static void ProgressPrefix()
{
int ElapsedSecs = (int) (time(0) - g_StartTime);
unsigned MemUseMB = (GetMemUseBytes() + 500000)/1000000;
unsigned RAMMB = (unsigned) ((GetRAMSize() + 500000)/1000000);
unsigned MemUsePct = (MemUseMB*100)/RAMMB;
fprintf(stderr, "%6d secs %6d Mb (%3d%%) ", ElapsedSecs, MemUseMB, MemUsePct);
Log("%6d secs %6d Mb (%3d%%) ", ElapsedSecs, MemUseMB, MemUsePct);
}
/***
Alignment parameters can be specified in three ways:
(1) All defaults.
(2) By -length and -pctid only.
(3) All parameters specified:
-wordsize -seedlength -seeddiffs -length -pctid
Optional parameters:
-maxmem (Default = 80% of RAM, 0 = no maximum)
-tube (Tube offset, Default = 32)
***/
void GetParams(int SeqLengthT, int SeqLengthQ, bool Self,
FilterParams *ptrFP, DPParams *ptrDP)
{
const char *strLength = ValueOpt("length");
const char *strPctId = ValueOpt("pctid");
const char *strWordSize = ValueOpt("wordsize");
const char *strSeedLength = ValueOpt("seedlength");
const char *strSeedErrors = ValueOpt("seeddiffs");
const char *strMaxMem = ValueOpt("maxmem");
const char *strTubeOffset = ValueOpt("tubeoffset");
const double MaxMem = (0 == strMaxMem) ? GetRAMSize()*RAM_FRACT : atof(strMaxMem);
const int TubeOffset = (0 == strTubeOffset) ? -1 : atoi(strTubeOffset);
// All parameters specified
if (0 != strWordSize || 0 != strSeedLength || 0 != strSeedErrors)
{
if (0 == strWordSize || 0 == strSeedLength || 0 == strSeedErrors ||
0 == strLength || 0 == strPctId)
Quit("Missing one or more of: -wordsize, -seedlength, -seeddiffs, -length, -pctid");
ptrFP->SeedDiffs = atoi(strSeedErrors);
ptrFP->SeedLength = atoi(strSeedLength);
ptrFP->WordSize = atoi(strWordSize);
ptrFP->TubeOffset = TubeOffset > 0 ? TubeOffset : ptrFP->SeedDiffs + TUBE_OFFSET_DELTA;
ptrDP->MinHitLength = atoi(strLength);
ptrDP->MinId = atoi(strPctId)/100.0;
}
// -length and -pctid
else if (0 != strLength || 0 != strPctId)
{
if (0 == strLength || 0 == strPctId)
Quit("Missing option -length or -pctid");
int Length = atoi(strLength);
double MinId = atof(strPctId)/100.0;
DefParams(Length, MinId, SeqLengthT, SeqLengthQ, Self, MaxMem, ptrFP, ptrDP);
}
// All defaults
else
{
DefParams(DEFAULT_LENGTH, DEFAULT_MIN_ID, SeqLengthT, SeqLengthQ,
Self, MaxMem, ptrFP, ptrDP);
}
}
double GetRAMSizeMB()
{
return GetRAMSize()/1e6;
}
