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containers.cpp
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containers.cpp
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/* sdm: simple demultiplexer
Copyright (C) 2013 Falk Hildebrand
email: [email protected]
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include <mutex>
#include "containers.h"
using namespace std;
void trim(string& str){
// trim trailing spaces
size_t endpos = str.find_last_not_of(" \t");
if( string::npos != endpos )
{
str = str.substr( 0, endpos+1 );
}
// trim leading spaces
size_t startpos = str.find_first_not_of(" \t");
if( string::npos != startpos )
{
str = str.substr( startpos );
}
}
//from http://stackoverflow.com/questions/8888748/how-to-check-if-given-c-string-or-char-contains-only-digits
bool is_digits(const std::string &str)
{
return std::all_of(str.begin(), str.end(), ::isdigit); // C++11
}
//
ReadSubset::ReadSubset(const string inf, const string default_outfile):
RemainderStrPos(-1), newHD(0), outFiles(0), outFilesIdx(0) {
string line;
ifstream in(inf.c_str());
if (!in){
cerr << "Could not find " << inf << " read subset file. Exiting.\n"; exit(90);
}
int ini_ColPerRow(0), cnt(0), skips(0);
//check read subset format
while (!safeGetline(in, line).eof()) {
if (line.substr(0, 1) == "#"){ skips++; continue; }
string segments;
int ColsPerRow = 0; // Initialize counter.
stringstream ss;
ss << line;
while (getline(ss, segments, '\t')) {
ColsPerRow++;
}
if (cnt == 0){
ini_ColPerRow = ColsPerRow;
}
else {
if (ColsPerRow != ini_ColPerRow){
cerr << "Number of columns in read subset file on line " << cnt + skips << " is " << ColsPerRow << ". Expected " << ini_ColPerRow << " columns.\n";
exit(91);
}
if (cnt > 1000){
break;
}
}
cnt++;
}
if (ini_ColPerRow == 0){
cerr << "Read Subset File exists, but appears to be badly formated (0 columns detected). Exiting\n"; exit(92);
}
if (cnt == 0){
cerr << "Read Subset File exists, but appears to be badly formated (0 lines detected). Exiting\n"; exit(92);
}
in.clear();
in.seekg(0, ios::beg);
//extract read subset content
cnt = 0;
map<string, int> tmpFiles;
map<string, int>::iterator tmpFilIT;
unordered_map <string, int>::iterator TarIT;
//parameters were set for in matrix, now read line by line
while (!safeGetline(in, line).eof()) {
// while(getline(in,line,'\n')) {
if (cnt != 0 && line.substr(0, 1) == "#"){ continue; }
if (line.length() < 5){ continue; }
stringstream ss; string segments; int cnt2 = 0;
ss << line;
while (getline(ss, segments, '\t')) {
if (cnt2 == 0){
//free target RD from paired end info
remove_paired_info(segments);
TarIT = Targets.find(segments);
if (TarIT == Targets.end()){
Targets[segments] = cnt;
} else {
break;
}
}
else if (cnt2 == 1){
newHD.push_back(segments);
}
else if (cnt2 == 2){
uint Idx(0);
//1: test if outfile already exists
tmpFilIT = tmpFiles.find(segments);
if (tmpFilIT != tmpFiles.end()){
Idx = (*tmpFilIT).second;
}
else {//create new key
Idx = (uint) outFiles.size();
outFiles.push_back(segments);
tmpFiles[segments] = Idx;
}
//2: add the index to outfile to this position
outFilesIdx.push_back(Idx);
}
cnt2++;
}
if (cnt2 == 1) {//no specific header
newHD.push_back("");
tmpFilIT = tmpFiles.find("Default");
uint Idx(0);
if (tmpFilIT != tmpFiles.end()) {
Idx = (*tmpFilIT).second;
} else {//create new key
Idx = (uint)outFiles.size();
outFiles.push_back("Default");
tmpFiles["Default"] = Idx;
}
outFilesIdx.push_back(Idx);
}
if (cnt2>0) { cnt++; }
}
//is extra file info in read subset file?
