/
aligner_swsse_ee_u8.cpp
1905 lines (1768 loc) · 61.2 KB
/
aligner_swsse_ee_u8.cpp
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/*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Bowtie 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
/**
* aligner_sw_sse.cpp
*
* Versions of key alignment functions that use vector instructions to
* accelerate dynamic programming. Based chiefly on the striped Smith-Waterman
* paper and implementation by Michael Farrar. See:
*
* Farrar M. Striped Smith-Waterman speeds database searches six times over
* other SIMD implementations. Bioinformatics. 2007 Jan 15;23(2):156-61.
* http://sites.google.com/site/farrarmichael/smith-waterman
*
* While the paper describes an implementation of Smith-Waterman, we extend it
* do end-to-end read alignment as well as local alignment. The change
* required for this is minor: we simply let vmax be the maximum element in the
* score domain rather than the minimum.
*
* The vectorized dynamic programming implementation lacks some features that
* make it hard to adapt to solving the entire dynamic-programming alignment
* problem. For instance:
*
* - It doesn't respect gap barriers on either end of the read
* - It just gives a maximum; not enough information to backtrace without
* redoing some alignment
* - It's a little difficult to handle st_ and en_, especially st_.
* - The query profile mechanism makes handling of ambiguous reference bases a
* little tricky (16 cols in query profile lookup table instead of 5)
*
* Given the drawbacks, it is tempting to use SSE dynamic programming as a
* filter rather than as an aligner per se. Here are a few ideas for how it
* can be extended to handle more of the alignment problem:
*
* - Save calculated scores to a big array as we go. We return to this array
* to find and backtrace from good solutions.
*/
#include <limits>
#include "aligner_sw.h"
static const size_t NBYTES_PER_REG = 16;
static const size_t NWORDS_PER_REG = 16;
// static const size_t NBITS_PER_WORD = 8;
static const size_t NBYTES_PER_WORD = 1;
// In end-to-end mode, we start high (255) and go low (0). Factoring in
// a query profile involves unsigned saturating subtraction, so all the
// query profile elements should be expressed as a positive penalty rather
// than a negative score.
typedef uint8_t TCScore;
/**
* Build query profile look up tables for the read. The query profile look
* up table is organized as a 1D array indexed by [i][j] where i is the
* reference character in the current DP column (0=A, 1=C, etc), and j is
* the segment of the query we're currently working on.
*/
void SwAligner::buildQueryProfileEnd2EndSseU8(bool fw) {
bool& done = fw ? sseU8fwBuilt_ : sseU8rcBuilt_;
if(done) {
return;
}
done = true;
const BTDnaString* rd = fw ? rdfw_ : rdrc_;
const BTString* qu = fw ? qufw_ : qurc_;
// daehwan - allows to align a portion of a read, not the whole.
// const size_t len = rd->length();
const size_t len = dpRows();
const size_t seglen = (len + (NWORDS_PER_REG-1)) / NWORDS_PER_REG;
// How many __m128i's are needed
size_t n128s =
64 + // slack bytes, for alignment?
(seglen * ALPHA_SIZE) // query profile data
* 2; // & gap barrier data
assert_gt(n128s, 0);
SSEData& d = fw ? sseU8fw_ : sseU8rc_;
d.profbuf_.resizeNoCopy(n128s);
assert(!d.profbuf_.empty());
d.maxPen_ = d.maxBonus_ = 0;
d.lastIter_ = d.lastWord_ = 0;
d.qprofStride_ = d.gbarStride_ = 2;
d.bias_ = 0; // no bias needed for end-to-end alignment; just use subtraction
// For each reference character A, C, G, T, N ...
for(size_t refc = 0; refc < ALPHA_SIZE; refc++) {
// For each segment ...
for(size_t i = 0; i < seglen; i++) {
size_t j = i;
uint8_t *qprofWords =
reinterpret_cast<uint8_t*>(d.profbuf_.ptr() + (refc * seglen * 2) + (i * 2));
uint8_t *gbarWords =
reinterpret_cast<uint8_t*>(d.profbuf_.ptr() + (refc * seglen * 2) + (i * 2) + 1);
// For each sub-word (byte) ...
for(size_t k = 0; k < NWORDS_PER_REG; k++) {
int sc = 0;
*gbarWords = 0;
if(j < len) {
int readc = (*rd)[j];
int readq = (*qu)[j];
sc = sc_->score(readc, (int)(1 << refc), readq - 33);
// Make score positive, to fit in an unsigned
sc = -sc;
assert_range(0, 255, sc);
size_t j_from_end = len - j - 1;
if(j < (size_t)sc_->gapbar ||
j_from_end < (size_t)sc_->gapbar)
{
// Inside the gap barrier
*gbarWords = 0xff;
}
}
if(refc == 0 && j == len-1) {
// Remember which 128-bit word and which smaller word has
// the final row
d.lastIter_ = i;
d.lastWord_ = k;
}
if((size_t)sc > d.maxPen_) {
d.maxPen_ = (size_t)sc;
}
*qprofWords = (uint8_t)sc;
gbarWords++;
qprofWords++;
j += seglen; // update offset into query
}
}
}
}
#ifndef NDEBUG
/**
* Return true iff the cell has sane E/F/H values w/r/t its predecessors.
