/
equiv.cpp
133 lines (116 loc) · 2.9 KB
/
equiv.cpp
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#include "myutils.h"
#include "syncmerindex.h"
#include "randseq.h"
static byte *Seq;
static bool Trace = false;
static void FindEquiv(SyncmerType ST, uint k, uint t)
{
SyncmerIndex SIS;
SIS.Create(ST, k, t, 0, Seq, BENCHL);
uint K = SIS.GetKmerCount();
uint SSize = SIS.GetIndexSize();
double SStride = K/double(SSize);
uint EstimatedWindow = SyncmerIndex::EstimateWindow(k, t);
uint wHi = UINT_MAX;
uint wLo = UINT_MAX;
double MStrideLo = 0.0;
double MStrideHi = 999.9;
for (int iw = int(EstimatedWindow); iw > 1; --iw)
{
uint w = uint(iw);
SyncmerIndex SIM;
SIM.Create(ST_Minimizer1, k, 0, w, Seq, BENCHL);
uint KM = SIM.GetKmerCount();
asserta(KM == K);
uint MSize = SIM.GetIndexSize();
double MStride = K/double(MSize);
if (Trace)
Log("(-) w %u, stride %.1f\n", w, MStride);
if (MStride <= t && MStride > MStrideLo)
{
MStrideLo = MStride;
wLo = w;
}
if (MStride >= t && MStride < MStrideHi)
{
MStrideHi = MStride;
wHi = w;
}
if (MStride <= t)
break;
}
for (uint w = EstimatedWindow; w < EstimatedWindow + 32; ++w)
{
SyncmerIndex SIM;
SIM.Create(ST_Minimizer1, k, 0, w, Seq, BENCHL);
uint KM = SIM.GetKmerCount();
asserta(KM == K);
uint MSize = SIM.GetIndexSize();
double MStride = K/double(MSize);
if (Trace)
Log("(+) w %u, stride %.1f\n", w, MStride);
if (MStride <= t && MStride > MStrideLo)
{
MStrideLo = MStride;
wLo = w;
}
if (MStride >= t && MStride < MStrideHi)
{
MStrideHi = MStride;
wHi = w;
}
if (MStride >= t)
break;
}
double DiffHi = MStrideHi - double(t);
double DiffLo = MStrideLo - double(t);
uint wBest;
double DiffBest;
if (fabs(DiffHi) <= fabs(DiffLo))
{
wBest = wHi;
DiffBest = DiffHi;
}
else
{
wBest = wLo;
DiffBest = DiffLo;
}
ProgressLog("k=%u", k);
ProgressLog(", t=%u", t);
ProgressLog(", SStride=%.2f", SStride);
ProgressLog(", wLo=%u", wLo);
ProgressLog(", MStrideLo=%.2f", MStrideLo);
ProgressLog(", wHi=%u", wHi);
ProgressLog(", MStrideHi=%.2f", MStrideHi);
ProgressLog(", MStrideHi=%.2f", MStrideHi);
ProgressLog(", wBest=%u", wBest);
ProgressLog(", dBest=%.2g", DiffBest);
ProgressLog(", wEst=%u", EstimatedWindow);
ProgressLog(", dw=%+d", int(wBest - EstimatedWindow));
ProgressLog("\n");
}
void cmd_equiv()
{
const string Name = opt(equiv);
ResetRand(1);
SyncmerType ST = StrToST(Name);
Seq = myalloc(byte, BENCHL);
MakeRandSeq(Seq, BENCHL);
for (uint k = 8; k <= 16; ++k)
for (uint t = 2; t <= 10; ++t)
FindEquiv(ST, k, t);
}
void cmd_equiv1()
{
const string Name = opt(equiv1);
ResetRand(1);
SyncmerType ST = StrToST(Name);
asserta(optset_k && optset_t);
const uint k = opt(k);
const uint t = opt(t);
Seq = myalloc(byte, BENCHL);
MakeRandSeq(Seq, BENCHL);
Trace = true;
FindEquiv(ST, k, t);
}