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#include "ParametersSolo.h"
#include "Parameters.h"
#include "ErrorWarning.h"
#include "streamFuns.h"
#include "SequenceFuns.h"
#include "serviceFuns.cpp"
#include <stdlib.h>
void ParametersSolo::initialize(Parameters *pPin)
{
pP=pPin;
cellFiltering();
if (pP->runMode=="soloCellFiltering") {//only filtering happens, do not need any other parameters
yes=true;
umiDedup.typesIn = {"NoDedup"}; //this does not affect the results - the dedup had been done when raw matrix was generated
umiDedup.initialize(this);
return;
};
//constants - may turn into parameters in the future
redistrReadsNfiles = 3*pP->runThreadN;
//////////////////////////////////////////////////////////////////////////////////////////////////////
///////////////////////////////--soloType
barcodeStart=barcodeEnd=0; //this means that the entire barcodeRead is considered barcode. Will change it for simple barcodes.
yes = true;
if (typeStr=="None" || typeStr=="SmartSeq") {//solo SAM attributes not allowed
if ( pP->outSAMattrPresent.CR || pP->outSAMattrPresent.CY || pP->outSAMattrPresent.UR
|| pP->outSAMattrPresent.UY || pP->outSAMattrPresent.CB || pP->outSAMattrPresent.UB
|| pP->outSAMattrPresent.sS || pP->outSAMattrPresent.sQ || pP->outSAMattrPresent.sM
|| pP->outSAMattrPresent.sF
) {
ostringstream errOut;
errOut <<"EXITING because of FATAL INPUT ERROR: --outSAMattributes contains CR/CY/UR/UY/CB/UB tags which are not allowed for --soloType " << typeStr <<'\n';
errOut <<"SOLUTION: re-run STAR without these attribures\n";
exitWithError(errOut.str(), std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
};
if (typeStr=="None") {
type = SoloTypes::None;
yes = false;
samAttrYes = false;
return;
} else if (typeStr=="CB_UMI_Simple" || typeStr=="Droplet") {
type=SoloTypes::CB_UMI_Simple;
if (umiL > 16) {
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: UMI length is too long: --soloUMIlen="<<umiL<<"\n";
errOut << "SOLUTION: UMI length cannot be longer than 16";
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
if (cbL > 31) {
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: CB length is too long: --soloCBlen="<<cbL<<"\n";
errOut << "SOLUTION: CB length cannot be longer than 31";
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
cbumiL=cbL+umiL;
if (bL==1)
bL=cbumiL;
barcodeStart=min(cbS,umiS)-1;
barcodeEnd=max(cbS+cbL,umiS+umiL)-2;
} else if (typeStr=="CB_UMI_Complex") {
type=SoloTypes::CB_UMI_Complex;
bL=0;//no fixed length for barcode sequence
cbumiL=0;
} else if (typeStr=="CB_samTagOut") {
type=SoloTypes::CB_samTagOut;
cbumiL=cbL+umiL;
if (bL==1)
bL=cbumiL;
barcodeStart=min(cbS,umiS)-1;
barcodeEnd=max(cbS+cbL,umiS+umiL)-2;
} else if (typeStr=="SmartSeq") {
type=SoloTypes::SmartSeq;
} else {
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: unrecognized option in --soloType="<<typeStr<<"\n";
errOut << "SOLUTION: use allowed option: None OR CB_UMI_Simple OR CB_UMI_Complex\n";
errOut << "Obsolete option Droplet should be replaced with CB_UMI_Simple";
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
/////////////////////////// CB type
if (CBtype.typeString=="Sequence") {
CBtype.type = 1;
} else if (CBtype.typeString=="String") {
if (soloCBwhitelist[0]!="None") {
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: --soloCBtype String cannot be used with passlist\n";
errOut << "SOLUTION: use --soloCBwhitelist None\n";
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
CBtype.type = 2;
CBtype.strMtx = new std::mutex;
CBtype.strMap.reserve(100000);
} else {
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: unrecognized option in --soloCBtype="<< CBtype.typeString <<"\n";
