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#ifndef CODE_ParametersSolo
#define CODE_ParametersSolo
#include <array>
#include "IncludeDefine.h"
#include "SoloBarcode.h"
#include "SoloFeatureTypes.h"
class Parameters;
class ParametersSolo;
class UMIdedup {
public:
const static uint32 tN = 6;
array<string,tN> typeNames { {"NoDedup", "Exact", "1MM_All", "1MM_Directional", "1MM_CR", "1MM_Directional_UMItools"} };
enum typeI : int32 { NoDedup=0, Exact=1, All=2, Directional=3, CR=4, Directional_UMItools=5 };
struct {
uint32_t N;
array<bool,tN> B;
bool &NoDedup=B[0], &Exact=B[1], &All=B[2], &Directional=B[3], &CR=B[4], &Directional_UMItools=B[5];
} yes;
struct {
//uint32_t N;
array<uint32_t,tN> I;
uint32_t &NoDedup=I[0], &Exact=I[1], &All=I[2], &Directional=I[3], &CR=I[4], &Directional_UMItools=I[5];
uint32_t main; //index for SAM/stats/filtering output
} countInd; //index in the countCellGennUMI
vector<string> typesIn; //UMIdedup types from user options
vector<int32> types; //the above converted to typeI numbers
int32 typeMain; //the type to be used in SAM/stats/filtering output - for now just types[0]
void initialize(ParametersSolo *pS);
protected:
int it;
};
class ParametersSolo {
public:
Parameters *pP;
//chemistry, library etc
string typeStr;
enum SoloTypes : int32 {None=0, CB_UMI_Simple=1, CB_UMI_Complex=2, CB_samTagOut=3, SmartSeq=4};
SoloTypes type;
bool yes;
string strandStr;
int32 strand;
uint32 barcodeRead, barcodeReadIn;//which read is the barcode read = 0,1,2?
uint32 barcodeStart, barcodeEnd;//start/end of barcode sequence on barcodeRead
bool barcodeReadSeparate;
//simple barcodes
uint32 cbS, cbL; //cell barcode start,length
uint32 umiS, umiL; //umi start,length
uint32 bL, cbumiL; //total barcode sequene length, CB+UMI length. Former does may not be equal to the latter
vector<string> cbPositionStr;
string umiPositionStr;
//complex barcodes
vector<SoloBarcode> cbV;
SoloBarcode umiV; //single UMI
bool adapterYes; //anchor?
string adapterSeq; //anchor sequence
uint32 adapterMismatchesNmax;//max number of mismatches in the anchor
//input from SAM files
vector<string> samAtrrBarcodeSeq, samAtrrBarcodeQual;
//whitelist - general
uint64 cbWLsize;
bool cbWLyes;
vector<string> soloCBwhitelist;
vector <uint64> cbWL;
vector<string> cbWLstr;
//features
vector<string> featureIn;//string of requested features
vector<uint32> features;
uint32 nFeatures;//=features.size(), number of requested features
array<bool,SoloFeatureTypes::N> featureYes; //which features are requested
array<bool,SoloFeatureTypes::N> readInfoYes;//which features will readInfo (for now only Gene)
array<int32,SoloFeatureTypes::N> featureInd;//index of each feature - skips unrequested features
//filtering
char QSbase,QSmax;//quality score base and cutoff
#ifdef MATCH_CellRanger
double cbMinP;//for CBs with non-exact matching to WL, min posterior probability
#else
float cbMinP;//for CBs with non-exact matching to WL, min posterior probability
#endif
//cell filtering
struct {
vector<string> type;
uint32 topCells;
struct {
double nExpectedCells;
double maxPercentile;
double maxMinRatio;
} knee;
struct {
uint32 indMin, indMax; //min/max cell index, sorted by UMI counts,for empty cells
uint32 umiMin;
double umiMinFracMedian;
uint32 candMaxN;
double FDR;
uint32 simN;
} eDcr;//EmptyDrops-CellRanger
} cellFilter;
//CB match
struct {
string type;
bool mm1; //1 mismatch allowed
bool mm1_multi; //1 mismatch, multiple matches to WL allowed
bool oneExact; //CBs require at least one exact match
bool mm1_multi_pc; //use psedocounts while calculating probabilities of multi-matches
bool mm1_multi_Nbase; //allow multimatching to WL for CBs with N-bases
} CBmatchWL;
//UMIdedup
UMIdedup umiDedup;
//multi-gene umi
struct {
vector<string> type;
bool MultiGeneUMI;
bool MultiGeneUMI_CR;
} umiFiltering;
//clusters
string clusterCBfile;
//output
vector<string> outFileNames;
struct {
string featuresGeneField3;
} outFormat;
bool samAttrYes;//post-processed SAM attributes: error-corrected CB and UMI
int32 samAttrFeature;//which feature to use for error correction
//processing
uint32 redistrReadsNfiles; //numer of files to resditribute reads into
//constants
uint32 umiMaskLow, umiMaskHigh; //low/high half bit-mask or UMIs
void initialize(Parameters *pPin);
void umiSwapHalves(uint32 &umi);
void complexWLstrings();
void cellFiltering();
};
#endif
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