*/
static bool cellOkEnd2EndU8(
SSEData& d,
size_t row,
size_t col,
int refc,
int readc,
int readq,
const Scoring& sc) // scoring scheme
{
TCScore floorsc = 0;
TAlScore ceilsc = MAX_I64;
TAlScore offsetsc = -0xff;
TAlScore sc_h_cur = (TAlScore)d.mat_.helt(row, col);
TAlScore sc_e_cur = (TAlScore)d.mat_.eelt(row, col);
TAlScore sc_f_cur = (TAlScore)d.mat_.felt(row, col);
if(sc_h_cur > floorsc) {
sc_h_cur += offsetsc;
}
if(sc_e_cur > floorsc) {
sc_e_cur += offsetsc;
}
if(sc_f_cur > floorsc) {
sc_f_cur += offsetsc;
}
bool gapsAllowed = true;
size_t rowFromEnd = d.mat_.nrow() - row - 1;
if(row < (size_t)sc.gapbar || rowFromEnd < (size_t)sc.gapbar) {
gapsAllowed = false;
}
bool e_left_trans = false, h_left_trans = false;
bool f_up_trans = false, h_up_trans = false;
bool h_diag_trans = false;
if(gapsAllowed) {
TAlScore sc_h_left = floorsc;
TAlScore sc_e_left = floorsc;
TAlScore sc_h_up = floorsc;
TAlScore sc_f_up = floorsc;
if(col > 0 && sc_e_cur > floorsc && sc_e_cur <= ceilsc) {
sc_h_left = d.mat_.helt(row, col-1) + offsetsc;
sc_e_left = d.mat_.eelt(row, col-1) + offsetsc;
e_left_trans = (sc_e_left > floorsc && sc_e_cur == sc_e_left - sc.readGapExtend());
h_left_trans = (sc_h_left > floorsc && sc_e_cur == sc_h_left - sc.readGapOpen());
assert(e_left_trans || h_left_trans);
// Check that we couldn't have got a better E score
assert_geq(sc_e_cur, sc_e_left - sc.readGapExtend());
assert_geq(sc_e_cur, sc_h_left - sc.readGapOpen());
}
if(row > 0 && sc_f_cur > floorsc && sc_f_cur <= ceilsc) {
sc_h_up = d.mat_.helt(row-1, col) + offsetsc;
sc_f_up = d.mat_.felt(row-1, col) + offsetsc;
f_up_trans = (sc_f_up > floorsc && sc_f_cur == sc_f_up - sc.refGapExtend());
h_up_trans = (sc_h_up > floorsc && sc_f_cur == sc_h_up - sc.refGapOpen());
assert(f_up_trans || h_up_trans);
// Check that we couldn't have got a better F score
assert_geq(sc_f_cur, sc_f_up - sc.refGapExtend());
assert_geq(sc_f_cur, sc_h_up - sc.refGapOpen());
}
} else {
assert_geq(floorsc, sc_e_cur);
assert_geq(floorsc, sc_f_cur);
}
if(col > 0 && row > 0 && sc_h_cur > floorsc && sc_h_cur <= ceilsc) {
TAlScore sc_h_upleft = d.mat_.helt(row-1, col-1) + offsetsc;
TAlScore sc_diag = sc.score(readc, (int)refc, readq - 33);
h_diag_trans = sc_h_cur == sc_h_upleft + sc_diag;
}
assert(
sc_h_cur <= floorsc ||
e_left_trans ||
h_left_trans ||
f_up_trans ||
h_up_trans ||
h_diag_trans ||
sc_h_cur > ceilsc ||
row == 0 ||
col == 0);
return true;
}
#endif /*ndef NDEBUG*/
#ifdef NDEBUG
#define assert_all_eq0(x)
#define assert_all_gt(x, y)
#define assert_all_gt_lo(x)
#define assert_all_lt(x, y)
#define assert_all_lt_hi(x)
#else
#define assert_all_eq0(x) { \
__m128i z = _mm_setzero_si128(); \
__m128i tmp = _mm_setzero_si128(); \
z = _mm_xor_si128(z, z); \
tmp = _mm_cmpeq_epi16(x, z); \
assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
}
#define assert_all_gt(x, y) { \
__m128i tmp = _mm_cmpgt_epu8(x, y); \
assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
}
#define assert_all_gt_lo(x) { \
__m128i z = _mm_setzero_si128(); \
__m128i tmp = _mm_setzero_si128(); \
z = _mm_xor_si128(z, z); \
tmp = _mm_cmpgt_epu8(x, z); \
assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
}
#define assert_all_lt(x, y) { \
__m128i z = _mm_setzero_si128(); \
z = _mm_xor_si128(z, z); \
__m128i tmp = _mm_subs_epu8(y, x); \
tmp = _mm_cmpeq_epi16(tmp, z); \
assert_eq(0x0000, _mm_movemask_epi8(tmp)); \
}
#define assert_all_lt_hi(x) { \
__m128i z = _mm_setzero_si128(); \
__m128i tmp = _mm_setzero_si128(); \
z = _mm_cmpeq_epu8(z, z); \
z = _mm_srli_epu8(z, 1); \
tmp = _mm_cmplt_epu8(x, z); \
assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
}
#endif
/**
* Aligns by filling a dynamic programming matrix with the SSE-accelerated,
* banded DP approach of Farrar. As it goes, it determines which cells we
* might backtrace from and tallies the best (highest-scoring) N backtrace
* candidate cells per diagonal. Also returns the alignment score of the best
* alignment in the matrix.