errOut << "SOLUTION: use allowed option: Sequence OR String\n";
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////input read files
barcodeRead=-1;
barcodeReadSeparate=false;
if (pP->readFilesTypeN != 10) {//input from FASTQ
if (type==SoloTypes::SmartSeq) {//no barcode read
//TODO: a lot of parameters should not be defined for SmartSeq option - check it here
} else {//all other types require barcode read
if (barcodeReadIn == 0) {//barcode read is separate - needs to be the last read in --readFilesIn
if (pP->readNends < 2) {
exitWithError("EXITING because of fatal PARAMETERS error: --soloType (except SmartSeq) with --soloBarcodeMate 0 (default) require 2 reads or 3 reads, where the last read is the barcode read.\n"
"SOLUTION: if barcode is in a separate mate, specify it as the last file in --readFilesIn. If barcode sequence is a part of one of the mates, specify that mate with --soloBarcodeMate 1 (or 2 or 3)"
,std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
pP->readNmates = pP->readNends-1; //true mates, excluding barcode read
barcodeRead = pP->readNends-1;//the barcode read is always the last one
} else if (barcodeReadIn > pP->readNends) {
exitWithError("EXITING because of fatal PARAMETERS error: --soloBarcodeMate " +to_string(barcodeReadIn)+ "is larger than number of mates " + to_string(pP->readNends) +
"\nSOLUTION: specify --soloBarcodeMate <= than the number of mates.",std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
} else {//barcode sequence is in one of the mates
if (type != SoloTypes::CB_UMI_Simple) {
exitWithError("EXITING because of fatal PARAMETERS error: --soloBarcodeMate " +to_string(barcodeReadIn)+ ">0 for is not allowed for --soloType " + typeStr +
"\nSOLUTION: specify --soloBarcodeMate 0 or --soloType CB_UMI_Simple",std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
barcodeRead = barcodeReadIn-1;
barcodeReadSeparate = true;
bL = 0; //>0 only for separate barcode read
if ( pP->pClip.in[0].N[barcodeRead] == 0 && pP->pClip.in[1].N[barcodeRead] == 0 ){//clipping not specified for the mate with barcodes
exitWithError("EXITING because of fatal PARAMETERS error: --soloBarcodeMate " +to_string(barcodeReadIn)+ " specifies that barcode sequence is a part of the mate " +to_string(barcodeReadIn)+
", which requires clipping the barcode off this mate."
"\nSOLUTION: clip the barcode sequence from 5' or/and 3' with --clip5pNbases or/and --clip3pNbases . The values for mate1 and mate2 have to specified, specify 0 for no clipping.",std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
};
};
} else if (pP->readFilesTypeN == 10) {//input from SAM
if (typeStr=="SmartSeq") {
exitWithError("EXITING because of fatal PARAMETERS error: --readFilesType SAM SE/PE cannot be used with --soloType SmartSeq\n"
"SOLUTION: for Smart-seq input from BAM files, use --soloType CB_UMI_Simple , create whitelist of SmartSeq file names, and specify the SAM tag that records these file names in --soloInputSAMattrBarcodeSeq"
, std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
if (samAtrrBarcodeSeq.at(0) == "-") {
exitWithError("EXITING because of fatal PARAMETERS error: --readFilesType SAM SE/PE requires --soloInputSAMattrBarcodeSeq.\n"
"SOLUTION: specify input SAM attributes for barcode sequence in --soloInputSAMattrBarcodeSeq, and (optionally) quality with --soloInputSAMattrBarcodeQual"
, std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
if (samAtrrBarcodeQual.at(0) == "-") {
warningMessage(" since --readFilesType SAM SE/PE --soloInputSAMattrBarcodeQual - : qualities for barcode read will be replaced with 'H'", pP->inOut->logMain,std::cerr, *pP);
samAtrrBarcodeQual.clear();
};
for (auto &tag: samAtrrBarcodeSeq) {
