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#include "readLoad.h"
#include "ErrorWarning.h"
int readLoad(istream& readInStream, Parameters& P, uint& Lread, uint& LreadOriginal, \
char* readName, char* Seq, char* SeqNum, char* Qual, vector<ClipMate> &clipOneMate, \
uint &iReadAll, uint32 &readFilesIndex, char &readFilter, string &readNameExtra)
{//load one read from a stream
int readFileType=0;
if (readInStream.peek()!='@' && readInStream.peek()!='>')
return -1; //end of the stream
string line1;
getline(readInStream, line1); //read 1st line
istringstream line1str(line1);
readName[0]=0;//clear char array
line1str >> readName; //TODO check that it does not overflow the array
if (strlen(readName)>=DEF_readNameLengthMax-1) {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR in reads input: read name is too long:" << readInStream.gcount()<<"\nRead Name="<<readName<<"\nDEF_readNameLengthMax="<<DEF_readNameLengthMax<<'\n';
errOut << "SOLUTION: increase DEF_readNameLengthMax in IncludeDefine.h and re-compile STAR\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
line1str >> iReadAll >> readFilter >> readFilesIndex; //extract read number TODO this is needed only for one mate
line1str >> std::ws; //skip whitespace before readNameExtra
getline(line1str, readNameExtra);
readInStream.getline(Seq,DEF_readSeqLengthMax+1); //extract sequence
Lread=readInStream.gcount()-1;
if (Lread<1) {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR in reads input: short read sequence line: " << Lread <<"\n";
errOut << "Read Name="<< readName <<'\n'<< "Read Sequence=\"" << Seq <<"\"\nDEF_readNameLengthMax="<< DEF_readNameLengthMax <<'\n'<< "DEF_readSeqLengthMax="<<DEF_readSeqLengthMax<<'\n';
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
if (Lread>DEF_readSeqLengthMax) {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR in reads input: Lread>=" << Lread << " while DEF_readSeqLengthMax=" << DEF_readSeqLengthMax <<'\n'<< "Read Name="<<readName<<'\n';
errOut << "SOLUTION: increase DEF_readSeqLengthMax in IncludeDefine.h and re-compile STAR\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
LreadOriginal=Lread;
convertNucleotidesToNumbers(Seq,SeqNum,Lread);
if (readName[0]=='@') {//fastq format: read the '+' line
readFileType=2;
readInStream.get(clipOneMate[0].clippedInfo); //this is used if clipChunk is activated, only 5' for now
readInStream.ignore(); //ignore one char: \n
};
//cout << readName <<'\t' << (uint32) line3char << '\n';
clipOneMate[0].clip(Lread, SeqNum); //5p clip
clipOneMate[1].clip(Lread, SeqNum); //3p clip
if (readName[0]=='@') {//fastq format, read qualities
readInStream.getline(Qual,DEF_readSeqLengthMax);//read qualities
if ((uint) readInStream.gcount() != LreadOriginal+1) {//inconsistent read sequence and quality
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR in reads input: quality string length is not equal to sequence length\n";
errOut << readName <<'\n'<< Seq <<'\n'<< Qual <<'\n'<< "SOLUTION: fix your fastq file\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
if (P.outQSconversionAdd!=0) {
for (uint ii=0;ii<LreadOriginal;ii++) {
int qs=int(Qual[ii])+P.outQSconversionAdd;
if (qs<33) {
qs=33;
} else if (qs>126) {
qs=126;
};
Qual[ii]=qs;
};
};
} else if (readName[0]=='>') {//fasta format, assign Qtop to all qualities
readFileType=1;
for (uint ii=0;ii<LreadOriginal;ii++)
Qual[ii]='A';
Qual[LreadOriginal]=0;
} else {//wrong header
ostringstream errOut;
errOut <<"Unknown reads file format: header line does not start with @ or > : "<< readName<<"\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
//trim read name TODO this is needed only for one mate
for (uint ii=0; ii<P.readNameSeparatorChar.size(); ii++) {
char* pSlash=strchr(readName,P.readNameSeparatorChar.at(ii)); //trim everything after ' '
if (pSlash!=NULL) *pSlash=0;
};
return readFileType;
};
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