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#include <alignment/MappingMetrics.hpp>
#include <iomanip>
#include <unistd.h>
//In order to use clock_gettime in LINUX, add -lrt
#ifdef __APPLE__
#if MAC_OS_X_VERSION_MAX_ALLOWED < 101200
int my_clock_gettime_(clockid_t clk_id, struct timespec *tp)
{
kern_return_t ret;
clock_serv_t clk;
clock_id_t clk_serv_id;
mach_timespec_t tm;
uint64_t start, end, delta, nano;
//task_basic_info_data_t tinfo;
//task_thread_times_info_data_t ttinfo;
//mach_msg_type_number_t tflag;
int retval = -1;
switch (clk_id) {
case CLOCK_REALTIME:
case CLOCK_MONOTONIC:
clk_serv_id = clk_id == CLOCK_REALTIME ? CALENDAR_CLOCK : SYSTEM_CLOCK;
if (KERN_SUCCESS ==
(ret = host_get_clock_service(mach_host_self(), clk_serv_id, &clk))) {
if (KERN_SUCCESS == (ret = clock_get_time(clk, &tm))) {
tp->tv_sec = tm.tv_sec;
tp->tv_nsec = tm.tv_nsec;
retval = 0;
}
}
if (KERN_SUCCESS != ret) {
errno = EINVAL;
retval = -1;
}
break;
case CLOCK_PROCESS_CPUTIME_ID:
case CLOCK_THREAD_CPUTIME_ID:
start = mach_absolute_time();
if (clk_id == CLOCK_PROCESS_CPUTIME_ID) {
getpid();
} else {
sched_yield();
}
end = mach_absolute_time();
delta = end - start;
if (0 == __clock_gettime_inf.denom) {
mach_timebase_info(&__clock_gettime_inf);
}
nano = delta * __clock_gettime_inf.numer / __clock_gettime_inf.denom;
tp->tv_sec = nano * 1e-9;
tp->tv_nsec = nano - (tp->tv_sec * 1e9);
retval = 0;
break;
default:
errno = EINVAL;
retval = -1;
}
return retval;
}
#define clock_gettime my_clock_gettime_
#endif // MAC_OS_X_VERSION_MAX_ALLOWED < 101200
#endif // __APPLE__
Timer::Timer(std::string _header)
{
keepHistogram = false;
keepList = false;
totalElapsedClock = 0;
header = _header;
elapsedClockMsec = 0;
elapsedTime = 0.0;
}
int Timer::ListSize() { return msecList.size(); }
void Timer::PrintHeader(std::ostream &out)
{
if (msecList.size() > 0) {
out << header << " ";
}
}
void Timer::PrintListValue(std::ostream &out, int index)
{
if (msecList.size() > 0) {
out << msecList[index] << " ";
}
}
void Timer::Tick() { clock_gettime(CLOCK_THREAD_CPUTIME_ID, &cpuclock[0]); }
void Timer::SetStoreElapsedTime(bool value) { keepList = value; }
void Timer::SetStoreHistgram(bool value) { keepHistogram = value; }
void Timer::Tock()
{
clock_gettime(CLOCK_THREAD_CPUTIME_ID, &cpuclock[1]);
elapsedClockMsec = (cpuclock[1].tv_nsec - cpuclock[0].tv_nsec) / 1000;
totalElapsedClock += elapsedClockMsec;
elapsedTime = ((1.0) * elapsedClockMsec);
if (keepHistogram) {
// keep a histogram in number of milliseconds per operation
if (histogram.find(elapsedClockMsec) == histogram.end()) {
histogram[elapsedClockMsec] = 1;
} else {
histogram[elapsedClockMsec]++;
}
}
if (keepList) {
msecList.push_back(elapsedClockMsec);
}
}
void Timer::Add(const Timer &rhs)
{
elapsedClockMsec += rhs.elapsedClockMsec;
elapsedTime += rhs.elapsedTime;
totalElapsedClock += rhs.totalElapsedClock;
msecList.insert(msecList.end(), rhs.msecList.begin(), rhs.msecList.end());
}
void Timer::SetHeader(std::string _header) { header = _header; }
void MappingClocks::AddCells(int nCells) { nCellsPerSample.push_back(nCells); }
void MappingClocks::AddBases(int nBases) { nBasesPerSample.push_back(nBases); }
int MappingClocks::GetSize() { return total.ListSize(); }
MappingClocks::MappingClocks()
{
total.SetHeader("Total");
findAnchors.SetHeader("FindAnchors");
mapToGenome.SetHeader("MapToGenome");
sortMatchPosList.SetHeader("SortMatchPosList");
findMaxIncreasingInterval.SetHeader("FindMaxIncreasingInterval");
alignIntervals.SetHeader("AlignIntervals");
}
void MappingClocks::PrintHeader(std::ostream &out)
{
total.PrintHeader(out);
findAnchors.PrintHeader(out);
mapToGenome.PrintHeader(out);
sortMatchPosList.PrintHeader(out);
findMaxIncreasingInterval.PrintHeader(out);
alignIntervals.PrintHeader(out);
}
void MappingClocks::PrintList(std::ostream &out, int index)
{
total.PrintListValue(out, index);
findAnchors.PrintListValue(out, index);
mapToGenome.PrintListValue(out, index);
sortMatchPosList.PrintListValue(out, index);
findMaxIncreasingInterval.PrintListValue(out, index);
alignIntervals.PrintListValue(out, index);
if (nCellsPerSample.size() > 0) {
out << nCellsPerSample[index] << " ";
}
if (nBasesPerSample.size() > 0) {