if (tag.size()!=2) {
exitWithError("EXITING because of fatal PARAMETERS error: --soloInputSAMattrBarcodeSeq attributes have to be two-letter strings.\n"
"SOLUTION: specify correct two-letter strings in --soloInputSAMattrBarcodeSeq",
std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
tag.insert(0,1,'\t');
};
for (auto &tag: samAtrrBarcodeQual) {
if (tag.size()!=2) {
exitWithError("EXITING because of fatal PARAMETERS error: --soloInputSAMattrBarcodeQual attributes have to be two-letter strings.\n"
"SOLUTION: specify correct two-letter strings in --soloInputSAMattrBarcodeQual",
std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
tag.insert(0,1,'\t');
};
};
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
///////////////////////////////////////////////// soloStrand
if (strandStr=="Unstranded") {
strand=-1;
} else if (strandStr=="Forward") {
strand=0;
} else if (strandStr=="Reverse") {
strand=1;
} else {
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: unrecognized option in --soloStrand="<<strandStr<<"\n";
errOut << "SOLUTION: use allowed option: Unstranded OR Forward OR Reverse";
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////// features
featureInd.fill(-1);
featureYes.fill(false);
featureFirst = -1;
for (auto &fin : featureIn) {
for (uint32 ii=0; ii<SoloFeatureTypes::Names.size(); ii++) {
if (fin==SoloFeatureTypes::Names[ii]) {
featureYes[ii]=true;
features.push_back(ii);
if (featureFirst == -1)
featureFirst = ii; //recored the first feature on the list
break;
};
};
};
nFeatures=features.size();
std::sort(features.begin(), features.end());
for (uint32 ii=0; ii<nFeatures; ii++)
featureInd[features[ii]]=ii;
if (nFeatures != featureIn.size()) {
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: unrecognized option(s) in --soloFeatures ";
for (auto &fname : featureIn)
errOut << fname <<" ";
errOut << "\nSOLUTION: use allowed option: ";
errOut <<SoloFeatureTypes::Names[0];
for (auto &fname : SoloFeatureTypes::Names)
errOut <<" OR "<< fname;
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
if (featureYes[SoloFeatureTypes::Velocyto] && type==SoloTypes::SmartSeq) {
string errOut = "EXITING because of fatal PARAMETERS error: --soloFeatures Velocyto is presently not compatible with --soloType SmartSeq .\n";
errOut += "SOLUTION: re-run without --soloFeatures Velocyto .";
exitWithError(errOut, std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
if (featureYes[SoloFeatureTypes::Gene]) {
pP->quant.gene.yes = true;
pP->quant.yes = true;
};
if (featureYes[SoloFeatureTypes::GeneFull]) {
pP->quant.geneFull.yes = true;
pP->quant.yes = true;
if (!featureYes[SoloFeatureTypes::Gene])
pP->quant.gene.yes=false; //if GeneFull is requested, but Gene is not, turn it off - it could have been turned on because of GX/GN attributes
};
if (featureYes[SoloFeatureTypes::GeneFull_Ex50pAS]) {
pP->quant.geneFull_Ex50pAS.yes = true;
pP->quant.yes = true;
if (!featureYes[SoloFeatureTypes::Gene])
pP->quant.gene.yes=false; //if GeneFull is requested, but Gene is not, turn it off - it could have been turned on because of GX/GN attributes
};
if (featureYes[SoloFeatureTypes::GeneFull_ExonOverIntron]) {
pP->quant.geneFull_ExonOverIntron.yes = true;
pP->quant.gene.yes = true; //needed to prioritize exons over introns
pP->quant.yes = true;
};
//initialize CB match to WL types
init_CBmatchWL();
////////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////umiDedup
umiDedup.initialize(this);
///////////// finished parameters input
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//make output directory if needed
if ( outFileNames[0].find_last_of("/") < outFileNames[0].size() ) {//need to create dir