*
* This routine does *not* maintain a matrix holding the entire matrix worth of
* scores, nor does it maintain any other dense O(mn) data structure, as this
* would quickly exhaust memory for queries longer than about 10,000 kb.
* Instead, in the fill stage it maintains two columns worth of scores at a
* time (current/previous, or right/left) - these take O(m) space. When
* finished with the current column, it determines which cells from the
* previous column, if any, are candidates we might backtrace from to find a
* full alignment. A candidate cell has a score that rises above the threshold
* and isn't improved upon by a match in the next column. The best N
* candidates per diagonal are stored in a O(m + n) data structure.
*/
TAlScore SwAligner::alignGatherEE8(int& flag, bool debug) {
assert_leq(rdf_, rd_->length());
assert_leq(rdf_, qu_->length());
assert_lt(rfi_, rff_);
assert_lt(rdi_, rdf_);
assert_eq(rd_->length(), qu_->length());
assert_geq(sc_->gapbar, 1);
assert(repOk());
#ifndef NDEBUG
for(size_t i = (size_t)rfi_; i < (size_t)rff_; i++) {
assert_range(0, 16, (int)rf_[i]);
}
#endif
SSEData& d = fw_ ? sseU8fw_ : sseU8rc_;
SSEMetrics& met = extend_ ? sseU8ExtendMet_ : sseU8MateMet_;
if(!debug) met.dp++;
buildQueryProfileEnd2EndSseU8(fw_);
assert(!d.profbuf_.empty());
assert_eq(0, d.maxBonus_);
size_t iter =
(dpRows() + (NWORDS_PER_REG-1)) / NWORDS_PER_REG; // iter = segLen
int dup;
// Now set up the score vectors. We just need two columns worth, which
// we'll call "left" and "right".
d.vecbuf_.resize(4 * 2 * iter);
d.vecbuf_.zero();
__m128i *vbuf_l = d.vecbuf_.ptr();
__m128i *vbuf_r = d.vecbuf_.ptr() + (4 * iter);
// This is the data structure that holds candidate cells per diagonal.
const size_t ndiags = rff_ - rfi_ + dpRows() - 1;
if(!debug) {
btdiag_.init(ndiags, 2);
}
// Data structure that holds checkpointed anti-diagonals
TAlScore perfectScore = sc_->perfectScore(dpRows());
bool checkpoint = true;
bool cpdebug = false;
#ifndef NDEBUG
cpdebug = dpRows() < 1000;
#endif
cper_.init(
dpRows(), // # rows
rff_ - rfi_, // # columns
cperPerPow2_, // checkpoint every 1 << perpow2 diags (& next)
perfectScore, // perfect score (for sanity checks)
true, // matrix cells have 8-bit scores?
cperTri_, // triangular mini-fills?
false, // alignment is local?
cpdebug); // save all cells for debugging?
// Many thanks to Michael Farrar for releasing his striped Smith-Waterman
// implementation:
//
// http://sites.google.com/site/farrarmichael/smith-waterman
//
// Much of the implmentation below is adapted from Michael's code.
// Set all elts to reference gap open penalty
__m128i rfgapo = _mm_setzero_si128();
__m128i rfgape = _mm_setzero_si128();
__m128i rdgapo = _mm_setzero_si128();
__m128i rdgape = _mm_setzero_si128();
__m128i vlo = _mm_setzero_si128();
__m128i vhi = _mm_setzero_si128();
__m128i ve = _mm_setzero_si128();
__m128i vf = _mm_setzero_si128();
__m128i vh = _mm_setzero_si128();
__m128i vhd = _mm_setzero_si128();
__m128i vhdtmp = _mm_setzero_si128();
__m128i vtmp = _mm_setzero_si128();
__m128i vzero = _mm_setzero_si128();
__m128i vhilsw = _mm_setzero_si128();
assert_gt(sc_->refGapOpen(), 0);
assert_leq(sc_->refGapOpen(), MAX_U8);
dup = (sc_->refGapOpen() << 8) | (sc_->refGapOpen() & 0x00ff);
rfgapo = _mm_insert_epi16(rfgapo, dup, 0);
rfgapo = _mm_shufflelo_epi16(rfgapo, 0);
rfgapo = _mm_shuffle_epi32(rfgapo, 0);
// Set all elts to reference gap extension penalty
assert_gt(sc_->refGapExtend(), 0);
assert_leq(sc_->refGapExtend(), MAX_U8);
assert_leq(sc_->refGapExtend(), sc_->refGapOpen());