if (ini_ColPerRow < 3){
outFilesIdx.resize(Targets.size(), 0);
outFiles.resize(1, default_outfile);
}
}
void ReadSubset::findMatches(shared_ptr<InputStreamer> IS, OutputStreamer* MD, bool mocatFix) {
vector<shared_ptr<DNA>> match; //shared_ptr<DNA> match2(NULL);
bool cont(true), cont2(true);
int idx(0);
int pairs = IS->pairNum();
unordered_map <string, int>::iterator SEEK;
bool b_doHD = newHD.size() > 0;
//bool sync(false);//meaningless placeholder
while (cont) {
match = IS->getDNApairs();
if (match[0] == NULL) { cont = false; break; }
//if (pairs > 1) { match2 = IS->getDNA(cont2, 1); }
string curID = match[0]->getPositionFreeId();
if (mocatFix && curID.length()>5 ) {
curID = header_stem(curID);
//cerr << curID << endl;
//exit(0);
}
//cerr << curID << endl;
SEEK = Targets.find(curID);
if (SEEK == Targets.end()) {//no hit
if (RemainderStrPos != -1) {
MD->writeSelectiveStream(match[0], 0, RemainderStrPos);
if (pairs > 1) {
MD->writeSelectiveStream(match[1], 1, RemainderStrPos);
}
} else {// nothing written, but still need to delete
// delete match; if (pairs > 1) {delete match2;}
}
continue;
}
//serious work
//cerr << "H";
idx = SEEK->second;
if (b_doHD && newHD[idx] != "" && pairs>1) {
match[0]->setHeader(newHD[idx] + "#1:0");
match[1]->setHeader(newHD[idx] + "#2:0");
}
MD->writeSelectiveStream(match[0], 0, outFilesIdx[idx]);
if (pairs > 1) {
MD->writeSelectiveStream(match[1], 1, outFilesIdx[idx]);
}
//finished, clean up to reduce search space (faster??)
Targets.erase(SEEK);
if (Targets.size() == 0 && RemainderStrPos==-1) {
return;
}
}
cerr << Targets.size() << " seqs remaining (not found in current file)\n";
}
OutputStreamer::OutputStreamer(Filters* fil, OptContainer* cmdArgs,
std::ios_base::openmode writeStatus,
shared_ptr<ReadSubset> RDSset,
int numThreads, string fileExt, int forceFmt) :
MFil(nullptr), subFilter(0), //DNAsP1(0), DNAsP2(0), DNAsS1(0), DNAsS2(0),
//DNAsNoHead(0), DNAsP1_alt(0), DNAsP2_alt(0), DNAsS1_alt(0), DNAsS2_alt(0),
//locBufGreen(2,""),
suppressOutWrite(0), write2File(true),// mem_used(false),
DNAinMem(0), writeThreadStatus(0),
fastQver(33),
fastQoutVer(33), BWriteQual(false),
BWriteFastQ(false), b_multiOutStream(false), pairedSeq(-1),
b_changeFQheadVer(false),
b_checkedHeaderChange(false),
b_oneLinerFasta(false), b_doDereplicate(false), b_writeGreenQual(true), b_writeYellowQual(true),
maxReadsPerOFile(0),
demultiBPperSR(0),
BPwrittenInSR(0), BPwrittenInSRmerg(0),
ReadsWritten(0),
maxRdsOut(-1), stopAll(false),
leadingOutf(""), locCmdArgs(cmdArgs), dereplicator(nullptr), cntDerep(0), wrMode(ios::out),
sFile(0), qFile(0), fqFile(0),
sPairFile(0), qPairFile(0), fqPairFile(0),
of_merged_fq(0),
//sFileStr(0), qFileStr(0), fqFileStr(0), fqNoBCFile(0),
totalFileStrms(0),doTIO(true),
bDoDemultiplexIntoFiles(false), demultiSinglFiles(0), //demultiSinglFilesF(0),
demultiMergeFiles(0),
onlyCompletePairsDemulti(false),
b_merge_pairs_demulti_(false), b_merge_pairs_filter_(false),
b_merge_pairs_(false), mergers(0,nullptr),
Nthrds(numThreads),_benchmark(nullptr)
{
MFil = fil;
fastQver = fil->getuserReqFastqVer();
fastQoutVer = fil->getuserReqFastqOutVer();
maxReadsPerOFile = fil->maxReadsOutput();
demultiBPperSR = fil->getDemultiBPperSR();
ReadsWritten = fil->writtenReads();