string dir1=pP->outFileNamePrefix+outFileNames[0].substr(0,outFileNames[0].find_last_of("/"));
if (mkdir(dir1.c_str(),pP->runDirPerm)!=0 && errno!=EEXIST) {
ostringstream errOut;
errOut << "EXITING because of fatal OUTPUT FILE error: could not create Solo output directory"<<dir1<<"\n";
errOut << "SOLUTION: check the path and permisssions";
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
};
QSbase=33;//TODO make these user-definable
QSmax=33;
cbMinP=0.975;
umiMaskLow=(uint32) ( (((uint64)1)<<umiL) - 1);
umiMaskHigh=~umiMaskLow;
//////////////////////////////////////////////////////CB whitelist
if (type==SoloTypes::CB_UMI_Simple || type==SoloTypes::CB_samTagOut) {//simple whitelist
if (soloCBwhitelist.size()>1) {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR in INPUT parameters: --soloCBwhitelist contains more than one file which is not allowed with --soloType CB_UMI_Simple \n";
errOut << "SOLUTION: in --soloCBwhitelist specify only one whitelist file \n";
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_INPUT_FILES, *pP);
} else if (soloCBwhitelist[0]=="-") {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR in INPUT parameters: --soloCBwhitelist is not defined\n";
errOut << "SOLUTION: in --soloCBwhitelist specify path to and name of the whitelist file, or None for CB demultiplexing without whitelist \n";
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_INPUT_FILES, *pP);
} else if (soloCBwhitelist[0]=="None") {
cbWLyes=false;
} else {
cbWLyes=true;
ifstream & cbWlStream = ifstrOpen(soloCBwhitelist[0], ERROR_OUT, "SOLUTION: check the path and permissions of the CB whitelist file: " + soloCBwhitelist[0], *pP);
string seq1;
while (cbWlStream >> seq1) {
if (seq1.size() != cbL) {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR in input CB whitelist file: "<< soloCBwhitelist[0] <<" the total length of barcode sequence is " << seq1.size() << " not equal to expected " <<bL <<"\n" ;
errOut << "SOLUTION: make sure that the barcode read is the second in --readFilesIn and check that is has the correct formatting\n";
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_INPUT_FILES, *pP);
};
uint64 cb1;
if (convertNuclStrToInt64(seq1,cb1)) {//convert to 2-bit format
cbWL.push_back(cb1);
} else {
pP->inOut->logMain << "WARNING: CB whitelist sequence contains non-ACGT base and is ignored: " << seq1 <<endl;
};
};
if (cbWL.size()==0) {//empty whitelist
exitWithError("EXITING because of FATAL ERROR: CB whitelist file " + soloCBwhitelist[0] + \
" is empty. \nSOLUTION: provide non-empty whitelist.\n" , \
std::cerr, pP->inOut->logMain, EXIT_CODE_INPUT_FILES, *pP);
};
};
std::sort(cbWL.begin(),cbWL.end());//sort
auto un1=std::unique(cbWL.begin(),cbWL.end());//collapse identical
cbWL.resize(std::distance(cbWL.begin(),un1));
cbWLsize=cbWL.size();
pP->inOut->logMain << "Number of CBs in the whitelist = " << cbWLsize <<endl;
cbWLstr.resize(cbWLsize);
for (uint64 ii=0; ii<cbWLsize; ii++)
cbWLstr[ii] = convertNuclInt64toString(cbWL[ii],cbL);
//////////////////////////////////////////////////////////////////////////////////
} else if (type==SoloTypes::SmartSeq) {
cbWLstr=pP->outSAMattrRG;
cbWLsize=cbWLstr.size();
cbWLyes=true;
/////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
} else if (type==SoloTypes::CB_UMI_Complex) {//complex barcodes: multiple whitelist (one for each CB), varying CB length
cbWLyes=true; //for complex barcodes, no-whitelist option is not allowed for now
adapterYes=false;
if (adapterSeq!="-")
adapterYes=true;
if (cbPositionStr.size() != soloCBwhitelist.size()) {
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETER error: number of barcodes in --soloCBposition : "<< cbPositionStr.size() <<" is not equal to the number of WhiteLists in --soloCBwhitelist : " << soloCBwhitelist.size() <<"\n" ;
