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//
// sffheader.cpp
// Mothur
//
// Created by Sarah Westcott on 6/10/20.
// Copyright © 2020 Schloss Lab. All rights reserved.
//
#include "sffheader.hpp"
//***************************************************************************************
SffCommonHeader::~SffCommonHeader(){
if (entireHeader.size() != 0) {
for (int i = 0; i < entireHeader.size(); i++) { delete[] entireHeader[i]; }
entireHeader.clear();
}
}
//***************************************************************************************
SffCommonHeader::SffCommonHeader(){
try {
m = MothurOut::getInstance();
padSize = 0;
magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlows=0; flogramFormatCode='s';
}
catch(exception& e) {
m->errorOut(e, "SffCommonHeader", "SffCommonHeader");
exit(1);
}
}
//***************************************************************************************
SffCommonHeader::SffCommonHeader(ifstream& in){
try {
m = MothurOut::getInstance();
read(in);
padSize = 0;
magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlows=0; flogramFormatCode='s';
}
catch(exception& e) {
m->errorOut(e, "SffCommonHeader", "SffCommonHeader");
exit(1);
}
}
//**********************************************************************************
bool SffCommonHeader::read(ifstream& in){
try {
bool goodHeader = true;
if (!in.eof()) {
//read magic number
char* magic = new char[4];
in.read(&(*magic), 4);
magicNumber = be_int4(*(unsigned int *)(magic));
entireHeader.push_back(magic);
//read version
char* cversion = new char[4];
in.read(&(*cversion), 4);
entireHeader.push_back(cversion);
version = "";
for (int i = 0; i < 4; i++) { version += toString((int)(cversion[i])); }
//read offset - ignored in print
char buffer2 [8];
in.read(buffer2, 8);
indexOffset = be_int8(*(unsigned long long *)(&buffer2));
//read index length - ignored in print
char buffer3 [4];
in.read(buffer3, 4);
indexLength = be_int4(*(unsigned int *)(&buffer3));
//read num reads - ignored in print and set to samples numReads
char rnumReads[4];
in.read(rnumReads, 4);
numReads = be_int4(*(unsigned int *)(&rnumReads));
if (m->getDebug()) { m->mothurOut("[DEBUG]: numReads = " + toString(numReads) + "\n"); }
//read header length
char* hlength = new char [2];
in.read(&(*hlength), 2);
entireHeader.push_back(hlength);
headerLength = be_int2(*(unsigned short *)(hlength));
//read key length
char* klength = new char [2];
in.read(&(*klength), 2);
entireHeader.push_back(klength);
keyLength = be_int2(*(unsigned short *)(klength));
//read number of flow reads
char* nflows = new char [2];
in.read(&(*nflows), 2);
entireHeader.push_back(nflows);
numFlows = be_int2(*(unsigned short *)(nflows));
//read format code
char* fcode = new char[1];
in.read(&(*fcode), 1);
entireHeader.push_back(fcode);
flogramFormatCode = (int)(fcode[0]);
//read flow chars
char* tempBuffer = new char[numFlows];
in.read(&(*tempBuffer), numFlows);
flowChars = tempBuffer;
if (flowChars.length() > numFlows) { flowChars = flowChars.substr(0, numFlows); }
entireHeader.push_back(tempBuffer);
//read key
char* tempBuffer2 = new char[keyLength];
in.read(&(*tempBuffer2), keyLength);
keySequence = tempBuffer2;
if (keySequence.length() > keyLength) { keySequence = keySequence.substr(0, keyLength); }
entireHeader.push_back(tempBuffer2);
/* Pad to 8 chars */
unsigned long long spotInFile = in.tellg();
unsigned long long spot = (spotInFile + 7)& ~7; // ~ inverts
char* padding = new char[spot-spotInFile];
entireHeader.push_back(padding);
padSize = spot-spotInFile;
//ensure good reset
in.seekg(spot);
//check magic number and version
if (magicNumber != 779314790) { m->mothurOut("[ERROR]: Magic Number is not correct, not a valid .sff file\n"); goodHeader = false; }
if (version != "0001") { m->mothurOut("[ERROR]: Version is not supported, only support version 0001.\n"); goodHeader = false; }
}else{ m->mothurOut("Error reading sff common header.\n"); goodHeader = false; }
return goodHeader;
}
catch(exception& e) {
m->errorOut(e, "SffCommonHeader", "read");
exit(1);
}
}
//****************************************************************************************
void SffCommonHeader::printSampleCommonHeader(ofstream& out, int numReads){
try {
//magic number
out.write(entireHeader[0], 4);
//version
out.write(entireHeader[1], 4);
//offset - read and discard, we will set it to 0
long long offset = 0;
char offsetBuffer[8];
offsetBuffer[0] = (offset >> 56) & 0xFF;
offsetBuffer[1] = (offset >> 48) & 0xFF;
offsetBuffer[2] = (offset >> 40) & 0xFF;
offsetBuffer[3] = (offset >> 32) & 0xFF;
offsetBuffer[4] = (offset >> 24) & 0xFF;
offsetBuffer[5] = (offset >> 16) & 0xFF;
offsetBuffer[6] = (offset >> 8) & 0xFF;
offsetBuffer[7] = offset & 0xFF; //index = 15
out.write(offsetBuffer, 8);
offset = 0;
char readIndexLength[4];
readIndexLength[0] = (offset >> 24) & 0xFF;
readIndexLength[1] = (offset >> 16) & 0xFF;
readIndexLength[2] = (offset >> 8) & 0xFF;
readIndexLength[3] = offset & 0xFF; //index = 19
out.write(readIndexLength, 4);
//change num reads
char numSampleReads[4];
numSampleReads[0] = (numReads >> 24) & 0xFF;
numSampleReads[1] = (numReads >> 16) & 0xFF;
numSampleReads[2] = (numReads >> 8) & 0xFF;
numSampleReads[3] = numReads & 0xFF; //index = 23
out.write(numSampleReads, 4);
//read header length
out.write(entireHeader[2], 2);
//read key length
out.write(entireHeader[3], 2);
//read number of flow reads
out.write(entireHeader[4], 2);
//read format code
out.write(entireHeader[5], 1);
//read flow chars
out.write(entireHeader[6], numFlows);
//read key
out.write(entireHeader[7], keyLength);
/* Pad to 8 chars */
out.write(entireHeader[8], padSize);
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "printSampleCommonHeader");
exit(1);
}
}
//***********************************************************************************
void SffCommonHeader::printSFFTxt(ofstream& out) {
try {
out << "Common Header:\nMagic Number: " << magicNumber << endl;
out << "Version: " << version << endl;
out << "Index Offset: " << indexOffset << endl;
out << "Index Length: " << indexLength << endl;
out << "Number of Reads: " << numReads << endl;
out << "Header Length: " << headerLength << endl;
out << "Key Length: " << keyLength << endl;
out << "Number of Flows: " << numFlows << endl;
out << "Format Code: " << flogramFormatCode << endl;
out << "Flow Chars: " << flowChars << endl;
out << "Key Sequence: " << keySequence << endl << endl;
}
catch(exception& e) {
m->errorOut(e, "SffCommonHeader", "printSFFTxt");
exit(1);
}
}
//***********************************************************************************
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