pairedSeq = MFil->isPaired();
if (cmdArgs->find("-suppressOutput") != cmdArgs->end()) {
suppressOutWrite = atoi( (*cmdArgs)["-suppressOutput"].c_str() );
}
if (cmdArgs->find("-pairedDemulti") != cmdArgs->end() && (*cmdArgs)["-pairedDemulti"] == "1") { //only demultiplex proper pairs
onlyCompletePairsDemulti = true;
}
if (cmdArgs->find("-oneLineFastaFormat") != cmdArgs->end() && (*cmdArgs)["-oneLineFastaFormat"] == "1") {
b_oneLinerFasta = true;
}
if (suppressOutWrite == 3 || suppressOutWrite == 1){
b_writeGreenQual = false;
}
if (suppressOutWrite == 3 || suppressOutWrite == 2){
b_writeYellowQual = false;
}
if (fil->doSubselReads() && RDSset != nullptr ) {
this->openSeveralOutstreams(locCmdArgs,RDSset, writeStatus);
} else {//standard one file output stream
this->openOutStreams(locCmdArgs, MFil->getFileIncrementor(),
writeStatus, fileExt, forceFmt);
}
if ((*cmdArgs)["-o_fastq_noBC"] != "") {
openNoBCoutstrean((*cmdArgs)["-o_fastq_noBC"]);
}
if (cmdArgs->find("-o_demultiplex") != cmdArgs->end()) {//demulti: always write mode out
bool gzDemulti = false;
if (cmdArgs->find("-o_demultiplex_gz") != cmdArgs->end()) {
if ((*cmdArgs)["-o_demultiplex_gz"] == "1") {
gzDemulti = true;
//cerr << "Gzip demulti output\n";
}
else {
//cerr << "\n\nNo Gzip demulti output\n";
}
}
generateDemultiOutFiles((*cmdArgs)["-o_demultiplex"],fil, ios::out, gzDemulti);
}
if (cmdArgs->find("-merge_pairs_filter") != cmdArgs->end()
&& (*cmdArgs)["-merge_pairs_filter"] == "1") {
b_merge_pairs_filter_ = true;
}
if (cmdArgs->find("-merge_pairs_demulti") != cmdArgs->end()
&& (*cmdArgs)["-merge_pairs_demulti"] == "1") {
b_merge_pairs_demulti_ = true;
}
if (b_merge_pairs_demulti_ || b_merge_pairs_filter_) {
b_merge_pairs_ = true;
}
setSubfilters(Nthrds);
if (this->pairedSeq != 2) {
onlyCompletePairsDemulti = false;
}
if ((*cmdArgs)["-threadIO"] == "1") { doTIO = true; }
if ((*cmdArgs)["-threadIO"] == "0") { doTIO = false; }
//threads = futures(num_threads);
//if (pairedSeq){cerr<<"paired MFil\n";}
}
OutputStreamer::~OutputStreamer(){
//delete MFil;
cdbg("Destr OutputStreamer" );
//delAllDNAvectors();
//cdbg(".. done\n" );
dmltMTX.lock();
this->closeOutStreams(true);
closeOutFilesDemulti();
for (uint i=0; i<subFilter.size();i++){
if (subFilter[i] != nullptr) { delete subFilter[i]; }
}
for (size_t x = 0; x < mergers.size(); x++) {
if (mergers[x] != nullptr) { delete mergers[x]; mergers[x] = nullptr; }
}
dmltMTX.unlock();
cdbg("Subfilters deleted, streams closed\n" );
//for (size_t x = 0; x < merger.size(); x++) { delete merger[x]; } merger.clear();
//delete optim;
}
void OutputStreamer::delAllDNAvectors() {
#ifdef DEBUG
cerr << "cleaning MD..";
#endif
//locBufGreen[0].clear(); locBufGreen[1].clear();
//hard delete all saved data, no write to HDD
for (size_t i = 0; i < sFile.size(); i++) {
for (size_t j = 0; j < sFile[i].size(); j++) {
if (sFile[i][j] != nullptr) {
sFile[i][j]->emptyStream();
}
}
}
for (size_t i = 0; i < qFile.size(); i++) {
for (size_t j = 0; j < qFile[i].size(); j++) {
if (qFile[i][j] != nullptr) {
qFile[i][j]->emptyStream();
}
}
}
for (size_t i = 0; i < fqFile.size(); i++) {
for (size_t j = 0; j < fqFile[i].size(); j++) {
if (fqFile[i][j] != nullptr) {
fqFile[i][j]->emptyStream();
}
}
}
//s/q/fqPairFile destructor..