errOut << "SOLUTION: make sure that the number of CB whitelists and CB positions are the same\n";
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_INPUT_FILES, *pP);
};
cbV.resize(cbPositionStr.size());
for (uint32 ii=0; ii<cbPositionStr.size(); ii++) {
cbV[ii].extractPositionsFromString(cbPositionStr[ii]);
};
umiV.extractPositionsFromString(umiPositionStr);
umiL = 0; //this will be defined when the first barcode is processed
umiV.adapterLength=adapterSeq.size();//one adapter for all
cbWLsize=1;
for (uint32 icb=0; icb<cbV.size(); icb++) {//cycle over WL files
cbV[icb].adapterLength=adapterSeq.size();//one adapter for all
ifstream & cbWlStream = ifstrOpen(soloCBwhitelist[icb], ERROR_OUT, "SOLUTION: check the path and permissions of the CB whitelist file: " + soloCBwhitelist[icb], *pP);
string seq1;
while (cbWlStream >> seq1) {//cycle over one WL file
uint64 cb1;
if (!convertNuclStrToInt64(seq1,cb1)) {//convert to 2-bit format
pP->inOut->logMain << "WARNING: CB whitelist sequence contains non-ACGT base and is ignored: " << seq1 <<endl;
continue;
};
uint32 len1=seq1.size();
if (len1>=cbV[icb].wl.size())
cbV[icb].wl.resize(len1+1);//add new possible lengths to this CB
cbV[icb].wl.at(len1).push_back(cb1);
};
cbV[icb].sortWhiteList(this);
cbV[icb].wlFactor=cbWLsize;
cbWLsize *= cbV[icb].totalSize;
};
complexWLstrings();
};
time_t rawTime;
time(&rawTime);
pP->inOut->logMain << timeMonthDayTime(rawTime) << " ... Finished reading, sorting and deduplicating CB whitelist sequences." <<endl;
//////////////////////////////////////////////////////////////SAM attributes
samAttrYes=false;
if ( (pP->outSAMattrPresent.CB || pP->outSAMattrPresent.UB) && type!=SoloTypes::CB_samTagOut) {
samAttrYes=true;
if (!pP->outBAMcoord) {
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: CB and/or UB attributes in --outSAMattributes can only be output in the sorted BAM file.\n";
errOut << "SOLUTION: re-run STAR with --outSAMtype BAM SortedByCoordinate ...\n";
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
} else if ( pP->outSAMattrPresent.UB && type==SoloTypes::CB_samTagOut) {
exitWithError("EXITING because of fatal PARAMETERS error: UB attribute (corrected UMI) in --outSAMattributes cannot be used with --soloType CB_samTagOut \n" \
"SOLUTION: instead, use UR (uncorrected UMI) in --outSAMattributes\n", std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
////////////////////////////////////////////////////////////////readInfoYes: which feature is used to fill readInfo. Only one feature is allowed
readInfoYes.fill(false);
if (featureYes[SoloFeatureTypes::VelocytoSimple] || featureYes[SoloFeatureTypes::Velocyto]) {//turn readInfo on for Gene needed by VelocytoSimple
readInfoYes[SoloFeatureTypes::Gene]=true;
};
samAttrFeature = featureFirst;
if (samAttrYes){//pSolo.samAttrFeature=0 by default, so need to check samAttrYes
if ( featureFirst == SoloFeatureTypes::Gene || featureFirst == SoloFeatureTypes::GeneFull ||
featureFirst == SoloFeatureTypes::GeneFull_Ex50pAS || featureFirst == SoloFeatureTypes::GeneFull_ExonOverIntron ) {
//all good
} else {
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: CB and/or UB attributes in --outSAMattributes require --soloFeatures Gene OR/AND GeneFull OR/AND GeneFull_Ex50pAS.\n";
errOut << "SOLUTION: re-run STAR adding Gene AND/OR GeneFull OR/AND GeneFull_Ex50pAS OR/AND GeneFull_ExonOverIntron to --soloFeatures\n";
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
readInfoYes[samAttrFeature]=true;
};
readIndexYes = readInfoYes;
/////////////////////////////////////////////////////////////////// readFlag output
readStats.yes = false;