dup = (sc_->refGapExtend() << 8) | (sc_->refGapExtend() & 0x00ff);
rfgape = _mm_insert_epi16(rfgape, dup, 0);
rfgape = _mm_shufflelo_epi16(rfgape, 0);
rfgape = _mm_shuffle_epi32(rfgape, 0);
// Set all elts to read gap open penalty
assert_gt(sc_->readGapOpen(), 0);
assert_leq(sc_->readGapOpen(), MAX_U8);
dup = (sc_->readGapOpen() << 8) | (sc_->readGapOpen() & 0x00ff);
rdgapo = _mm_insert_epi16(rdgapo, dup, 0);
rdgapo = _mm_shufflelo_epi16(rdgapo, 0);
rdgapo = _mm_shuffle_epi32(rdgapo, 0);
// Set all elts to read gap extension penalty
assert_gt(sc_->readGapExtend(), 0);
assert_leq(sc_->readGapExtend(), MAX_U8);
assert_leq(sc_->readGapExtend(), sc_->readGapOpen());
dup = (sc_->readGapExtend() << 8) | (sc_->readGapExtend() & 0x00ff);
rdgape = _mm_insert_epi16(rdgape, dup, 0);
rdgape = _mm_shufflelo_epi16(rdgape, 0);
rdgape = _mm_shuffle_epi32(rdgape, 0);
vhi = _mm_cmpeq_epi16(vhi, vhi); // all elts = 0xffff
vlo = _mm_xor_si128(vlo, vlo); // all elts = 0
// vhilsw: topmost (least sig) word set to 0x7fff, all other words=0
vhilsw = _mm_shuffle_epi32(vhi, 0);
vhilsw = _mm_srli_si128(vhilsw, NBYTES_PER_REG - NBYTES_PER_WORD);
// Points to a long vector of __m128i where each element is a block of
// contiguous cells in the E, F or H matrix. If the index % 3 == 0, then
// the block of cells is from the E matrix. If index % 3 == 1, they're
// from the F matrix. If index % 3 == 2, then they're from the H matrix.
// Blocks of cells are organized in the same interleaved manner as they are
// calculated by the Farrar algorithm.
const __m128i *pvScore; // points into the query profile
const size_t colstride = ROWSTRIDE_2COL * iter;
// Initialize the H and E vectors in the first matrix column
__m128i *pvELeft = vbuf_l + 0; __m128i *pvERight = vbuf_r + 0;
/* __m128i *pvFLeft = vbuf_l + 1; */ __m128i *pvFRight = vbuf_r + 1;
__m128i *pvHLeft = vbuf_l + 2; __m128i *pvHRight = vbuf_r + 2;
// Maximum score in final row
bool found = false;
TCScore lrmax = MIN_U8;
for(size_t i = 0; i < iter; i++) {
_mm_store_si128(pvERight, vlo); pvERight += ROWSTRIDE_2COL;
// Could initialize Hs to high or low. If high, cells in the lower
// triangle will have somewhat more legitiate scores, but still won't
// be exhaustively scored.
_mm_store_si128(pvHRight, vlo); pvHRight += ROWSTRIDE_2COL;
}
assert_gt(sc_->gapbar, 0);
size_t nfixup = 0;
// Fill in the table as usual but instead of using the same gap-penalty
// vector for each iteration of the inner loop, load words out of a
// pre-calculated gap vector parallel to the query profile. The pre-
// calculated gap vectors enforce the gap barrier constraint by making it
// infinitely costly to introduce a gap in barrier rows.
//
// AND use a separate loop to fill in the first row of the table, enforcing
// the st_ constraints in the process. This is awkward because it
// separates the processing of the first row from the others and might make
// it difficult to use the first-row results in the next row, but it might
// be the simplest and least disruptive way to deal with the st_ constraint.
for(size_t i = (size_t)rfi_; i < (size_t)rff_; i++) {
// Swap left and right; vbuf_l is the vector on the left, which we
// generally load from, and vbuf_r is the vector on the right, which we
// generally store to.
swap(vbuf_l, vbuf_r);
pvELeft = vbuf_l + 0; pvERight = vbuf_r + 0;
/* pvFLeft = vbuf_l + 1; */ pvFRight = vbuf_r + 1;
pvHLeft = vbuf_l + 2; pvHRight = vbuf_r + 2;
// Fetch the appropriate query profile. Note that elements of rf_ must
// be numbers, not masks.