for (size_t i = 0; i < fqPairFile.size(); i++) {
if (fqPairFile[i] != nullptr) {
delete fqPairFile[i];
}
}
for (size_t i = 0; i < qPairFile.size(); i++) {
if (qPairFile[i] != nullptr) {
delete qPairFile[i];
}
}
for (size_t i = 0; i < sPairFile.size(); i++) {
if (sPairFile[i] != nullptr) {
delete sPairFile[i];
}
}
}
void OutputStreamer::analyzeDNA(shared_ptr<DNA> d, int FilterUse, int pair, int& idx, int thr) {
if (!d){
return ;
}
if (d->isFailed()) { return; }
Filters * curFil = this->getFilters(thr);
bool isP1 = max(0, pair) == 0;
if (isP1 && curFil->getcut5PR1()) {
d->cutSeq(0,curFil->getcut5PR1());
} else if (!isP1 && curFil->getcut5PR2()) {
d->cutSeq(0, curFil->getcut5PR2());
}
if ( !curFil->doFilterAtAll() ) {
if (idx < 0 && !isP1 && !curFil->doubleBarcodes()) {
;
} else if (idx < 0) {
idx = curFil->detectCutBC(d, isP1); //still need to check for BC
}
if (idx >= 0) { //prevent second read pair_ from being flagged as true
d->setPassed(true);
}
return;
}
//pricipally safe to call from thread
curFil->checkYellowAndGreen(d, pair, idx, false);
//bit redundant.. but better safe than sorry
if (!curFil->secondaryOutput() && d->isYellowQual() && ! d->isGreenQual()) {
d->failed();
}
if (idx == -1 ) {
d->setBarcodeDetected(false);
}
return;
/*
if (curFil->secondaryOutput() ){
//make this primary routine..
} else if (FilterUse==-1){
curFil->check(d, false, pair, idx);
} else {
cerr << "Invalid control path in analyzeDNA\n"; exit(55);
//Filters* f = subFilter[FilterUse];
//subFilter[FilterUse].check(d, false, pair_, idx);
//f->check(d, false, pair, idx);
}
*/
//count this as failure if BC was present
//d->prepareWrite(fastQoutVer);
}
vector<bool> OutputStreamer::analyzeDNA(shared_ptr<DNA> p1, shared_ptr<DNA> p2, shared_ptr<DNA> mid,
bool changePHead, int FilterUse) {
cerr << "deprecated analuze DNA"; exit(2323);
vector<bool> ret(2, true);
//1st: check if DNA pointer valid
if (p1 == NULL){
ret[0] = false;
}
if (p2 == NULL){
ret[1] = false;
}
if (mid == NULL){//no MID? kill
ret[1] = false; ret[0] = false; return ret;
}
else {
mid->setMIDseq(true);
}
//2nd: check if basic DNA signatures are valid
//3rd: check if all quality criteria are met, BC is true etc.
//if (FilterUse == -1){
//ret = curFil->check_pairs(p1, p2, mid, ret, changePHead);
//} else { //mutithread, to avoid race conditions etc use separate filter
// ret = subFilter[FilterUse]->check_pairs(p1, p2, mid, ret, changePHead);
//}
//if (ret[0]){ p1->prepareWrite(fastQoutVer); }
//if (ret[1]){ p2->prepareWrite(fastQoutVer);}
return ret;
}
bool OutputStreamer::checkFastqHeadVersion(shared_ptr<DNA> d,bool disable) {
if (!b_checkedHeaderChange) {
return b_changeFQheadVer;
}
b_checkedHeaderChange = true;
if (pairedSeq == 1) { b_changeFQheadVer = false; return false; }
drpMTX.lock();
b_changeFQheadVer = false;
int fastQheadVer = 0;
string head = d->getId();
int shouldVer = MFil->FQheadV();
if (head.find("/1") != string::npos || head.find("/2") != string::npos){
fastQheadVer = 1;
