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Encode horizontal deltas using +1/-1 indicators for up to 20% speed gain #214

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Encode horizontal deltas using +1/-1 indicators for up to 20% speed gain #214

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49 changes: 31 additions & 18 deletions edlib/src/edlib.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -401,46 +401,45 @@ static inline unsigned char* createReverseCopy(const unsigned char* const seq, c
* @param [in] Pv Bitset, Pv[i] == 1 if vin is +1, otherwise Pv[i] == 0.
* @param [in] Mv Bitset, Mv[i] == 1 if vin is -1, otherwise Mv[i] == 0.
* @param [in] Eq Bitset, Eq[i] == 1 if match, 0 if mismatch.
* @param [in] hin Will be +1, 0 or -1.
* @param [in] Phin Bitset, 00..01 when hin == +1.
* @param [in] Mhin Bitset, 00..01 when hin == -1.
* @param [out] PvOut Bitset, PvOut[i] == 1 if vout is +1, otherwise PvOut[i] == 0.
* @param [out] MvOut Bitset, MvOut[i] == 1 if vout is -1, otherwise MvOut[i] == 0.
* @param [out] hout Will be +1, 0 or -1.
* @param [out] Phout Bitset, 00..01 when hout == +1.
* @param [out] Mhout Bitset, 00..01 when hout == -1.
*/
static inline int calculateBlock(Word Pv, Word Mv, Word Eq, const int hin,
static inline pair<Word, Word> calculateBlock(Word Pv, Word Mv, Word Eq, const Word Phin, const Word Mhin,
Word &PvOut, Word &MvOut) {
// hin can be 1, -1 or 0.
// 1 -> 00...01
// 0 -> 00...00
// -1 -> 11...11 (2-complement)

Word hinIsNeg = static_cast<Word>(hin >> 2) & WORD_1; // 00...001 if hin is -1, 00...000 if 0 or 1

Word Xv = Eq | Mv;
// This is instruction below written using 'if': if (hin < 0) Eq |= (Word)1;
Eq |= hinIsNeg;
Eq |= Mhin;
Word Xh = (((Eq & Pv) + Pv) ^ Pv) | Eq;

Word Ph = Mv | ~(Xh | Pv);
Word Mh = Pv & Xh;

int hout = 0;
// This is instruction below written using 'if': if (Ph & HIGH_BIT_MASK) hout = 1;
hout = (Ph & HIGH_BIT_MASK) >> (WORD_SIZE - 1);
Word Phout = Ph >> (WORD_SIZE - 1);
// This is instruction below written using 'if': if (Mh & HIGH_BIT_MASK) hout = -1;
hout -= (Mh & HIGH_BIT_MASK) >> (WORD_SIZE - 1);
Word Mhout = Mh >> (WORD_SIZE - 1);

Ph <<= 1;
Mh <<= 1;

// This is instruction below written using 'if': if (hin < 0) Mh |= (Word)1;
Mh |= hinIsNeg;
Mh |= Mhin;
// This is instruction below written using 'if': if (hin > 0) Ph |= (Word)1;
Ph |= static_cast<Word>((hin + 1) >> 1);
Ph |= Phin;

PvOut = Mh | ~(Xv | Ph);
MvOut = Ph & Xv;

return hout;
return {Phout, Mhout};
}

/**
Expand Down Expand Up @@ -581,17 +580,22 @@ static int myersCalcEditDistanceSemiGlobal(

int bestScore = -1;
vector<int> positions; // TODO: Maybe put this on heap?
const int startHout = mode == EDLIB_MODE_HW ? 0 : 1; // If 0 then gap before query is not penalized;
const Word PstartHout = mode == EDLIB_MODE_HW ? 0 : 1; // If 0 then gap before query is not penalized;
const unsigned char* targetChar = target;
for (int c = 0; c < targetLength; c++) { // for each column
const Word* Peq_c = Peq + (*targetChar) * maxNumBlocks;

//----------------------- Calculate column -------------------------//
int hout = startHout;
Word Phout = PstartHout;
Word Mhout = 0;
int hout = 0;
bl = blocks + firstBlock;
Peq_c += firstBlock;
for (int b = firstBlock; b <= lastBlock; b++) {
hout = calculateBlock(bl->P, bl->M, *Peq_c, hout, bl->P, bl->M);
pair<Word,Word> PMhout = calculateBlock(bl->P, bl->M, *Peq_c, Phout, Mhout, bl->P, bl->M);
Phout = PMhout.first;
Mhout = PMhout.second;
hout = Phout - Mhout;
bl->score += hout;
bl++; Peq_c++;
}
Expand All @@ -605,7 +609,8 @@ static int myersCalcEditDistanceSemiGlobal(
lastBlock++; bl++; Peq_c++;
bl->P = static_cast<Word>(-1); // All 1s
bl->M = static_cast<Word>(0);
bl->score = (bl - 1)->score - hout + WORD_SIZE + calculateBlock(bl->P, bl->M, *Peq_c, hout, bl->P, bl->M);
pair<Word, Word> PMhout = calculateBlock(bl->P, bl->M, *Peq_c, Phout, Mhout, bl->P, bl->M);
bl->score = (bl - 1)->score - hout + WORD_SIZE + PMhout.first - PMhout.second;
} else {
while (lastBlock >= firstBlock && bl->score >= k + WORD_SIZE) {
lastBlock--; bl--; Peq_c--;
Expand Down Expand Up @@ -780,9 +785,14 @@ static int myersCalcEditDistanceNW(const Word* const Peq, const int W, const int

//----------------------- Calculate column -------------------------//
int hout = 1;
Word Phout = 1;
Word Mhout = 0;
bl = blocks + firstBlock;
for (int b = firstBlock; b <= lastBlock; b++) {
hout = calculateBlock(bl->P, bl->M, Peq_c[b], hout, bl->P, bl->M);
pair<Word, Word> PMhout = calculateBlock(bl->P, bl->M, Peq_c[b], Phout, Mhout, bl->P, bl->M);
Phout = PMhout.first;
Mhout = PMhout.second;
hout = Phout - Mhout;
bl->score += hout;
bl++;
}
Expand All @@ -806,7 +816,10 @@ static int myersCalcEditDistanceNW(const Word* const Peq, const int W, const int
lastBlock++; bl++;
bl->P = static_cast<Word>(-1); // All 1s
bl->M = static_cast<Word>(0);
int newHout = calculateBlock(bl->P, bl->M, Peq_c[lastBlock], hout, bl->P, bl->M);
pair<Word, Word> PMhout = calculateBlock(bl->P, bl->M, Peq_c[lastBlock], Phout, Mhout, bl->P, bl->M);
Phout = PMhout.first;
Mhout = PMhout.second;
int newHout = Phout - Mhout;
bl->score = (bl - 1)->score - hout + WORD_SIZE + newHout;
hout = newHout;
}
Expand Down