readStatsYes.fill(false);
if (readStats.type == "Standard") {
readStats.yes = true;
readStatsYes.fill(true);
readStatsYes[SoloFeatureTypes::VelocytoSimple] = false; //this could be allowed, but it will have the same info as Gene
readStatsYes[SoloFeatureTypes::Velocyto] = false;
readStatsYes[SoloFeatureTypes::SJ] = false; //output for SJ requires careful consideration for SoloReadFeature_record.cpp, for output of reads that do not have splice junction
for (uint32 ff=0; ff<readIndexYes.size(); ff++) {//merge with previous values
readIndexYes[ff] |= readStatsYes[ff];
};
} else if (readStats.type != "None" ) {
exitWithError("EXITING because of fatal PARAMETERS error: unrecognized option in --soloCellReadStats" + readStats.type
+ "\nSOLUTION: use allowed options: None OR Standard \n",
std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
///////////////////////////////////////////////////////////////////umi filtering
if (umiFiltering.type[0]=="MultiGeneUMI") {
umiFiltering.MultiGeneUMI = true;
umiFiltering.yes = true;
} else if (umiFiltering.type[0]=="MultiGeneUMI_All") {
umiFiltering.MultiGeneUMI_All = true;
umiFiltering.yes = true;
} else if (umiFiltering.type[0]=="MultiGeneUMI_CR") {
umiFiltering.MultiGeneUMI_CR = true;
if (umiDedup.typesIn.size()>1 || umiDedup.typesIn.at(0) != "1MM_CR")
exitWithError("EXITING because of fatal PARAMETERS error: --soloUMIfiltering MultiGeneUMI_CR only works with --soloUMIdedup 1MM_CR"
"\nSOLUTION: rerun with --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR \n",
std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
} else if (umiFiltering.type[0]=="-") {
//nothing to do
} else {
exitWithError("EXITING because of fatal PARAMETERS error: unrecognized option in --soloUMIfiltering=" + umiFiltering.type[0]
+ "\nSOLUTION: use allowed options: - or MultiGeneUMI or MultiGeneUMI_CR \n",
std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
//////////////////////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////// MultiMappers
multiMap.initialize(this);
if (multiMap.yes.multi) {
if (type==SoloTypes::CB_samTagOut || type==SoloTypes::SmartSeq) {
exitWithError("EXITING because of fatal PARAMETERS error: multimapping options do not work for --soloType " +typeStr+
"\nSOLUTION: use default option --soloMultiMappers Unique\n",
std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
readIndexYes[SoloFeatureTypes::Gene]=true;
readIndexYes[SoloFeatureTypes::GeneFull]=true;
readIndexYes[SoloFeatureTypes::GeneFull_Ex50pAS]=true;
readIndexYes[SoloFeatureTypes::GeneFull_ExonOverIntron]=true;
};
};
/////////////////////////////////
void ParametersSolo::umiSwapHalves(uint32 &umi) {
uint32 high=umi>>(umiL);
umi &= umiMaskLow; //remove high
umi <<= (umiL); //move low to high
umi |= high; //add high
};
void ParametersSolo::complexWLstrings() {
cbWLstr.resize(cbWLsize);
for (auto &cb : cbV) {//initialize
cb.iCB=0;
cb.iLen=cb.minLen;
};
for (uint32 ii=0; ii<cbWLsize; ii++) {//cycle over full WL
for (uint64 ii=0; ii<cbV.size(); ii++) {//check for overflow and re-calculate all indexes
SoloBarcode &cb=cbV[ii];
if (cb.iCB == cb.wl[cb.iLen].size()) {//advance length
cb.iLen++;
cb.iCB=0;//reset iCB
};
if (cb.iLen == cb.wl.size()){//advance barcode
cbV[ii+1].iCB++;
cb.iLen=cb.minLen;//reset length
};
};
for (auto &cb : cbV)
cbWLstr[ii] += convertNuclInt64toString(cb.wl[cb.iLen][cb.iCB], cb.iLen) + "_";
cbWLstr[ii].pop_back();
cbV[0].iCB++;//shift by one for the next CB
};
};
void ParametersSolo::cellFiltering()
{//cell filtering
string pars1;
for (auto s=cellFilter.type.begin()+1; s!=cellFilter.type.end(); s++)
pars1 += ' ' + *s; //concatenate parameters into one string - easier to process that way