}
if (head.find(" 1:") != string::npos|| head.find(" 2:") != string::npos){
fastQheadVer = 2;
}
if (shouldVer!=0 && shouldVer != fastQheadVer){
b_changeFQheadVer=true;
}
bool ret = b_changeFQheadVer;
if (disable){
b_changeFQheadVer = false;
}
drpMTX.unlock();
return ret;
}
void OutputStreamer::closeOutFilesDemulti() {
// cout << "FILES TO t DEMULTIPLEX OUT " << demultiSinglFiles.size() << endl;
//cout << "domeulti: " << bDoDemultiplexIntoFiles << endl;
cdbg("OutputStreamer::closeOutFilesDemulti");
if (!bDoDemultiplexIntoFiles) { return; }
for (size_t i = 0; i < demultiSinglFiles.size(); i++) {
//cout << " do fancy demultiplexing for " << i << endl;
if (demultiSinglFiles[i][0] != nullptr) {
//cout << "yaas" << endl;
delete demultiSinglFiles[i][0];
demultiSinglFiles[i][0] = nullptr;
}
if (demultiSinglFiles[i][1] != nullptr)
{
delete demultiSinglFiles[i][1];
demultiSinglFiles[i][1] = nullptr;
}
}
for (size_t i = 0; i < demultiMergeFiles.size(); i++) {
if (demultiMergeFiles[i] != nullptr) {
delete demultiMergeFiles[i];
demultiMergeFiles[i] = nullptr;
}
}
//cout << " closeOutFilesDemulti" << endl;
return;
}
/*
void OutputStreamer::writeAllStoredDNA(){
#ifdef DEBUG
printStorage();
cerr << "Writting stored DNA" << DNApairStreams[0].size() <<" " << DNApairStreams[1].size()<<endl;
#endif
#ifdef _THREADED
if (writeThreadStatus>0){
if (writeThreadStatus>1){wrThread.join();}
writeThreadStatus++;
wrThread = thread(&OutputStreamer::writeAllStoredDNA2t,this);
} else {
writeAllStoredDNA2();
}
#else
writeAllStoredDNA2();
#endif
}
void OutputStreamer::writeAllStoredDNA2(){
mem_used=false;
//
//this is handled by ofbufstream now..
if (b_writeGreenQual) {
//
if (DNAsP1.size() != DNAsP2.size()) {
for (unsigned int i = 0; i < DNAsP1.size(); i++) {
writeAndDel(DNAsP1[i], 0);
ReadsWritten++;
}
for (unsigned int i = 0; i < DNAsP2.size(); i++) {
writeAndDel(DNAsP2[i], 1);
}
} else {
for (unsigned int i = 0; i < DNAsP1.size(); i++) {
writeAndDel(DNAsP1[i], 0);
writeAndDel(DNAsP2[i], 1);
ReadsWritten++;
}
}
for (unsigned int i = 0; i < DNAsS1.size(); i++) {
writeAndDel(DNAsS1[i], 2);
}
for (unsigned int i = 0; i < DNAsS2.size(); i++) {
writeAndDel(DNAsS2[i], 3);
}
DNAsP1.resize(0); DNAsP2.resize(0);
DNAsS1.resize(0); DNAsS2.resize(0);
}
if (b_writeYellowQual) {
//Xtra file
if (DNAsP1_alt.size() != DNAsP2_alt.size()) {
for (unsigned int i = 0; i < DNAsP1_alt.size(); i++) {
writeAndDel(DNAsP1_alt[i], 0);
ReadsWritten++;
}
for (unsigned int i = 0; i < DNAsP2_alt.size(); i++) {
writeAndDel(DNAsP2_alt[i], 1);
}
} else {
for (unsigned int i = 0; i < DNAsP1_alt.size(); i++) {
writeAndDel(DNAsP1_alt[i], 0);
writeAndDel(DNAsP2_alt[i], 1);
ReadsWritten++;
}
}
for (unsigned int i = 0; i < DNAsS1_alt.size(); i++) {
writeAndDel(DNAsS1_alt[i], 2);
}
for (unsigned int i = 0; i < DNAsS2_alt.size(); i++) {
writeAndDel(DNAsS2_alt[i], 3);
}
DNAsP1_alt.resize(0); DNAsP2_alt.resize(0);
DNAsS1_alt.resize(0); DNAsS2_alt.resize(0);
}
//just to be on the safe side..
