utils.h

Go to the documentation of this file.

#ifndef __LREZ_UTILS__
#define __LREZ_UTILS__
 
#include <string>
#include <vector>
#include "api/BamReader.h"
#include "api/BamIndex.h"
#include "api/BamAux.h"
#include "robin_hood.h"
#include <sstream>
#include <regex>
#include "barcodesList.h"
 
#define BXTAG "BX:Z"
 
#define no_argument 0
#define required_argument 1 
#define optional_argument 2
 
using namespace std;
using namespace BamTools;
 
typedef vector<bool> barcode;
 
enum SequencingTechnology {Undefined = 0, TenX, Haplotagging, TELLSeq, stLFR};
 
extern SequencingTechnology techno;
 
SequencingTechnology determineSequencingTechnology(const string& barcode);
 
string retrieveNucleotidesContent(const string& barcode);
 
bool isValidBarcode(const string& barcode);
 
barcode stringToBarcode(const string& str);
 
vector<string> splitString(string s, string delimiter);
 
BamRegion stringToBamRegion(BamReader& reader, string s);
 
vector<string> extractRegions(string chromosome, int32_t chromosomeSize, unsigned regionSize);
 
vector<string> extractRegionsList(BamReader& reader, unsigned regionSize);
 
string convertToSam(const BamAlignment& a, RefVector m_references);
 
#endif