const int refc = (int)rf_[i];
// Fetch the appropriate query profile
size_t off = (size_t)firsts5[refc] * iter * 2;
pvScore = d.profbuf_.ptr() + off; // even elts = query profile, odd = gap barrier
// Set all cells to low value
vf = _mm_xor_si128(vf, vf);
// Load H vector from the final row of the previous column
vh = _mm_load_si128(pvHLeft + colstride - ROWSTRIDE_2COL);
// Shift 2 bytes down so that topmost (least sig) cell gets 0
vh = _mm_slli_si128(vh, NBYTES_PER_WORD);
// Fill topmost (least sig) cell with high value
vh = _mm_or_si128(vh, vhilsw);
// For each character in the reference text:
size_t j;
for(j = 0; j < iter; j++) {
// Load cells from E, calculated previously
ve = _mm_load_si128(pvELeft);
vhd = _mm_load_si128(pvHLeft);
assert_all_lt(ve, vhi);
pvELeft += ROWSTRIDE_2COL;
// Store cells in F, calculated previously
vf = _mm_subs_epu8(vf, pvScore[1]); // veto some ref gap extensions
_mm_store_si128(pvFRight, vf);
pvFRight += ROWSTRIDE_2COL;
// Factor in query profile (matches and mismatches)
vh = _mm_subs_epu8(vh, pvScore[0]);
// Update H, factoring in E and F
vh = _mm_max_epu8(vh, vf);
// Update vE value
vhdtmp = vhd;
vhd = _mm_subs_epu8(vhd, rdgapo);
vhd = _mm_subs_epu8(vhd, pvScore[1]); // veto some read gap opens
ve = _mm_subs_epu8(ve, rdgape);
ve = _mm_max_epu8(ve, vhd);
vh = _mm_max_epu8(vh, ve);
// Save the new vH values
_mm_store_si128(pvHRight, vh);
pvHRight += ROWSTRIDE_2COL;
vtmp = vh;
assert_all_lt(ve, vhi);
// Load the next h value
vh = vhdtmp;
pvHLeft += ROWSTRIDE_2COL;
// Save E values
_mm_store_si128(pvERight, ve);
pvERight += ROWSTRIDE_2COL;
// Update vf value
vtmp = _mm_subs_epu8(vtmp, rfgapo);
vf = _mm_subs_epu8(vf, rfgape);
assert_all_lt(vf, vhi);
vf = _mm_max_epu8(vf, vtmp);
pvScore += 2; // move on to next query profile / gap veto
}
// pvHStore, pvELoad, pvEStore have all rolled over to the next column
pvFRight -= colstride; // reset to start of column
vtmp = _mm_load_si128(pvFRight);
pvHRight -= colstride; // reset to start of column
vh = _mm_load_si128(pvHRight);
pvScore = d.profbuf_.ptr() + off + 1; // reset veto vector
// vf from last row gets shifted down by one to overlay the first row
// rfgape has already been subtracted from it.
vf = _mm_slli_si128(vf, NBYTES_PER_WORD);
vf = _mm_subs_epu8(vf, *pvScore); // veto some ref gap extensions
vf = _mm_max_epu8(vtmp, vf);
vtmp = _mm_subs_epu8(vf, vtmp);
vtmp = _mm_cmpeq_epi8(vtmp, vzero);
int cmp = _mm_movemask_epi8(vtmp);
// If any element of vtmp is greater than H - gap-open...
j = 0;
while(cmp != 0xffff) {
// Store this vf
_mm_store_si128(pvFRight, vf);
pvFRight += ROWSTRIDE_2COL;
// Update vh w/r/t new vf
vh = _mm_max_epu8(vh, vf);
// Save vH values
_mm_store_si128(pvHRight, vh);
pvHRight += ROWSTRIDE_2COL;
pvScore += 2;
assert_lt(j, iter);
if(++j == iter) {
pvFRight -= colstride;
vtmp = _mm_load_si128(pvFRight); // load next vf ASAP
pvHRight -= colstride;
vh = _mm_load_si128(pvHRight); // load next vh ASAP
pvScore = d.profbuf_.ptr() + off + 1;
j = 0;
vf = _mm_slli_si128(vf, NBYTES_PER_WORD);
} else {
vtmp = _mm_load_si128(pvFRight); // load next vf ASAP
vh = _mm_load_si128(pvHRight); // load next vh ASAP
}
// Update F with another gap extension
vf = _mm_subs_epu8(vf, rfgape);
vf = _mm_subs_epu8(vf, *pvScore); // veto some ref gap extensions
vf = _mm_max_epu8(vtmp, vf);
vtmp = _mm_subs_epu8(vf, vtmp);
vtmp = _mm_cmpeq_epi8(vtmp, vzero);
cmp = _mm_movemask_epi8(vtmp);
nfixup++;
}
// Check in the last row for the maximum so far
__m128i *vtmp = vbuf_r + 2 /* H */ + (d.lastIter_ * ROWSTRIDE_2COL);
// Note: we may not want to extract from the final row
TCScore lr = ((TCScore*)(vtmp))[d.lastWord_];
found = true;
if(lr > lrmax) {
lrmax = lr;
}
// Now we'd like to know whether the bottommost element of the right
// column is a candidate we might backtrace from. First question is:
// did it exceed the minimum score threshold?