if (cellFilter.type[0]=="CellRanger2.2") {
if (cellFilter.type.size()==1) {
pP->inOut->logMain << "ParametersSolo: using hardcoded filtering parameters for --soloCellFilterType CellRanger2.2" <<endl;
pars1="3000 0.99 10";
} else if (cellFilter.type.size()<4) {
string errOut="EXITING because of fatal PARAMETERS error: --soloCellFilterType CellRanger2.2 requires exactly 3 numerical parameters";
errOut += "\nSOLUTION: re-run with --soloCellFilterType CellRanger2.2 <nExpectedCells> <maxPercentile> <maxMinRatio>\n";
exitWithError(errOut, std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
pP->inOut->logMain << "ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters: " << pars1 <<endl;
istringstream parsStream(pars1);
parsStream >> cellFilter.knee.nExpectedCells >> cellFilter.knee.maxPercentile >> cellFilter.knee.maxMinRatio;
} else if (cellFilter.type[0]=="EmptyDrops_CR") {
if (cellFilter.type.size()==1) {
pP->inOut->logMain << "ParametersSolo: using hardcoded filtering parameters for --soloCellFilterType EmptyDrops_CR\n";
pars1="3000 0.99 10 45000 90000 500 0.01 20000 0.01 10000";
} else if (cellFilter.type.size()<11) {
string errOut="EXITING because of fatal PARAMETERS error: --soloCellFilterType EmptyDrops_CR requires exactly 10 numerical parameters";
errOut += "\nSOLUTION: re-run with --soloCellFilterType EmptyDrops_CR ";
errOut += "<nExpectedCells> <maxPercentile> <maxMinRatio> <indMin> <indMax> <umiMin> <umiMinFracMedian> <candMaxN> <FDR> <simN>\n";
exitWithError(errOut, std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
pP->inOut->logMain << "ParametersSolo: --soloCellFilterType EmptyDrops_CR filtering parameters: " << pars1 <<endl;
istringstream parsStream(pars1);
parsStream >> cellFilter.knee.nExpectedCells >> cellFilter.knee.maxPercentile >> cellFilter.knee.maxMinRatio;
parsStream >> cellFilter.eDcr.indMin >> cellFilter.eDcr.indMax >> cellFilter.eDcr.umiMin >> cellFilter.eDcr.umiMinFracMedian;
parsStream >> cellFilter.eDcr.candMaxN >> cellFilter.eDcr.FDR >> cellFilter.eDcr.simN;
} else if (cellFilter.type[0]=="TopCells") {
if (cellFilter.type.size()<2) {
string errOut="EXITING because of fatal PARAMETERS error: number of cells not specified for --soloCellFilterType TopCells";
errOut += "\nSOLUTION: --soloCellFilterType TopCells <NumberOfCells>\n";
exitWithError(errOut, std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
cellFilter.topCells=stoi(cellFilter.type[1]);
} else if (cellFilter.type[0]=="None") {
//nothing to do
} else {
exitWithError("EXITING because of fatal PARAMETERS error: unrecognized option in --soloCellFilterType=" + cellFilter.type[0] + "\nSOLUTION: use allowed options: CellRanger2.2 or None\n",
std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
};
void UMIdedup::initialize(ParametersSolo *pS)
{
yes.N = 0;
countInd.I.fill((uint32_t) -1); //marks types not used
yes.B.fill(false);
for (uint32_t iin=0; iin<typesIn.size(); iin++) {
uint32_t itype;
for (itype=0; itype<tN; itype++) {
if (typesIn[iin] == typeNames[itype])
break; //found match
};
if (itype==tN) {//no match
std::string tall;
for (auto &t: typeNames)
tall +=" " + t; // concatenate allowed values
exitWithError("EXITING because of fatal PARAMETERS error: unrecognzied option --soloUMIdedup = " + typesIn[iin] + '\n'
+ "SOLUTION: use allowed values: " + tall + '\n'
,std::cerr, pS->pP->inOut->logMain, EXIT_CODE_PARAMETER, *pS->pP);
};
types.push_back(itype);
yes.B[itype] = true;
yes.N++;
countInd.I[itype] = iin + 1; //for each type, which column itype's recorded in
if (pS->type == pS->SoloTypes::SmartSeq && (yes.All || yes.Directional || yes.CR) )
exitWithError("EXITING because of fatal PARAMETERS error: --soloUMIdedup = " + typesIn[iin] + " is not allowed for --soloType SmartSeq\n"