delAllDNAvectors();
#ifdef DEBUG
cerr << " .. Finished" << endl;
#endif
}
*/
#ifdef _THREADED
void OutputStreamer::writeAllStoredDNA2t(){
std::lock_guard<std::mutex> guard(mutex);
write2File=true;mem_used=false;
if (DNAsP1.size() != DNAsP2.size()){
for (unsigned int i=0; i<DNAsP1.size();i++){
writeAndDel(DNAsP1[i],0);
}
for (unsigned int i=0; i<DNAsP2.size();i++){
writeAndDel(DNAsP2[i],1);
}
}else {
for (unsigned int i=0; i<DNAsP1.size();i++){
writeAndDel(DNAsP1[i],0);
writeAndDel(DNAsP2[i],1);
}
}
for (unsigned int i=0; i<DNAsS1.size();i++){
writeAndDel(DNAsS1[i],2);
}
for (unsigned int i=0; i<DNAsS2.size();i++){
writeAndDel(DNAsS2[i],3);
}
DNAsP1.resize(0);DNAsP2.resize(0);
DNAsS1.resize(0);DNAsS2.resize(0);
}
#endif
void OutputStreamer::write2Demulti(shared_ptr<DNA> d1, shared_ptr<DNA> d2, int BCoffset,
int curThread) {
if (!this->Demulti2Fls()) {
return;
}
bool demultFini = demultiBPperSR > 0 && (uint)BPwrittenInSR > demultiBPperSR;
bool demultMrgFini = demultiBPperSR > 0 && (uint) BPwrittenInSRmerg > demultiBPperSR;
if (demultFini && demultMrgFini) {
return;
}
int idx = d1->getBCnumber() - BCoffset; //correct for BC offset as well..
if (idx < 0) {
return;
}
bool green1(d1->isGreenQual());
bool green2(false);
if (d2 != nullptr) {
green2 = d2->isGreenQual();
}
bool mergeWr(false);
//merging attempts/prep, requires paired reads
if (this->isPEseq() == 2 &&
(green1 || green2) && b_merge_pairs_demulti_ && d1->merge_seed_pos_ > 0) {
shared_ptr<DNA> dna_merged = mergers[curThread]->merge(d1, d2);
if (dna_merged) {
// write out merged DNA
dna_merged->prepareWrite(fastQoutVer);
//dmltMTX.lock();
*(demultiMergeFiles[idx]) << dna_merged->writeFastQ();
BPwrittenInSRmerg += d1->length();
//dmltMTX.unlock();
//mergeWr = true;
}
}
if (mergeWr) {
return;
}
//check for paired reads
if ((onlyCompletePairsDemulti && (!green1 || !green2) )) {
return;
}
/*
string x = d2->getShortId();
if (x.find("M04428:252:000000000-BM3M5:1:2106:11089:1656") != string::npos) {
bool x = true; // DEBUG
}
/**/
string dn1(""), dn2("");
if (green1) {
//cout << "trouble" << endl;
d1->prepareWrite(fastQoutVer);
//dmltMTX.lock();
BPwrittenInSR += d1->length();
//dmltMTX.unlock();
d1->writeFastQ(dn1,false);
}
if (green2) {
//cout << "trouble" << endl;
d2->prepareWrite(fastQoutVer);
//dmltMTX.lock();
//dmltMTX.unlock();
d2->writeFastQ(dn2,false);
}
//cerr << dn2 << "WEW";
//move them closer together..
dmltMTX.lock();
*(demultiSinglFiles[idx][0]) << dn1;
//cdbg("write2Demulti4"+itos(idx) + "X "+itos(demultiSinglFiles[idx].size())+"Y"+ dn2);
*(demultiSinglFiles[idx][1]) << dn2;
dmltMTX.unlock();
}
void OutputStreamer::write2Demulti(shared_ptr<DNA> d, int p, int BCoffset) {//this->getBCoffset()
if (!this->Demulti2Fls()) {
return;
}
if (demultiBPperSR > 0 && (uint)BPwrittenInSR > demultiBPperSR) {
return;
}
int idx = d->getBCnumber() - BCoffset; //correct for BC offset as well..