TAlScore score = (TAlScore)(lr - 0xff);
if(lr == MIN_U8) {
score = MIN_I64;
}
if(!debug && score >= minsc_) {
DpBtCandidate cand(dpRows() - 1, i - rfi_, score);
btdiag_.add(i - rfi_, cand);
}
// Save some elements to checkpoints
if(checkpoint) {
__m128i *pvE = vbuf_r + 0;
__m128i *pvF = vbuf_r + 1;
__m128i *pvH = vbuf_r + 2;
size_t coli = i - rfi_;
if(coli < cper_.locol_) cper_.locol_ = coli;
if(coli > cper_.hicol_) cper_.hicol_ = coli;
if(cperTri_) {
size_t rc_mod = coli & cper_.lomask_;
assert_lt(rc_mod, cper_.per_);
int64_t row = -rc_mod-1;
int64_t row_mod = row;
int64_t row_div = 0;
size_t idx = coli >> cper_.perpow2_;
size_t idxrow = idx * cper_.nrow_;
assert_eq(4, ROWSTRIDE_2COL);
bool done = false;
while(true) {
row += (cper_.per_ - 2);
row_mod += (cper_.per_ - 2);
for(size_t j = 0; j < 2; j++) {
row++;
row_mod++;
if(row >= 0 && (size_t)row < cper_.nrow_) {
// Update row divided by iter_ and mod iter_
while(row_mod >= (int64_t)iter) {
row_mod -= (int64_t)iter;
row_div++;
}
size_t delt = idxrow + row;
size_t vecoff = (row_mod << 6) + row_div;
assert_lt(row_div, 16);
int16_t h_sc = ((uint8_t*)pvH)[vecoff];
int16_t e_sc = ((uint8_t*)pvE)[vecoff];
int16_t f_sc = ((uint8_t*)pvF)[vecoff];
if(h_sc == 0) h_sc = MIN_I16;
else h_sc -= 0xff;
if(e_sc == 0) e_sc = MIN_I16;
else e_sc -= 0xff;
if(f_sc == 0) f_sc = MIN_I16;
else f_sc -= 0xff;
assert_leq(h_sc, cper_.perf_);
assert_leq(e_sc, cper_.perf_);
assert_leq(f_sc, cper_.perf_);
CpQuad *qdiags = ((j == 0) ? cper_.qdiag1s_.ptr() : cper_.qdiag2s_.ptr());
qdiags[delt].sc[0] = h_sc;
qdiags[delt].sc[1] = e_sc;
qdiags[delt].sc[2] = f_sc;
} // if(row >= 0 && row < nrow_)
else if(row >= 0 && (size_t)row >= cper_.nrow_) {
done = true;
break;
}
} // end of loop over anti-diags
if(done) {
break;
}
idx++;
idxrow += cper_.nrow_;
}
} else {
// If this is the first column, take this opportunity to
// pre-calculate the coordinates of the elements we're going to
// checkpoint.
if(coli == 0) {
size_t cpi = cper_.per_-1;
size_t cpimod = cper_.per_-1;
size_t cpidiv = 0;
cper_.commitMap_.clear();
while(cpi < cper_.nrow_) {
while(cpimod >= iter) {
cpimod -= iter;
cpidiv++;
}
size_t vecoff = (cpimod << 6) + cpidiv;
cper_.commitMap_.push_back(vecoff);
cpi += cper_.per_;
cpimod += cper_.per_;
}
}
// Save all the rows
size_t rowoff = 0;
size_t sz = cper_.commitMap_.size();
for(size_t i = 0; i < sz; i++, rowoff += cper_.ncol_) {
size_t vecoff = cper_.commitMap_[i];
int16_t h_sc = ((uint8_t*)pvH)[vecoff];
//int16_t e_sc = ((uint8_t*)pvE)[vecoff];
int16_t f_sc = ((uint8_t*)pvF)[vecoff];
if(h_sc == 0) h_sc = MIN_I16;
else h_sc -= 0xff;
//if(e_sc == 0) e_sc = MIN_I16;
//else e_sc -= 0xff;
if(f_sc == 0) f_sc = MIN_I16;
else f_sc -= 0xff;
assert_leq(h_sc, cper_.perf_);
//assert_leq(e_sc, cper_.perf_);
assert_leq(f_sc, cper_.perf_);
CpQuad& dst = cper_.qrows_[rowoff + coli];
dst.sc[0] = h_sc;
//dst.sc[1] = e_sc;
dst.sc[2] = f_sc;
}
// Is this a column we'd like to checkpoint?
if((coli & cper_.lomask_) == cper_.lomask_) {
// Save the column using memcpys
assert_gt(coli, 0);
size_t wordspercol = cper_.niter_ * ROWSTRIDE_2COL;
size_t coloff = (coli >> cper_.perpow2_) * wordspercol;
__m128i *dst = cper_.qcols_.ptr() + coloff;
memcpy(dst, vbuf_r, sizeof(__m128i) * wordspercol);
}
}
if(cper_.debug_) {
// Save the column using memcpys
size_t wordspercol = cper_.niter_ * ROWSTRIDE_2COL;
size_t coloff = coli * wordspercol;
__m128i *dst = cper_.qcolsD_.ptr() + coloff;
memcpy(dst, vbuf_r, sizeof(__m128i) * wordspercol);
}
}
}
// Update metrics
if(!debug) {
size_t ninner = (rff_ - rfi_) * iter;
met.col += (rff_ - rfi_); // DP columns
met.cell += (ninner * NWORDS_PER_REG); // DP cells
met.inner += ninner; // DP inner loop iters
met.fixup += nfixup; // DP fixup loop iters
}
flag = 0;
// Did we find a solution?