+ "SOLUTION: use allowed options: Exact and/or NoDedup\n"
,std::cerr, pS->pP->inOut->logMain, EXIT_CODE_PARAMETER, *pS->pP);
};
//hard-coded for now
typeMain = types[0]; //main is the 0th entry in typesIn
countInd.main = 1; //hard-coded - 1 column is always main
};
void MultiMappers::initialize(ParametersSolo* pS)
{
yes.N = 0;
countInd.I.fill((uint32) -1); //marks types not used
yes.B.fill(false);
for (uint32 iin=0; iin<typesIn.size(); iin++) {
uint32 itype;
for (itype=0; itype<tN; itype++) {
if (typesIn[iin] == typeNames[itype])
break; //found match
};
if (itype==tN) {//no match
std::string tall;
for (auto &t: typeNames)
tall +=" " + t; // concatenate allowed values
exitWithError("EXITING because of fatal PARAMETERS error: unrecognzied option --soloMultiMappers = " + typesIn[iin] + '\n'
+ "SOLUTION: use allowed values: " + tall + '\n'
,std::cerr, pS->pP->inOut->logMain, EXIT_CODE_PARAMETER, *pS->pP);
};
if (itype == typeI::Unique)
continue; //Unique type does not have to be recorded TODO use it to perform filtering and stats
types.push_back(itype);
yes.B[itype] = true;
yes.N++;
};
if (yes.N==0) {//only Unique, no multimappers
yes.multi=false;
return;
};
uint32 ind1=1; //start
for (const auto &itype : types) {
countInd.I[itype] = ind1;
ind1 += pS->umiDedup.yes.N;
};
//hard-coded for now
typeMain = types[0]; //main is the 0th entry in typesIn
countInd.main = 1; //hard-coded - 1 column is always main
yes.multi = yes.Uniform | yes.Rescue | yes.PropUnique | yes.EM;
};
////////////////////////////////////////////////////
void ParametersSolo::init_CBmatchWL()
{//CBmatchWL
bool incomp1 = typeStr=="CB_UMI_Complex" && (CBmatchWL.type!="Exact" && CBmatchWL.type!="1MM" && CBmatchWL.type!="EditDist_2");
incomp1 = incomp1 || (typeStr=="CB_samTagOut" && (CBmatchWL.type!="Exact" && CBmatchWL.type!="1MM"));
incomp1 = incomp1 || (typeStr!="CB_UMI_Complex" && CBmatchWL.type=="EditDist_2");
if ( incomp1 ) {
ostringstream errOut;
errOut << "EXITING because of fatal PARAMETERS error: --soloCBmatchWLtype "<< CBmatchWL.type << " does not work with --soloType " << typeStr << "\n";
errOut << "SOLUTION: use allowed option: use --soloCBmatchWLtype Exact (exact matches only) OR 1MM (one match with 1 mismatched base)\n";
exitWithError(errOut.str(),std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
CBmatchWL.mm1 = false;
CBmatchWL.mm1_multi = false;
CBmatchWL.mm1_multi_pc = false;
CBmatchWL.mm1_multi_Nbase = false;
CBmatchWL.oneExact = false; //if true, for a CB matching with 1 mismatch to a WL-CB, requires at least one other read to match this WL-CB.
//this is true for all options except pseudocount
CBmatchWL.EditDist_2 = false;
if (CBmatchWL.type=="Exact") {
CBmatchWL.oneExact=true;
} else if (CBmatchWL.type=="1MM") {
CBmatchWL.mm1=true;
CBmatchWL.oneExact=true;
} else if (CBmatchWL.type=="1MM_multi") {
CBmatchWL.mm1=true;
CBmatchWL.mm1_multi=true;
CBmatchWL.oneExact=true;
} else if (CBmatchWL.type=="1MM_multi_pseudocounts") {
CBmatchWL.mm1=true;
CBmatchWL.mm1_multi=true;
CBmatchWL.mm1_multi_pc=true;
} else if (CBmatchWL.type=="1MM_multi_Nbase_pseudocounts") {
CBmatchWL.mm1=true;
CBmatchWL.mm1_multi=true;
CBmatchWL.mm1_multi_pc=true;
CBmatchWL.mm1_multi_Nbase = true;
} else if (CBmatchWL.type=="EditDist_2") {
CBmatchWL.EditDist_2=true;
} else {
exitWithError("EXITING because of fatal PARAMETERS error: unrecognized option in --soloCBmatchWLtype " +CBmatchWL.type + "\nSOLUTION: use allowed options: Exact or 1MM or 1MM_multi or 1MM_multi_pseudocounts 1MM_multi_Nbase_pseudocounts\n",
std::cerr, pP->inOut->logMain, EXIT_CODE_PARAMETER, *pP);
};
};
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