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#ifndef H_SoloFeature
#define H_SoloFeature
#include <fstream>
#include <unordered_map>
#include <unordered_set>
#include "IncludeDefine.h"
#include "ReadAlignChunk.h"
#include "Transcriptome.h"
#include "SoloCommon.h"
#include "SoloRead.h"
#include "ReadAlignChunk.h"
#include "SoloFilteredCells.h"
class SoloFeature {
private:
Parameters &P;
ReadAlignChunk **RAchunk;
Transcriptome &Trans;
const int32 featureType;
SoloFeature **soloFeatAll;
static const uint32 umiArrayStride=3;
enum {rguG, rguU, rguR};
uint32 rguStride;
public:
ParametersSolo &pSolo;
SoloReadFeature *readFeatSum, **readFeatAll;
SoloReadBarcode *readBarSum;
uint64 nReadsMapped, nReadsInput; //total number of mapped reads
uint32 nCB;
uint32 featuresNumber; //number of features (i.e. genes, SJs, etc)
uint32 *rGeneUMI;//mapped reads sorted by CB
uint32 *rCBn;//number of reads for detected CBs in the whitelist
uint32 **rCBp;//array of pointers to each CB sub-array
vector<uint32> indCB;//index of detected CBs in the whitelist
vector<uint32> indCBwl; //reverse of indCB: index of WL CBs in detected CB list
vector<uint32> nUMIperCB, nUMIperCBsorted;//number of UMIs per CB, and the same sorted (descendant)
vector<uint32> nGenePerCB;//number of genes (with >0 UMIs) per CB
vector<uint32> nReadPerCB;//number of reads per CB
vector<uint32> countCellGeneUMI;//sparsified matrix for the counts, each entry is: geneID count1 count2 ... countNcounts
vector<uint32> countCellGeneUMIindex;//index of CBs in the count matrix
uint32 countMatStride; //number of counts per entry in the count matrix
vector<unordered_map<uint32, unordered_set<uint64>>> cbFeatureUMImap; //for SmartSeq counting
string outputPrefix, outputPrefixFiltered;
SoloFilteredCells filteredCells;
array<vector<uint64>,2> sjAll;
vector<readInfoStruct> readInfo; //corrected CB/UMI information for each read
vector<uint32> redistrFilesCBindex, redistrFilesCBfirst; //redistr file for each CB, CB boundaries in redistributed files
vector<uint64> redistrFilesNreads; //number of reads in each file
vector <fstream*> redistrFilesStreams;
SoloFeature(Parameters &Pin, ReadAlignChunk **RAchunk, Transcriptome &inTrans, int32 feTy, SoloReadBarcode *readBarSumIn, SoloFeature **soloFeatAll);
void processRecords();
void sumThreads();
void countSmartSeq();
void countCBgeneUMI();
void countVelocyto();
void quantTranscript();
void collapseUMI(uint32 iCB, uint32 *umiArray);
void collapseUMI_CR(uint32 iCB, uint32 *umiArray);
void collapseUMIall(uint32 iCB, uint32 *umiArray);
uint32 umiArrayCorrect_CR (const uint32 nU0, uintUMI *umiArr, const bool readInfoRec, const bool nUMIyes, unordered_map <uintUMI,uintUMI> &umiCorr);
uint32 umiArrayCorrect_Directional(const uint32 nU0, uintUMI *umiArr, const bool readInfoRec, const bool nUMIyes, unordered_map <uintUMI,uintUMI> &umiCorr, const int32 dirCountAdd);
uint32 umiArrayCorrect_Graph (const uint32 nU0, uintUMI *umiArr, const bool readInfoRec, const bool nUMIyes, unordered_map <uintUMI,uintUMI> &umiCorr);
void outputResults(bool cellFilterYes, string outputPrefixMat);
void addBAMtags(char *&bam0, uint32 &size0, char* bam1);
void statsOutput();
void redistributeReadsByCB();
void cellFiltering();
void emptyDrops_CR();
void loadRawMatrix();
};
#endif
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