out << nBasesPerSample[index] << " ";
}
out << std::endl;
}
void MappingClocks::SetStoreList(bool value)
{
total.SetStoreElapsedTime(value);
findAnchors.SetStoreElapsedTime(value);
mapToGenome.SetStoreElapsedTime(value);
sortMatchPosList.SetStoreElapsedTime(value);
findMaxIncreasingInterval.SetStoreElapsedTime(value);
alignIntervals.SetStoreElapsedTime(value);
}
void MappingClocks::AddClockTime(const MappingClocks &rhs)
{
total.Add(rhs.total);
findAnchors.Add(rhs.findAnchors);
mapToGenome.Add(rhs.mapToGenome);
sortMatchPosList.Add(rhs.sortMatchPosList);
findMaxIncreasingInterval.Add(rhs.findMaxIncreasingInterval);
alignIntervals.Add(rhs.alignIntervals);
}
MappingMetrics::MappingMetrics()
{
numReads = 0;
numMappedReads = 0;
numMappedBases = 0;
anchorsPerRead = 0;
totalAnchorsForMappedReads = 0;
totalAnchors = 0;
}
void MappingMetrics::StoreSDPPoint(int nBases, int nSDPAnchors, int nClock)
{
sdpBases.push_back(nBases);
sdpAnchors.push_back(nSDPAnchors);
sdpClock.push_back(nClock);
}
void MappingMetrics::SetStoreList(bool value) { clocks.SetStoreList(value); }
void MappingMetrics::PrintSeconds(std::ostream &out, long sec) { out << sec << " Msec"; }
void MappingMetrics::PrintFraction(std::ostream &out, float frac)
{
out << std::setprecision(2) << frac;
}
void MappingMetrics::RecordNumAlignedBases(int nBases) { mappedBases.push_back(nBases); }
void MappingMetrics::RecordNumCells(int nCells) { cellsPerAlignment.push_back(nCells); }
void MappingMetrics::Collect(MappingMetrics &rhs)
{
clocks.AddClockTime(rhs.clocks);
totalAnchors += rhs.totalAnchors;
numReads += rhs.numReads;
numMappedReads += rhs.numMappedReads;
totalAnchorsForMappedReads += rhs.totalAnchorsForMappedReads;
mappedBases.insert(mappedBases.end(), rhs.mappedBases.begin(), rhs.mappedBases.end());
cellsPerAlignment.insert(cellsPerAlignment.end(), rhs.cellsPerAlignment.begin(),
rhs.cellsPerAlignment.end());
}
void MappingMetrics::CollectSDPMetrics(MappingMetrics &rhs)
{
sdpAnchors.insert(sdpAnchors.end(), rhs.sdpAnchors.begin(), rhs.sdpAnchors.end());
sdpBases.insert(sdpBases.end(), rhs.sdpBases.begin(), rhs.sdpBases.end());
sdpClock.insert(sdpClock.end(), rhs.sdpClock.begin(), rhs.sdpClock.end());
}
void MappingMetrics::PrintSDPMetrics(std::ostream &out)
{
out << "nbases ncells time" << std::endl;
for (size_t i = 0; i < sdpAnchors.size(); i++) {
out << sdpBases[i] << " " << sdpAnchors[i] << " " << sdpClock[i] << std::endl;
}
}
void MappingMetrics::PrintFullList(std::ostream &out)
{
//
// Print the full header
//
clocks.PrintHeader(out);
out << " MappedBases Cells " << std::endl;
//
// Print all values: clocks + bases and cells.
//
int i;
for (i = 0; i < clocks.GetSize(); i++) {
clocks.PrintList(out, i);
// out << mappedBases[i] << " " << cellsPerAlignment[i] << std::endl;
}
}
void MappingMetrics::PrintSummary(std::ostream &out)
{
out << "Examined " << numReads << std::endl;
out << "Mapped " << numMappedReads << std::endl;
out << "Total mapping time\t";
PrintSeconds(out, clocks.total.elapsedClockMsec);
out << " \t";
PrintSeconds(out, (1.0 * clocks.total.elapsedClockMsec) / numReads);
out << " /read" << std::endl;
out << " find anchors\t";
PrintSeconds(out, clocks.mapToGenome.elapsedClockMsec);
out << " \t";
PrintSeconds(out, (1.0 * clocks.mapToGenome.elapsedClockMsec) / numReads);
out << std::endl;
out << " sort anchors\t";
PrintSeconds(out, clocks.sortMatchPosList.elapsedClockMsec);
out << " \t";
PrintSeconds(out, (1.0 * clocks.sortMatchPosList.elapsedClockMsec) / numReads);
out << std::endl;
out << " find max interval\t";
PrintSeconds(out, clocks.findMaxIncreasingInterval.elapsedClockMsec);
out << " \t";
PrintSeconds(out, (1.0 * clocks.findMaxIncreasingInterval.elapsedClockMsec) / numReads);
out << std::endl;
out << "Total anchors: " << totalAnchors << std::endl;
out << " Anchors per read: " << (1.0 * totalAnchors) / numReads << std::endl;
out << "Total mapped: " << totalAnchorsForMappedReads << std::endl;
out << " Anchors per mapped read: " << (1.0 * totalAnchorsForMappedReads) / numMappedReads
<< std::endl;
}
void MappingMetrics::AddClock(MappingClocks &clocks) { clocks.AddClockTime(clocks); }
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