1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500
|
/*
* 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/>.
*/
#ifndef ALIGNER_SWSSE_H_
#define ALIGNER_SWSSE_H_
#include "ds.h"
#include "mem_ids.h"
#include "random_source.h"
#include "scoring.h"
#include "mask.h"
#include "sse_util.h"
#include <strings.h>
struct SSEMetrics {
SSEMetrics():mutex_m() { reset(); }
void clear() { reset(); }
void reset() {
dp = dpsat = dpfail = dpsucc =
col = cell = inner = fixup =
gathsol = bt = btfail = btsucc = btcell =
corerej = nrej = 0;
}
void merge(const SSEMetrics& o, bool getLock = false) {
ThreadSafe ts(&mutex_m, getLock);
dp += o.dp;
dpsat += o.dpsat;
dpfail += o.dpfail;
dpsucc += o.dpsucc;
col += o.col;
cell += o.cell;
inner += o.inner;
fixup += o.fixup;
gathsol += o.gathsol;
bt += o.bt;
btfail += o.btfail;
btsucc += o.btsucc;
btcell += o.btcell;
corerej += o.corerej;
nrej += o.nrej;
}
uint64_t dp; // DPs tried
uint64_t dpsat; // DPs saturated
uint64_t dpfail; // DPs failed
uint64_t dpsucc; // DPs succeeded
uint64_t col; // DP columns
uint64_t cell; // DP cells
uint64_t inner; // DP inner loop iters
uint64_t fixup; // DP fixup loop iters
uint64_t gathsol; // DP gather solution cells found
uint64_t bt; // DP backtraces
uint64_t btfail; // DP backtraces failed
uint64_t btsucc; // DP backtraces succeeded
uint64_t btcell; // DP backtrace cells traversed
uint64_t corerej; // DP backtrace core rejections
uint64_t nrej; // DP backtrace N rejections
MUTEX_T mutex_m;
};
/**
* Encapsulates matrix information calculated by the SSE aligner.
*
* Matrix memory is laid out as follows:
*
* - Elements (individual cell scores) are packed into __m128i vectors
* - Vectors are packed into quartets, quartet elements correspond to: a vector
* from E, one from F, one from H, and one that's "reserved"
* - Quartets are packed into columns, where the number of quartets is
* determined by the number of query characters divided by the number of
* elements per vector
*
* Regarding the "reserved" element of the vector quartet: we use it for two
* things. First, we use the first column of reserved vectors to stage the
* initial column of H vectors. Second, we use the "reserved" vectors during
* the backtrace procedure to store information about (a) which cells have been
* traversed, (b) whether the cell is "terminal" (in local mode), etc.
*/
struct SSEMatrix {
// Each matrix element is a quartet of vectors. These constants are used
// to identify members of the quartet.
const static size_t E = 0;
const static size_t F = 1;
const static size_t H = 2;
const static size_t TMP = 3;
SSEMatrix(int cat = 0) : nvecPerCell_(4), matbuf_(cat) { }
/**
* Return a pointer to the matrix buffer.
*/
inline __m128i *ptr() {
assert(inited_);
return matbuf_.ptr();
}
/**
* Return a pointer to the E vector at the given row and column. Note:
* here row refers to rows of vectors, not rows of elements.
*/
inline __m128i* evec(size_t row, size_t col) {
assert_lt(row, nvecrow_);
assert_lt(col, nveccol_);
size_t elt = row * rowstride() + col * colstride() + E;
assert_lt(elt, matbuf_.size());
return ptr() + elt;
}
/**
* Like evec, but it's allowed to ask for a pointer to one column after the
* final one.
*/
inline __m128i* evecUnsafe(size_t row, size_t col) {
assert_lt(row, nvecrow_);
assert_leq(col, nveccol_);
size_t elt = row * rowstride() + col * colstride() + E;
assert_lt(elt, matbuf_.size());
return ptr() + elt;
}
/**
* Return a pointer to the F vector at the given row and column. Note:
* here row refers to rows of vectors, not rows of elements.
*/
inline __m128i* fvec(size_t row, size_t col) {
assert_lt(row, nvecrow_);
assert_lt(col, nveccol_);
size_t elt = row * rowstride() + col * colstride() + F;
assert_lt(elt, matbuf_.size());
return ptr() + elt;
}
/**
* Return a pointer to the H vector at the given row and column. Note:
* here row refers to rows of vectors, not rows of elements.
*/
inline __m128i* hvec(size_t row, size_t col) {
assert_lt(row, nvecrow_);
assert_lt(col, nveccol_);
size_t elt = row * rowstride() + col * colstride() + H;
assert_lt(elt, matbuf_.size());
return ptr() + elt;
}
/**
* Return a pointer to the TMP vector at the given row and column. Note:
* here row refers to rows of vectors, not rows of elements.
*/
inline __m128i* tmpvec(size_t row, size_t col) {
assert_lt(row, nvecrow_);
assert_lt(col, nveccol_);
size_t elt = row * rowstride() + col * colstride() + TMP;
assert_lt(elt, matbuf_.size());
return ptr() + elt;
}
/**
* Like tmpvec, but it's allowed to ask for a pointer to one column after
* the final one.
