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#include "Genome_Index.h"
CGenome_Index::CGenome_Index(void)
{
this->initialization();
}
CGenome_Index::~CGenome_Index(void)
{
delete this->pgenomeNT;
delete this->pgenomeNTInBits;
}
int CGenome_Index::initialization(void)
{
this->NO_OF_BUCKET = 0x4000000; // 64M buckets, 256 MB 4^13
// this->NO_OF_BUCKET = 0x1000000; // 16M buckets, 64 MB, 4^12
// this->NO_OF_BUCKET = 0x400000; // 4M buckets, 16 MB, 4^11
this->pgenomeNT = NULL;
this->pgenomeNTInBits = NULL;
this->fpHashValue = NULL;
this->fpSeedKey = NULL;
this->caRefName[0] = '\0';
this->bEXTEND_SEED = true;
this->iHashDigits = 0;
this->iKeyDigits = 0;
return(0);
}
unsigned int CGenome_Index::getHashValue(char* slide_window) const
{
CReadInBits r(slide_window);
return(this->getHashValue(r) & (NO_OF_BUCKET - 1));
}
// generate Key for sorting
unsigned int CGenome_Index::getSeedKey(char* slide_window) const
{
CReadInBits r(slide_window);
return(getSeedKey(r));
}
unsigned int CGenome_Index::getHashValue(CReadInBits r) const
{
if (this->fpHashValue != NULL)
return(this->fpHashValue(r) & (NO_OF_BUCKET - 1)); // DEBUG
else
return(0);
}
unsigned int CGenome_Index::getSeedKey(CReadInBits r) const
{
if (this->fpSeedKey != NULL)
return(this->fpSeedKey(r, this->iKeyDigits));
else
return(0);
}
int CGenome_Index::chooseHashFunction(unsigned int uiReadLength, unsigned int chosenSeedId)
{
const char* F0SeedRepeat = "111";
const char* F1SeedRepeat = "1110";
const char* F2SeedRepeat = "1110100";
const char* S11SeedRepeat = "1111001000";
const char* F3SeedRepeat = "11101001000";
const char* S20SeedRepeat = "11110010000";
const char* S12SeedRepeat = "11110010000000"; //Only for read length 44 - 50
const char* F4SeedRepeat = "1100010000";
const char* SeedRepeatPattern;
// (1) choose SeedRepeatPattern and Hash function to bucket ID
switch (chosenSeedId) {
case 0:
SeedRepeatPattern = F0SeedRepeat;
this->fpHashValue = selectF0(uiReadLength);
break;
case 1:
SeedRepeatPattern = F1SeedRepeat;
this->fpHashValue = selectF1(uiReadLength);
break;
case 2:
SeedRepeatPattern = F2SeedRepeat;
this->fpHashValue = selectF2(uiReadLength);
break;
case 11: // full sensitive to three mismatches but two of them must to be consecutive.
SeedRepeatPattern = S11SeedRepeat;
this->fpHashValue = selectS1_1(uiReadLength);
break;
case 20: // full sensitive to 2 pairs of consecutive mismatches
SeedRepeatPattern = S20SeedRepeat;
this->fpHashValue = selectS2_0(uiReadLength);
break;
case 3:
SeedRepeatPattern = F3SeedRepeat;
this->fpHashValue = selectF3(uiReadLength);
break;
case 12: // full sensitive to four mismatches but two of them must to be consecutive.
