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// Author: Martin C. Frith 2019
// SPDX-License-Identifier: GPL-3.0-or-later
#include "GappedXdropAligner.hh"
#include "GappedXdropAlignerInl.hh"
//#include <iostream> // for debugging
namespace cbrc {
const int seqLoadLen = simdBytes;
const int delimiter = 4;
int GappedXdropAligner::alignDna(BigPtr seq1,
const uchar *seq2,
bool isForward,
const ScoreMatrixRow *scorer,
int delOpenCost,
int delGrowCost,
int insOpenCost,
int insGrowCost,
int maxScoreDrop,
int maxMatchScore,
const uchar *toUnmasked) {
int badScoreDrop = maxScoreDrop + 1;
delGrowCost = std::min(delGrowCost, badScoreDrop);
delOpenCost = std::min(delOpenCost, badScoreDrop - delGrowCost);
insGrowCost = std::min(insGrowCost, badScoreDrop);
insOpenCost = std::min(insOpenCost, badScoreDrop - insGrowCost);
const SimdUint1 mNegInf = simdOnes1();
const SimdUint1 mDelOpenCost = simdFill1(delOpenCost);
const SimdUint1 mDelGrowCost = simdFill1(delGrowCost);
const SimdUint1 mInsOpenCost = simdFill1(insOpenCost);
const SimdUint1 mInsGrowCost = simdFill1(insGrowCost);
const int seqIncrement = isForward ? 1 : -1;
const int scoreOffset = maxMatchScore * 2;
const SimdUint1 scorer4x4 =
simdSet1(
scorer[3][3], scorer[3][2], scorer[3][1], scorer[3][0],
scorer[2][3], scorer[2][2], scorer[2][1], scorer[2][0],
scorer[1][3], scorer[1][2], scorer[1][1], scorer[1][0],
scorer[0][3], scorer[0][2], scorer[0][1], scorer[0][0],
scorer[3][3], scorer[3][2], scorer[3][1], scorer[3][0],
scorer[2][3], scorer[2][2], scorer[2][1], scorer[2][0],
scorer[1][3], scorer[1][2], scorer[1][1], scorer[1][0],
scorer[0][3], scorer[0][2], scorer[0][1], scorer[0][0]);
int numCells = 1;
size_t seq1end = 1;
size_t diagPos = xdropPadLen - 1;
size_t horiPos = xdropPadLen * 2 - 1;
size_t thisPos = xdropPadLen * 2;
int bestScore = 0;
SimdUint1 mBestScore = mNegInf;
SimdUint1 mBadScore = simdFill1(scoreOffset + badScoreDrop);
SimdUint1 mScoreRise1 = simdZero1();
SimdUint1 mScoreRise2 = simdZero1();
initTiny(scoreOffset);
seq1queue.clear();
seq2queue.clear();
bool isDna = (toUnmasked[*seq1] < 4 && toUnmasked[*seq2] < 4);
for (int i = 0; i < seqLoadLen; ++i) {
uchar x = toUnmasked[*seq1];
seq1 += seqIncrement * (x != delimiter);
seq1queue.push(x, i);
seq2queue.push(toUnmasked[*seq2], i);
}
seq2 += seqIncrement;
size_t antidiagonal;
for (antidiagonal = 2; /* noop */; ++antidiagonal) {
int n = numCells - 1;
const uchar *s1 = &seq1queue.fromEnd(n + seqLoadLen);
const uchar *s2 = seq2queue.begin();
initAntidiagonalTiny(antidiagonal, seq1end, thisPos, numCells);
thisPos += xdropPadLen;
TinyScore *x0 = &xTinyScores[thisPos];
TinyScore *y0 = &yTinyScores[thisPos];
TinyScore *z0 = &zTinyScores[thisPos];
const TinyScore *y1 = &yTinyScores[horiPos];
const TinyScore *z1 = &zTinyScores[horiPos + 1];
const TinyScore *x2 = &xTinyScores[diagPos];
const SimdUint1 mScoreRise12 = simdAdd1(mScoreRise1, mScoreRise2);
const SimdUint1 mDelGrowCost1 = simdAdd1(mDelGrowCost, mScoreRise1);
const SimdUint1 mInsGrowCost1 = simdAdd1(mInsGrowCost, mScoreRise1);
if (isDna) {
for (int i = 0; i < numCells; i += simdBytes) {
SimdUint1 fwd1 = simdLoad1(s1+i);
SimdUint1 rev2 = simdLoad1(s2+i);
SimdUint1 j = simdOr1(simdQuadruple1(fwd1), rev2);
SimdUint1 s = simdChoose1(scorer4x4, j);
SimdUint1 x = simdAdds1(simdLoad1(x2+i), mScoreRise12);
SimdUint1 y = simdAdds1(simdLoad1(y1+i), mDelGrowCost1);
SimdUint1 z = simdAdds1(simdLoad1(z1+i), mInsGrowCost1);
SimdUint1 b = simdMin1(simdMin1(x, y), z);
SimdUint1 isDrop = simdGe1(b, mBadScore);
mBestScore = simdMin1(b, mBestScore);
simdStore1(x0+i, simdOr1(simdSub1(b, s), isDrop));
simdStore1(y0+i, simdMin1(simdAdds1(b, mDelOpenCost), y));
simdStore1(z0+i, simdMin1(simdAdds1(b, mInsOpenCost), z));
}
} else {
bool isDelimiter1 = (s1[n] == delimiter);
