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#include "Parameters.h"
#include "ErrorWarning.h"
#include "streamFuns.h"
#include <fstream>
#include <sys/stat.h>
#include "serviceFuns.cpp"
void Parameters::readFilesInit()
{//initialize read files - but do not open yet
if (readFilesType.at(0) == "Fastx") {
readFilesTypeN=1;
} else if (readFilesType.at(0) == "SAM"){
readFilesTypeN=10;
readFiles.samAttrKeepAll = false;
readFiles.samAttrKeepNone = false;
if (readFiles.samAttrKeepIn.at(0) == "All") {
readFiles.samAttrKeepAll = true;
} else if (readFiles.samAttrKeepIn.at(0) == "None") {
readFiles.samAttrKeepNone = true;
} else {
for (auto &tag: readFiles.samAttrKeepIn) {
if (tag.size()!=2) {
exitWithError("EXITING because of FATAL PARAMETER ERROR: each SAM tags in --readFilesSAMtagsKeep should contain two letters\n\
SOLUTION: specify only two-letter tags in --readFilesSAMtagsKeep.",
std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
//array<char,2> taga = {tag[0], tag[1]};
uint16_t tagn = * ( (uint16_t*) tag.c_str() );
readFiles.samAttrKeep.insert(tagn);
};
};
} else {
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: unknown/unimplemented value for --readFilesType: "<<readFilesType.at(0) <<"\n";
errOut <<"SOLUTION: specify one of the allowed values: Fastx or SAM\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
readFilesPrefixFinal=(readFilesPrefix=="-" ? "" : readFilesPrefix);
if (readFilesManifest[0]=="-") {//no manifest, file names in readFilesIn
readFilesNames.resize(readFilesIn.size());
for (uint32 imate=0; imate<readFilesNames.size(); imate++) {
splitString(readFilesIn[imate], ',', readFilesNames[imate]);
if (readFilesNames[imate].back().empty()) {//extra comma at the end
readFilesNames[imate].pop_back();
};
if (imate>0 && readFilesNames[imate].size() != readFilesNames[imate-1].size() ) {
ostringstream errOut;
errOut <<"EXITING: because of fatal INPUT ERROR: number of input files for mate" << imate+1 <<"="<< readFilesNames[imate].size() <<" is not equal to that for mate"<< imate-1 <<"="<< readFilesNames[imate-1].size() <<"\n";
errOut <<"Make sure that the number of files in --readFilesIn is the same for both mates\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
for ( auto &fn : readFilesNames[imate] )
fn = readFilesPrefixFinal + fn; //add prefix
};
readFilesN = readFilesNames[0].size();
//read groups
if (outSAMattrRGline.at(0)!="-") {
string linefull;
for (uint ii=0;ii<outSAMattrRGline.size(); ii++) {//concatenate into one line
if (ii==0 || outSAMattrRGline.at(ii)==",") {//start new entry
if (ii>0) ++ii;//skip comma
outSAMattrRGlineSplit.push_back(outSAMattrRGline.at(ii)); //start new RG line with the first field which must be ID:xxx
if (outSAMattrRGlineSplit.back().substr(0,3)!="ID:") {
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: the first word of a line from --outSAMattrRGline="<<outSAMattrRGlineSplit.back()<<" does not start with ID:xxx read group identifier\n";
errOut <<"SOLUTION: re-run STAR with all lines in --outSAMattrRGline starting with ID:xxx\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
outSAMattrRG.push_back(outSAMattrRGlineSplit.back().substr(3)); //this adds the ID field
} else {//keep adding fields to this RG line, until the next comma
outSAMattrRGlineSplit.back()+="\t" + outSAMattrRGline.at(ii);
};
};
};
if (outSAMattrRG.size()>1 && outSAMattrRG.size()!=readFilesN) {
ostringstream errOut;
errOut <<"EXITING: because of fatal INPUT ERROR: number of input read files: "<< readFilesN << " does not agree with number of read group RG entries: "<< outSAMattrRG.size() <<"\n";
errOut <<"Make sure that the number of RG lines in --outSAMattrRGline is equal to either 1, or the number of input read files in --readFilesIn\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
} else if (outSAMattrRG.size()==1) {//use the same read group for all files
for (uint32 ifile=1; ifile<readFilesN; ifile++) {
outSAMattrRG.push_back(outSAMattrRG.at(0));
};
};
} else {//read file names from manifest
//TODO check that outSAMattrRGline and readFilesIn are not set, throw an error
ifstream & rfM = ifstrOpen(readFilesManifest[0], ERROR_OUT, "SOLUTION: check the path and permissions for readFilesManifest = " + readFilesManifest[0], *this);
inOut->logMain << "Reading input file names and read groups from readFileManifest " << readFilesManifest[0] << endl;
readFilesNames.resize(2);
string rfMline;
while (getline(rfM, rfMline)) {
if (rfMline.find_first_not_of(" \t")>=rfMline.size())
continue; //skip blank lines
uint32 itab1=0, itab2=0;
for (uint32 imate=0; imate<2; imate++) {//SE manifest 2nd column contains "-"
itab2=rfMline.find('\t',itab1);
if (itab2>=rfMline.size()) {
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT FILE error: readFileManifest file " << readFilesManifest[0] << " has to contain at least 3 tab separated columns\n";
errOut <<"SOLUTION: fix the formatting of the readFileManifest file: Read1 <tab> Read2 <tab> ReadGroup. For single-end reads, use - in the 2nd column.\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_INPUT_FILES, *this);
};
readFilesNames[imate].push_back( readFilesPrefixFinal + rfMline.substr(itab1,itab2-itab1) );
itab1=itab2+1;
inOut->logMain << readFilesNames[imate].back() <<'\t';
};
outSAMattrRGlineSplit.push_back(rfMline.substr(itab2+1));
if (outSAMattrRGlineSplit.back().substr(0,3)!="ID:")
outSAMattrRGlineSplit.back().insert(0,"ID:");
itab2=outSAMattrRGlineSplit.back().find('\t');
outSAMattrRG.push_back(outSAMattrRGlineSplit.back().substr(3,itab2-3));
inOut->logMain << outSAMattrRGlineSplit.back() <<'\n';
};
rfM.close();
readNends = ( readFilesNames[1][0].back()=='-' ? 1 : 2);
readFilesNames.resize(readNends);//resize if readFilesN=1
readFilesN = readFilesNames[0].size();
};
inOut->logMain << "Number of fastq files for each mate = " << readFilesN << endl;
readFilesCommandString="";
if (readFilesCommand.at(0)=="-") {
if (readFilesN>1)
readFilesCommandString="cat ";//concatenate multiple files
} else {
for (uint ii=0; ii<readFilesCommand.size(); ii++)
readFilesCommandString+=readFilesCommand.at(ii)+" "; //concatenate into one string
};
if (readFilesTypeN==1) {
readNends=readFilesNames.size(); //for now the number of mates is defined by the number of input files
} else if (readFilesTypeN==10) {//find the number of mates from the SAM file
if (readFilesType.size()==2 && readFilesType.at(1)=="SE") {
readNends=1;
} else if (readFilesType.size()==2 && readFilesType.at(1)=="PE") {
readNends=2;
} else {
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: --readFilesType SAM requires specifying SE or PE reads"<<"\n";
errOut <<"SOLUTION: specify --readFilesType SAM SE for single-end reads or --readFilesType SAM PE for paired-end reads\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
};
readNmates=readNends; //this may be changed later if one of the reads is barcode rea
};
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