TAlScore score = MIN_I64;
if(!found) {
flag = -1; // no
if(!debug) met.dpfail++;
return MIN_I64;
} else {
score = (TAlScore)(lrmax - 0xff);
if(score < minsc_) {
flag = -1; // no
if(!debug) met.dpfail++;
return score;
}
}
// Could we have saturated?
if(lrmax == MIN_U8) {
flag = -2; // yes
if(!debug) met.dpsat++;
return MIN_I64;
}
// Now take all the backtrace candidates in the btdaig_ structure and
// dump them into the btncand_ array. They'll be sorted later.
if(!debug) {
btdiag_.dump(btncand_);
assert(!btncand_.empty());
}
// Return largest score
if(!debug) met.dpsucc++;
return score;
}
/**
* Solve the current alignment problem using SSE instructions that operate on 16
* unsigned 8-bit values packed into a single 128-bit register.
*/
TAlScore SwAligner::alignNucleotidesEnd2EndSseU8(int& flag, bool debug) {
assert_leq(rdf_, rd_->length());
assert_leq(rdf_, qu_->length());
assert_lt(rfi_, rff_);
assert_lt(rdi_, rdf_);
assert_eq(rd_->length(), qu_->length());
assert_geq(sc_->gapbar, 1);
assert(repOk());
#ifndef NDEBUG
for(size_t i = (size_t)rfi_; i < (size_t)rff_; i++) {
assert_range(0, 16, (int)rf_[i]);
}
#endif
SSEData& d = fw_ ? sseU8fw_ : sseU8rc_;
SSEMetrics& met = extend_ ? sseU8ExtendMet_ : sseU8MateMet_;
if(!debug) met.dp++;
buildQueryProfileEnd2EndSseU8(fw_);
assert(!d.profbuf_.empty());
assert_eq(0, d.maxBonus_);
size_t iter =
(dpRows() + (NWORDS_PER_REG-1)) / NWORDS_PER_REG; // iter = segLen
int dup;
// Many thanks to Michael Farrar for releasing his striped Smith-Waterman
// implementation:
//
// http://sites.google.com/site/farrarmichael/smith-waterman
//
// Much of the implmentation below is adapted from Michael's code.
// Set all elts to reference gap open penalty
__m128i rfgapo = _mm_setzero_si128();
__m128i rfgape = _mm_setzero_si128();
__m128i rdgapo = _mm_setzero_si128();
__m128i rdgape = _mm_setzero_si128();
__m128i vlo = _mm_setzero_si128();
__m128i vhi = _mm_setzero_si128();
__m128i ve = _mm_setzero_si128();
__m128i vf = _mm_setzero_si128();
__m128i vh = _mm_setzero_si128();
#if 0
__m128i vhd = _mm_setzero_si128();
__m128i vhdtmp = _mm_setzero_si128();
#endif
__m128i vtmp = _mm_setzero_si128();
__m128i vzero = _mm_setzero_si128();
__m128i vhilsw = _mm_setzero_si128();
assert_gt(sc_->refGapOpen(), 0);
assert_leq(sc_->refGapOpen(), MAX_U8);
dup = (sc_->refGapOpen() << 8) | (sc_->refGapOpen() & 0x00ff);
rfgapo = _mm_insert_epi16(rfgapo, dup, 0);
rfgapo = _mm_shufflelo_epi16(rfgapo, 0);
rfgapo = _mm_shuffle_epi32(rfgapo, 0);
// Set all elts to reference gap extension penalty
assert_gt(sc_->refGapExtend(), 0);
assert_leq(sc_->refGapExtend(), MAX_U8);
assert_leq(sc_->refGapExtend(), sc_->refGapOpen());
dup = (sc_->refGapExtend() << 8) | (sc_->refGapExtend() & 0x00ff);
rfgape = _mm_insert_epi16(rfgape, dup, 0);
rfgape = _mm_shufflelo_epi16(rfgape, 0);
rfgape = _mm_shuffle_epi32(rfgape, 0);
// Set all elts to read gap open penalty
assert_gt(sc_->readGapOpen(), 0);
assert_leq(sc_->readGapOpen(), MAX_U8);
dup = (sc_->readGapOpen() << 8) | (sc_->readGapOpen() & 0x00ff);
rdgapo = _mm_insert_epi16(rdgapo, dup, 0);
rdgapo = _mm_shufflelo_epi16(rdgapo, 0);
rdgapo = _mm_shuffle_epi32(rdgapo, 0);
// Set all elts to read gap extension penalty
assert_gt(sc_->readGapExtend(), 0);
assert_leq(sc_->readGapExtend(), MAX_U8);
assert_leq(sc_->readGapExtend(), sc_->readGapOpen());
dup = (sc_->readGapExtend() << 8) | (sc_->readGapExtend() & 0x00ff);
rdgape = _mm_insert_epi16(rdgape, dup, 0);
rdgape = _mm_shufflelo_epi16(rdgape, 0);
rdgape = _mm_shuffle_epi32(rdgape, 0);
vhi = _mm_cmpeq_epi16(vhi, vhi); // all elts = 0xffff
vlo = _mm_xor_si128(vlo, vlo); // all elts = 0
// vhilsw: topmost (least sig) word set to 0x7fff, all other words=0
vhilsw = _mm_shuffle_epi32(vhi, 0);
vhilsw = _mm_srli_si128(vhilsw, NBYTES_PER_REG - NBYTES_PER_WORD);
// Points to a long vector of __m128i where each element is a block of
// contiguous cells in the E, F or H matrix. If the index % 3 == 0, then
// the block of cells is from the E matrix. If index % 3 == 1, they're
// from the F matrix. If index % 3 == 2, then they're from the H matrix.