if (uiReadLength >= 44) {
SeedRepeatPattern = S12SeedRepeat;
this->fpHashValue = getS1_2SeedHashValue;
break;
} // otherwise use F4
case 4:
SeedRepeatPattern = F4SeedRepeat;
this->fpHashValue = selectF4(uiReadLength);
this->fpSeedKey = &returnDummyHashKey; // DEFAULT
break;
default:
SeedRepeatPattern = F3SeedRepeat; // DEFAULT
LOG_INFO("\nInfo %d: The sensitivity threshold haven't been implemented.\n",\
INFO_LOG);
LOG_INFO("\nInfo %d: Use seed pattern which is full sensitivit to 3 mismatches instead.\n",\
INFO_LOG);
}
if (this->fpHashValue == NULL) {
string seedStr = seedSymbol(chosenSeedId);
LOG_INFO("Info %d: Read length is too short (or long) for the seed %s.\n" \
, ERROR_LOG, seedStr.c_str());
return(-1);
}
// (2) Get the hashkey function for binary search
int DEFAULT_HASHING_BITS = 13;
this->uiNoOfShift = (unsigned int)strlen(SeedRepeatPattern) - 1;
if (bEXTEND_SEED) {
this->iHashDigits = getNoOfCaredPositions4FullRead(SeedRepeatPattern, uiReadLength);
// Speical setting to extend 34-bp and 32 reads because the min weight is twelve only
if (uiReadLength == 34 &&
(chosenSeedId == FULL_SENSITIVE_OPT_TO_TWO_BASE_MIS || chosenSeedId == 3)) {
DEFAULT_HASHING_BITS = 12;
} else if (uiReadLength == 32 && chosenSeedId == 3) {
DEFAULT_HASHING_BITS = 10;
}
int seedWeight = getNoOfCaredPositions(SeedRepeatPattern, uiReadLength);
if (DEFAULT_HASHING_BITS > seedWeight) {
string msg("The mapping could be slow.\n");
LOG_INFO("Info %d: Seed weight %d is low due to the short read length.%s" \
, INFO_LOG, seedWeight, msg.c_str());
this->iHashDigits = getNoOfCaredPositions(SeedRepeatPattern, uiReadLength);
this->bEXTEND_SEED = false;
}
} else {
this->iHashDigits = getNoOfCaredPositions(SeedRepeatPattern, uiReadLength);
}
if (this->iHashDigits > DEFAULT_HASHING_BITS) {
this->iKeyDigits = this->iHashDigits - DEFAULT_HASHING_BITS;
this->iHashDigits = DEFAULT_HASHING_BITS;
} else {
this->iKeyDigits = 0;
}
// When hashing index, use this->uiSeedLength to filter out sliding windows with N
this->uiSeedLength = uiReadLength - this->uiNoOfShift;
// If extended seed method is used, this->uiSeedLength will be changed to read length.
// (3) chooose See key function
return(this->chooseSeedKeyFunction(uiReadLength, chosenSeedId));
}
int CGenome_Index::chooseSeedKeyFunction(unsigned int uiReadLength, unsigned int chosenSeedId)
{
switch (chosenSeedId) {
case 0:
if (iKeyDigits > 0) {
this->fpSeedKey = &getF0SeedKey;
} else {
this->fpSeedKey = &returnDummyHashKey;
}
break;
case 1:
if (iKeyDigits > 0) {
this->fpSeedKey = &getF1SeedKey;
} else {
this->fpSeedKey = &returnDummyHashKey;
}
break;
case 2: // Full sensitivie to 2 mis
if (iKeyDigits > 0) {
this->fpSeedKey = &getF2SeedKey;
} else {
this->fpSeedKey = &returnDummyHashKey;
}
break;
case 11: // Full sensitivie to 1 color + 1 base mis
if (iKeyDigits > 0) {
this->fpSeedKey = &getS1_1SeedKey;
} else {
this->fpSeedKey = &returnDummyHashKey;
}
break;
case 20: // full sensitive to 2 pairs of consecutive mis.
if (iKeyDigits > 0) {
if (uiReadLength == 34) {
this->fpSeedKey = &getS2_0SeedKey4ReadLength34;
} else
this->fpSeedKey = &getS2_0SeedKey;
} else {
this->fpSeedKey = &returnDummyHashKey;
}
break;
case 3: // Full sensitivie to 3 mis
if (iKeyDigits > 0) {
if (uiReadLength == 34) {
this->fpSeedKey = &getF3SeedKey4ReadLength34;
} else if (uiReadLength == 32) {
this->fpSeedKey = &getF3SeedKey4ReadLength32;
} else
this->fpSeedKey = &getF3SeedKey;
} else {
this->fpSeedKey = &returnDummyHashKey; // DEBUG
}
break;
case 12: // Full sensitive to 1 color + 2 mis
if (iKeyDigits > 0) {
if (46 <= uiReadLength && uiReadLength <= 49) {
this->fpSeedKey = &getS1_2SeedKey4ReadLength46_49;
} else {
this->fpSeedKey = &returnDummyHashKey; // DEFAULT
}
break;
} // otherwise use F4
case 4:
this->fpSeedKey = &returnDummyHashKey; // DEFAULT
break;
default:
this->fpSeedKey = &returnDummyHashKey; // DEFAULT
if (chosenSeedId > MAX_MISMATCH_THRESHOLD) {
LOG_INFO("Info %d: No Seed key function is defined for\
full sensitive opt %d!\n", WARNING_LOG, chosenSeedId);
return(-1);
}
}
return (0);
}
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