if (idx < 0 || !d->isGreenQual()) {
return;
}
d->prepareWrite(fastQoutVer);
*(demultiSinglFiles[idx][p]) << d->writeFastQ(false);
BPwrittenInSR += d->length();
}
void OutputStreamer::generateDemultiOutFiles(string path, Filters* fil,
std::ios_base::openmode writeStatus, bool demulti2gz) {
//fill in demultiSinglFiles vector
vector<ofbufstream*> empVec(2, NULL);
//vector<string> empVec2(2, "");
bool doMC = Nthrds > 1;
string gzSuffiz = "";
string gzReport = "";
if (demulti2gz) {
gzSuffiz = ".gz";
gzReport = "gzipped ";
}
bool displayInfo(false);
if (fil->getReadsWritten() == 0) {
displayInfo = true;
}
struct stat info;
if (stat(path.c_str(), &info) != 0) {
cerr << "Output path for demultiplexed files does not exist, please create this directory:\n" << path << endl;
exit(833);
}
else if (info.st_mode & S_IFDIR) { // S_ISDIR() doesn't exist on my windows
if (displayInfo) {
cerr << "\nWriting " << gzReport << "demultiplexed files to : " << path << endl;// printf(" % s is a directory\n", path);
}
}
else {
cerr << path << " is no directory\n"; exit(834);
}
path += "/";
bDoDemultiplexIntoFiles = true;
bool openOstreams = true; uint ostrCnt(0);
size_t bufS = OUTPUT_BUFFER_SIZE;
//save as .gz? -> no for dada2..
demultiSinglFiles.resize(fil->SampleID.size(), empVec);
demultiMergeFiles.resize(fil->SampleID.size(), nullptr);
//demultiSinglFilesF.resize(fil->SampleID.size(), empVec2);
for (size_t i = 0; i < fil->SampleID.size(); i++) {
//actually needs to know if paired files..
//if (ostrCnt > maxFileStreams) {openOstreams = false;}
if (pairedSeq == 1 || pairedSeq == -1) {
string nfile = path + fil->SampleID[i] + ".fq" + gzSuffiz;
if (openOstreams) {
if (demultiSinglFiles[i][0] != nullptr) { delete demultiSinglFiles[i][0]; }
demultiSinglFiles[i][0] = DBG_NEW ofbufstream(nfile.c_str(), writeStatus, doMC, (size_t)bufS);
}
//demultiSinglFilesF[i][0] = nfile;
ostrCnt++;
}
else {
string nfile = path + fil->SampleID[i] + ".1.fq" + gzSuffiz;
if (openOstreams) {
if (demultiSinglFiles[i][0] != nullptr) { delete demultiSinglFiles[i][0]; }
demultiSinglFiles[i][0] = DBG_NEW ofbufstream(nfile.c_str(), writeStatus, doMC, size_t(bufS * 0.8));
}
//demultiSinglFilesF[i][0] = nfile;
nfile = path + fil->SampleID[i] + ".2.fq" + gzSuffiz;
if (openOstreams) {
if (demultiSinglFiles[i][1] != nullptr) { delete demultiSinglFiles[i][1]; }
demultiSinglFiles[i][1] = DBG_NEW ofbufstream(nfile.c_str(), writeStatus, doMC, size_t(bufS * 1.2)); }
//demultiSinglFilesF[i][1] = nfile;
nfile = path + fil->SampleID[i] + ".merg.fq" + gzSuffiz;
if (openOstreams) {
if (demultiMergeFiles[i] != nullptr) { delete demultiMergeFiles[i]; }
demultiMergeFiles[i] = DBG_NEW ofbufstream(nfile.c_str(), writeStatus, doMC, (size_t)bufS);
}
ostrCnt += 2;
}
}
}
void OutputStreamer::incrementOutputFile(){
//TODO has to be made threadsafe
MFil->incrementFileIncrementor();
this->closeOutStreams(true);
//this is definetely a new file
//TODO needs to be threadsafe
this->openOutStreams(locCmdArgs,MFil->getFileIncrementor(),ios_base::out);
ReadsWritten = 0;
}
// CHECK THIS METHOD AFTER IMPLEMENTING MULTIPLE STATS OBJECTs
//
//void Filters::addToStatistics(shared_ptr<DNA> d, Statistics &statistics) {
// //here should be the only place to count Barcodes!