// Blocks of cells are organized in the same interleaved manner as they are
// calculated by the Farrar algorithm.
const __m128i *pvScore; // points into the query profile
d.mat_.init(dpRows(), rff_ - rfi_, NWORDS_PER_REG);
const size_t colstride = d.mat_.colstride();
//const size_t rowstride = d.mat_.rowstride();
assert_eq(ROWSTRIDE, colstride / iter);
// Initialize the H and E vectors in the first matrix column
__m128i *pvHTmp = d.mat_.tmpvec(0, 0);
__m128i *pvETmp = d.mat_.evec(0, 0);
// Maximum score in final row
bool found = false;
TCScore lrmax = MIN_U8;
for(size_t i = 0; i < iter; i++) {
_mm_store_si128(pvETmp, vlo);
_mm_store_si128(pvHTmp, vlo); // start high in end-to-end mode
pvETmp += ROWSTRIDE;
pvHTmp += ROWSTRIDE;
}
// These are swapped just before the innermost loop
__m128i *pvHStore = d.mat_.hvec(0, 0);
__m128i *pvHLoad = d.mat_.tmpvec(0, 0);
__m128i *pvELoad = d.mat_.evec(0, 0);
__m128i *pvEStore = d.mat_.evecUnsafe(0, 1);
__m128i *pvFStore = d.mat_.fvec(0, 0);
__m128i *pvFTmp = NULL;
assert_gt(sc_->gapbar, 0);
size_t nfixup = 0;
// Fill in the table as usual but instead of using the same gap-penalty
// vector for each iteration of the inner loop, load words out of a
// pre-calculated gap vector parallel to the query profile. The pre-
// calculated gap vectors enforce the gap barrier constraint by making it
// infinitely costly to introduce a gap in barrier rows.
//
// AND use a separate loop to fill in the first row of the table, enforcing
// the st_ constraints in the process. This is awkward because it
// separates the processing of the first row from the others and might make
// it difficult to use the first-row results in the next row, but it might
// be the simplest and least disruptive way to deal with the st_ constraint.
colstop_ = rff_ - 1;
lastsolcol_ = 0;
for(size_t i = (size_t)rfi_; i < (size_t)rff_; i++) {
assert(pvFStore == d.mat_.fvec(0, i - rfi_));
assert(pvHStore == d.mat_.hvec(0, i - rfi_));
// Fetch the appropriate query profile. Note that elements of rf_ must
// be numbers, not masks.
const int refc = (int)rf_[i];
size_t off = (size_t)firsts5[refc] * iter * 2;
pvScore = d.profbuf_.ptr() + off; // even elts = query profile, odd = gap barrier
// Set all cells to low value
vf = _mm_xor_si128(vf, vf);
// Load H vector from the final row of the previous column
vh = _mm_load_si128(pvHLoad + colstride - ROWSTRIDE);
// Shift 2 bytes down so that topmost (least sig) cell gets 0
vh = _mm_slli_si128(vh, NBYTES_PER_WORD);
// Fill topmost (least sig) cell with high value
vh = _mm_or_si128(vh, vhilsw);
// For each character in the reference text:
size_t j;
for(j = 0; j < iter; j++) {
// Load cells from E, calculated previously
ve = _mm_load_si128(pvELoad);
#if 0
vhd = _mm_load_si128(pvHLoad);
#endif
assert_all_lt(ve, vhi);
pvELoad += ROWSTRIDE;
// Store cells in F, calculated previously
vf = _mm_subs_epu8(vf, pvScore[1]); // veto some ref gap extensions
_mm_store_si128(pvFStore, vf);
pvFStore += ROWSTRIDE;
// Factor in query profile (matches and mismatches)
vh = _mm_subs_epu8(vh, pvScore[0]);
// Update H, factoring in E and F
vh = _mm_max_epu8(vh, ve);
vh = _mm_max_epu8(vh, vf);
// Save the new vH values
_mm_store_si128(pvHStore, vh);
pvHStore += ROWSTRIDE;
// Update vE value
vtmp = vh;
#if 0
vhdtmp = vhd;
vhd = _mm_subs_epu8(vhd, rdgapo);
vhd = _mm_subs_epu8(vhd, pvScore[1]); // veto some read gap opens
ve = _mm_subs_epu8(ve, rdgape);
ve = _mm_max_epu8(ve, vhd);
#else
vh = _mm_subs_epu8(vh, rdgapo);
vh = _mm_subs_epu8(vh, pvScore[1]); // veto some read gap opens
ve = _mm_subs_epu8(ve, rdgape);
ve = _mm_max_epu8(ve, vh);
#endif
assert_all_lt(ve, vhi);
// Load the next h value
#if 0
vh = vhdtmp;