHeader* header = new CommonHeader();
+ readCommonHeader(in, header);
+ cout << strlen(header->flowChars) << endl;
//cout << "magic = " << header->magicNumber << endl << "version = " << header->version << endl << "index offset = " << header->indexOffset << endl << "index length = "<< header->indexLength << endl << "numreads = " << header->numReads << endl << "header length = " << header->headerLength << endl << "key length = " << header->keyLength << endl;
//cout << "numflowreads = "<< header->numFlowsPerRead << endl << "flow format code = "<< header->flogramFormatCode << endl << "flow chars = " << header->flowChars << endl << "key sequence = " << header->keySequence << endl << endl;
cout << in.tellg() << endl;
//read through the sff file
while (!in.eof()) {
-
+ //print common header
+ printCommonHeader(out, header, true);
+
//read header
- Header* readheader = readHeader(in);
-
- //read data
- seqRead* read = readSeqData(in, header->numFlowsPerRead, readheader->numBases);
+ Header* readheader = new Header();
+ readHeader(in, readheader);
cout << in.tellg() << endl;
- //print common header
- printCommonHeader(out, header, true);
-
//print header
printHeader(out, readheader, true);
+ //read data
+ seqRead* read = new seqRead();
+ readSeqData(in, read, header->numFlowsPerRead, readheader->numBases);
+
+ cout << in.tellg() << endl;
+
//print data
printSeqData(out, read, true);
}
}
//**********************************************************************************************************************
-CommonHeader* SffInfoCommand::readCommonHeader(ifstream& in){
+int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader*& header){
try {
- CommonHeader* header = new CommonHeader();
-
+
if (!in.eof()) {
- string tempBuf = "";
-
+
//read magic number
char* buffer = new char(sizeof(header->magicNumber));
in.read(buffer, sizeof(header->magicNumber));
- header->magicNumber = be_int4(*(uint32_t *)(buffer));
+ 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);
- tempBuf = buffer;
- if (tempBuf.length() > 4) { tempBuf = tempBuf.substr(0, 4); strcpy(header->version, tempBuf.c_str()); }
-
+ string tempBuf0 = header->version;
+ 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;
//read offset
buffer = new char(sizeof(header->indexOffset));
in.read(buffer, sizeof(header->indexOffset));
- header->indexOffset = be_int8(*(uint64_t *)(buffer));
+ header->indexOffset = be_int8(*(unsigned long int *)(buffer));
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(*(uint32_t *)(buffer));
+ header->indexLength = be_int4(*(unsigned int *)(buffer));
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(*(uint32_t *)(buffer));
+ header->numReads = be_int4(*(unsigned int *)(buffer));
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(*(uint16_t *)(buffer));
+ header->headerLength = be_int2(*(unsigned short *)(buffer));
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(*(uint16_t *)(buffer));
+ header->keyLength = be_int2(*(unsigned short *)(buffer));
delete[] buffer;
-
+
+//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(*(uint16_t *)(buffer));
+ header->numFlowsPerRead = be_int2(*(unsigned short *)(buffer));
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(*(uint8_t *)(buffer));
+ header->flogramFormatCode = be_int1(*(char *)(buffer));
delete[] buffer;
-
+ //cout << "here " << header->flogramFormatCode << '\t' << in.tellg() << endl;
+
//read flow chars
+ //header->numFlowsPerRead = 800;
header->flowChars = new char(header->numFlowsPerRead);
- in.read(header->flowChars, header->numFlowsPerRead);
- tempBuf = buffer;
- if (tempBuf.length() > header->numFlowsPerRead) { tempBuf = tempBuf.substr(0, header->numFlowsPerRead); strcpy(header->flowChars, tempBuf.c_str()); }
+ buffer = new char(header->numFlowsPerRead);
+ //cout << "here" << endl;
+ //in.read(header->flowChars, header->numFlowsPerRead);
+ 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;
//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;
in.read(header->keySequence, header->keyLength);
- tempBuf = header->keySequence;
- if (tempBuf.length() > header->keyLength) { tempBuf = tempBuf.substr(0, header->keyLength); strcpy(header->keySequence, tempBuf.c_str()); }
-
+ 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;
+
+ /* Pad to 8 chars */
+ int spotInFile = in.tellg();
+ //cout << spotInFile << endl;
+ int spot = floor((spotInFile + 7) /(float) 8) * 8;
+ //cout << spot << endl;
+ in.seekg(spot);
+
+ //exit(1);
+
}else{
m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
}
- return header;
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "readCommonHeader");
}
}
//**********************************************************************************************************************
-Header* SffInfoCommand::readHeader(ifstream& in){
+int SffInfoCommand::readHeader(ifstream& in, Header*& header){
try {
- Header* header = new Header();
if (!in.eof()) {
string tempBuf = "";
in.read(buffer, sizeof(header->clipAdapterRight));
header->clipAdapterRight = be_int2(*(unsigned short *)(buffer));
delete[] buffer;
-
+
//read name
header->name = new char(header->nameLength);
+ //buffer = new char(header->nameLength);
in.read(header->name, header->nameLength);
- tempBuf = header->name;
- if (tempBuf.length() > header->nameLength) { tempBuf = tempBuf.substr(0, header->nameLength); strcpy(header->name, tempBuf.c_str()); }
-
+ //memcpy(header->name, buffer, header->nameLength);
+ //delete[] buffer;
+
}else{
m->mothurOut("Error reading sff header info."); m->mothurOutEndLine();
}
- return header;
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "readHeader");
}
}
//**********************************************************************************************************************
-seqRead* SffInfoCommand::readSeqData(ifstream& in, int numFlowReads, int numBases){
+int SffInfoCommand::readSeqData(ifstream& in, seqRead*& read, int numFlowReads, int numBases){
try {
- seqRead* read = new seqRead();
if (!in.eof()) {
m->mothurOut("Error reading."); m->mothurOutEndLine();
}
- return read;
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "readSeqData");
projects / mothur.git / blobdiff