// statistics.total2++;
// if (d->isGreenQual() || d->isYellowQual()) {
//// this->DNAstatLQ(d, easyPair, d->isYellowQual());
// statistics.totalSuccess++;
// } else {
// statistics.totalRejected++;
// }
//
// //some general stats that always apply:
// if (d->QualCtrl.PrimerFwdFail) {
// statistics.PrimerFail++;
// }
// if (d->QualCtrl.PrimerRevFail) {
// statistics.PrimerRevFail++;
// }
// if (d->QualCtrl.minLqualTrim) {
// statistics.minLqualTrim++;
// }
// if (d->QualCtrl.TagFail) {
// statistics.TagFail++;
// }
// if (d->QualCtrl.fail_correct_BC) {
// statistics.fail_correct_BC++;
// }
// if (d->QualCtrl.suc_correct_BC) {
// statistics.suc_correct_BC++;
// }
// if (d->QualCtrl.RevPrimFound) {
// statistics.RevPrimFound++;
// }
// if (d->QualCtrl.QWinTrimmed || d->QualCtrl.AccErrTrimmed) {
// statistics.Trimmed++;
// }
// if (d->getTA_cut()) {
// statistics.adapterRem++;
// }
//
////exit(0);
//
// if (d->isGreenQual() || d->isYellowQual()) {
//// countBCdetected(d->getBCnumber(), easyPair, false);
// //and register as success
// } else {
// if (d->getBarcodeDetected()) {
// //DNA is no longer useful
//// failedStats2(d, easyPair);
// }
// //delete d;
// if (d->QualCtrl.AvgQual) {
// statistics.AvgQual++;
// }
// if (d->QualCtrl.minL) {
// statistics.minL++;
// }
// if (d->QualCtrl.maxL) {
// statistics.maxL++;
// }
// if (d->QualCtrl.HomoNT) {
// statistics.HomoNT++;
// }
// if (d->QualCtrl.MaxAmb) {
// statistics.MaxAmb++;
// }
// if (d->QualCtrl.BinomialErr) {
// statistics.BinomialErr++;
// }
// if (d->QualCtrl.QualWin) {
// statistics.QualWin++;
// }
// }
// if (d->isDereplicated()) {
// if (d->getBarcodeDetected() && !d->isGreenQual() && !d->isYellowQual()) {
// this->statAddDerepBadSeq(d->getBCnumber());
// }
// }
//}
void Filters::addDNAtoCStats(shared_ptr<DNA> d,int Pair) {
//here should be the only place to count Barcodes!
int easyPair = Pair < 3 ? Pair - 1 : Pair - 3;
//csMTX[easyPair]->lock();
collectStatistics[easyPair]->total2++;
if (d->isGreenQual() || d->isYellowQual()) {
this->DNAstatLQ(d, easyPair, d->isYellowQual());
collectStatistics[easyPair]->totalSuccess++;
if (d->isYellowQual()) {
collectStatistics[easyPair]->totalMid++;
}
} else {
collectStatistics[easyPair]->totalRejected++;
}
//some general stats that always apply:
if (d->QualCtrl.PrimerFwdFail) {
collectStatistics[easyPair]->PrimerFail++;
}
if (d->QualCtrl.PrimerRevFail) {
collectStatistics[easyPair]->PrimerRevFail++;
}
if (d->QualCtrl.minLqualTrim) {
collectStatistics[easyPair]->minLqualTrim++;
}
if (d->QualCtrl.TagFail) {
collectStatistics[easyPair]->TagFail++;
}
if (d->QualCtrl.fail_correct_BC) {
collectStatistics[easyPair]->fail_correct_BC++;
}
if (d->QualCtrl.suc_correct_BC) {
collectStatistics[easyPair]->suc_correct_BC++;
}
if (d->QualCtrl.RevPrimFound) {
collectStatistics[easyPair]->RevPrimFound++;
}
if (d->QualCtrl.QWinTrimmed || d->QualCtrl.AccErrTrimmed) {
collectStatistics[easyPair]->Trimmed++;
}
if (d->getTA_cut()) {
collectStatistics[easyPair]->adapterRem++;
}
//exit(0);
if (d->isGreenQual() ){//|| d->isYellowQual()) {
countBCdetected(d->getBCnumber(), easyPair, false);
//and register as success
} else {
if (d->getBarcodeDetected()) {
//DNA is no longer useful
failedStats2(d, easyPair);
}
//delete d;
if (d->QualCtrl.AvgQual) {
collectStatistics[easyPair]->AvgQual++;
}
if (d->QualCtrl.minL) {
collectStatistics[easyPair]->minL++;
}
if (d->QualCtrl.maxL) {
collectStatistics[easyPair]->maxL++;
}
if (d->QualCtrl.HomoNT) {
collectStatistics[easyPair]->HomoNT++;
}
if (d->QualCtrl.MaxAmb) {
collectStatistics[easyPair]->MaxAmb++;