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#ifndef _BLASR_MAPPING_METRICS_HPP_
#define _BLASR_MAPPING_METRICS_HPP_
#include <iostream>
#include <time.h>
#include <map>
#include <vector>
//In order to use clock_gettime in LINUX, add -lrt
#ifdef __APPLE__
#include <mach/mach.h>
#include <mach/clock.h>
#include <mach/mach_time.h>
#include <errno.h>
typedef enum {
CLOCK_REALTIME,
CLOCK_MONOTONIC,
CLOCK_PROCESS_CPUTIME_ID,
CLOCK_THREAD_CPUTIME_ID
} clockid_t;
static mach_timebase_info_data_t __clock_gettime_inf;
int clock_gettime(clockid_t clk_id, struct timespec *tp);
#endif // __APPLE__
class Timer {
public:
bool keepHistogram, keepList;
timespec cpuclock[2];
int elapsedClockMsec;
float elapsedTime;
std::map<int,int> histogram;
std::vector<int> msecList;
long long totalElapsedClock;
std::string header;
Timer(std::string _header="");
int ListSize();
void PrintHeader(std::ostream &out);
void PrintListValue(std::ostream &out, int index);
void Tick();
void SetStoreElapsedTime(bool value);
void SetStoreHistgram(bool value);
void Tock();
void Add(const Timer &rhs);
void SetHeader(std::string _header);
};
class MappingClocks {
public:
Timer total;
Timer findAnchors;
Timer mapToGenome;
Timer sortMatchPosList;
Timer findMaxIncreasingInterval;
Timer alignIntervals;
std::vector<int> nCellsPerSample;
std::vector<int> nBasesPerSample;
void AddCells(int nCells);
void AddBases(int nBases);
int GetSize();
MappingClocks();
void PrintHeader(std::ostream &out);
void PrintList(std::ostream &out, int index);
void SetStoreList(bool value=true);
void AddClockTime(const MappingClocks &rhs);
};
class MappingMetrics {
public:
MappingClocks clocks;
int numReads;
int numMappedReads;
int numMappedBases;
std::vector<int> mappedBases;
std::vector<int> cellsPerAlignment;
std::vector<int> anchorsPerAlignment;
std::vector<int> sdpAnchors, sdpBases, sdpClock;
long totalAnchors;
int anchorsPerRead;
long totalAnchorsForMappedReads;
MappingMetrics();
void StoreSDPPoint(int nBases, int nSDPAnchors, int nClock);
void SetStoreList(bool value=true);
void PrintSeconds(std::ostream &out, long sec);
void PrintFraction(std::ostream &out, float frac);
void RecordNumAlignedBases(int nBases);
void RecordNumCells(int nCells);
void Collect(MappingMetrics &rhs);
void CollectSDPMetrics(MappingMetrics &rhs);
void PrintSDPMetrics(std::ostream &out);
void PrintFullList(std::ostream &out);
void PrintSummary(std::ostream &out);
void AddClock(MappingClocks &clocks);
};
#endif // _BLASR_MAPPING_METRICS_HPP_
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