bool isDelimiter2 = (s2[0] == delimiter);
if (isDelimiter1 || isDelimiter2) {
badScoreDrop = std::min(badScoreDrop, n * maxMatchScore);
mBadScore = simdFill1(scoreOffset + badScoreDrop);
}
for (int i = 0; i < numCells; i += simdBytes) {
SimdUint1 s = simdSet1(
scorer[s1[31]][s2[31]],
scorer[s1[30]][s2[30]],
scorer[s1[29]][s2[29]],
scorer[s1[28]][s2[28]],
scorer[s1[27]][s2[27]],
scorer[s1[26]][s2[26]],
scorer[s1[25]][s2[25]],
scorer[s1[24]][s2[24]],
scorer[s1[23]][s2[23]],
scorer[s1[22]][s2[22]],
scorer[s1[21]][s2[21]],
scorer[s1[20]][s2[20]],
scorer[s1[19]][s2[19]],
scorer[s1[18]][s2[18]],
scorer[s1[17]][s2[17]],
scorer[s1[16]][s2[16]],
scorer[s1[15]][s2[15]],
scorer[s1[14]][s2[14]],
scorer[s1[13]][s2[13]],
scorer[s1[12]][s2[12]],
scorer[s1[11]][s2[11]],
scorer[s1[10]][s2[10]],
scorer[s1[9]][s2[9]],
scorer[s1[8]][s2[8]],
scorer[s1[7]][s2[7]],
scorer[s1[6]][s2[6]],
scorer[s1[5]][s2[5]],
scorer[s1[4]][s2[4]],
scorer[s1[3]][s2[3]],
scorer[s1[2]][s2[2]],
scorer[s1[1]][s2[1]],
scorer[s1[0]][s2[0]]);
SimdUint1 x = simdAdds1(simdLoad1(x2+i), mScoreRise12);
SimdUint1 y = simdAdds1(simdLoad1(y1+i), mDelGrowCost1);
SimdUint1 z = simdAdds1(simdLoad1(z1+i), mInsGrowCost1);
SimdUint1 b = simdMin1(simdMin1(x, y), z);
SimdUint1 isDrop = simdGe1(b, mBadScore);
mBestScore = simdMin1(b, mBestScore);
simdStore1(x0+i, simdOr1(simdSub1(b, s), isDrop));
simdStore1(y0+i, simdMin1(simdAdds1(b, mDelOpenCost), y));
simdStore1(z0+i, simdMin1(simdAdds1(b, mInsOpenCost), z));
s1 += simdBytes;
s2 += simdBytes;
}
if (isDelimiter2) x0[0] = droppedTinyScore;
if (isDelimiter1) x0[n] = droppedTinyScore; // maybe n=0
}
mScoreRise2 = mScoreRise1;
mScoreRise1 = simdZero1();
int newBestScore = simdHorizontalMin1(mBestScore);
int rise = 0;
if (newBestScore < scoreOffset) {
rise = scoreOffset - newBestScore;
bestScore += rise;
bestAntidiagonal = antidiagonal;
mBestScore = mNegInf;
mScoreRise1 = simdFill1(rise);
}
scoreRises[antidiagonal] = rise;
diagPos = horiPos;
horiPos = thisPos - 1;
thisPos += numCells;
if (x0[n] != droppedTinyScore) {
++numCells;
++seq1end;
uchar x = toUnmasked[*seq1];
seq1 += seqIncrement * (x != delimiter);
seq1queue.push(x, n + seqLoadLen);
uchar z = seq1queue.fromEnd(seqLoadLen);
if (z >= 4) {
isDna = false;
}
}
if (x0[0] != droppedTinyScore) {
uchar y = toUnmasked[*seq2];
seq2queue.push(y, n + seqLoadLen);
seq2 += seqIncrement;
if (y >= 4) {
isDna = false;
}
} else {
--numCells;
if (numCells == 0) break;
++diagPos;
++horiPos;
}
}
bestAntidiagonal -= 2;
calcBestSeq1positionTiny(scoreOffset);
numOfAntidiagonals = antidiagonal - 1;
return bestScore;
}
bool GappedXdropAligner::getNextChunkDna(size_t &end1,
size_t &end2,
size_t &length,
int delOpenCost,
int delGrowCost,
int insOpenCost,
int insGrowCost) {
if (bestAntidiagonal == 0) return false;
end1 = bestSeq1position;
end2 = bestAntidiagonal - bestSeq1position;
const size_t *origins = &scoreEndsAndOrigins[1];
size_t h, d;
int x, y, z;
do {
bestAntidiagonal -= 2;
bestSeq1position -= 1;
h = origins[bestAntidiagonal * 2 + 2] + bestSeq1position - 1;
d = origins[bestAntidiagonal * 2] + bestSeq1position - 1;
x = xTinyScores[d] + scoreRises[bestAntidiagonal];
y = yTinyScores[h] + delGrowCost;
z = zTinyScores[h + 1] + insGrowCost;
} while (x <= y && x <= z && bestAntidiagonal > 0);
length = end1 - bestSeq1position;
if (bestAntidiagonal == 0) return true;
while (1) {
bool isDel = (y <= z);
bestAntidiagonal -= 1;
bestSeq1position -= isDel;
h = d - isDel;
d = origins[bestAntidiagonal * 2] + bestSeq1position - 1;
x = xTinyScores[d] + scoreRises[bestAntidiagonal];
y = yTinyScores[h] + delGrowCost;
z = zTinyScores[h + 1] + insGrowCost;
if (isDel) {
y -= delOpenCost;
} else {
z -= insOpenCost;
}
if (x <= y && x <= z) return true;
}
}
}
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