*/
inline __m128i* tmpvecUnsafe(size_t row, size_t col) {
assert_lt(row, nvecrow_);
assert_leq(col, nveccol_);
size_t elt = row * rowstride() + col * colstride() + TMP;
assert_lt(elt, matbuf_.size());
return ptr() + elt;
}
/**
* Given a number of rows (nrow), a number of columns (ncol), and the
* number of words to fit inside a single __m128i vector, initialize the
* matrix buffer to accomodate the needed configuration of vectors.
*/
void init(
size_t nrow,
size_t ncol,
size_t wperv);
/**
* Return the number of __m128i's you need to skip over to get from one
* cell to the cell one column over from it.
*/
inline size_t colstride() const { return colstride_; }
/**
* Return the number of __m128i's you need to skip over to get from one
* cell to the cell one row down from it.
*/
inline size_t rowstride() const { return rowstride_; }
/**
* Given a row, col and matrix (i.e. E, F or H), return the corresponding
* element.
*/
int eltSlow(size_t row, size_t col, size_t mat) const;
/**
* Given a row, col and matrix (i.e. E, F or H), return the corresponding
* element.
*/
inline int elt(size_t row, size_t col, size_t mat) const {
assert(inited_);
assert_lt(row, nrow_);
assert_lt(col, ncol_);
assert_lt(mat, 3);
// Move to beginning of column/row
size_t rowelt = row / nvecrow_;
size_t rowvec = row % nvecrow_;
size_t eltvec = (col * colstride_) + (rowvec * rowstride_) + mat;
assert_lt(eltvec, matbuf_.size());
if(wperv_ == 16) {
return (int)((uint8_t*)(matbuf_.ptr() + eltvec))[rowelt];
} else {
assert_eq(8, wperv_);
return (int)((int16_t*)(matbuf_.ptr() + eltvec))[rowelt];
}
}
/**
* Return the element in the E matrix at element row, col.
*/
inline int eelt(size_t row, size_t col) const {
return elt(row, col, E);
}
/**
* Return the element in the F matrix at element row, col.
*/
inline int felt(size_t row, size_t col) const {
return elt(row, col, F);
}
/**
* Return the element in the H matrix at element row, col.
*/
inline int helt(size_t row, size_t col) const {
return elt(row, col, H);
}
/**
* Return true iff the given cell has its reportedThru bit set.
*/
inline bool reportedThrough(
size_t row, // current row
size_t col) const // current column
{
return (masks_[row][col] & (1 << 0)) != 0;
}
/**
* Set the given cell's reportedThru bit.
*/
inline void setReportedThrough(
size_t row, // current row
size_t col) // current column
{
masks_[row][col] |= (1 << 0);
}
/**
* Return true iff the H mask has been set with a previous call to hMaskSet.
*/
bool isHMaskSet(
size_t row, // current row
size_t col) const; // current column
/**
* Set the given cell's H mask. This is the mask of remaining legal ways to
* backtrack from the H cell at this coordinate. It's 5 bits long and has
* offset=2 into the 16-bit field.
*/
void hMaskSet(
size_t row, // current row
size_t col, // current column
int mask);
/**
* Return true iff the E mask has been set with a previous call to eMaskSet.
*/
bool isEMaskSet(
size_t row, // current row
size_t col) const; // current column
/**
* Set the given cell's E mask. This is the mask of remaining legal ways to
* backtrack from the E cell at this coordinate. It's 2 bits long and has
* offset=8 into the 16-bit field.
*/
void eMaskSet(
size_t row, // current row
size_t col, // current column
int mask);
/**
* Return true iff the F mask has been set with a previous call to fMaskSet.
*/
bool isFMaskSet(
size_t row, // current row
size_t col) const; // current column
/**
* Set the given cell's F mask. This is the mask of remaining legal ways to
* backtrack from the F cell at this coordinate. It's 2 bits long and has
* offset=11 into the 16-bit field.
*/
void fMaskSet(
size_t row, // current row
size_t col, // current column
int mask);
/**
* Analyze a cell in the SSE-filled dynamic programming matrix. Determine &
* memorize ways that we can backtrack from the cell. If there is at least one
* way to backtrack, select one at random and return the selection.
*
* There are a few subtleties to keep in mind regarding which cells can be at
* the end of a backtrace. First of all: cells from which we can backtrack
* should not be at the end of a backtrace. But have to distinguish between
* cells whose masks eventually become 0 (we shouldn't end at those), from
* those whose masks were 0 all along (we can end at those).
*/
void analyzeCell(
size_t row, // current row
size_t col, // current column
size_t ct, // current cell type: E/F/H
int refc,
int readc,
int readq,
const Scoring& sc, // scoring scheme
int64_t offsetsc, // offset to add to each score
RandomSource& rand, // rand gen for choosing among equal options
bool& empty, // out: =true iff no way to backtrace
int& cur, // out: =type of transition
bool& branch, // out: =true iff we chose among >1 options
bool& canMoveThru, // out: =true iff ...
bool& reportedThru); // out: =true iff ...
/**
* Initialize the matrix of masks and backtracking flags.
*/
void initMasks();
/**
* Return the number of rows in the dynamic programming matrix.
*/
size_t nrow() const {
return nrow_;
}
/**
* Return the number of columns in the dynamic programming matrix.
*/
size_t ncol() const {
return ncol_;
}
/**
* Prepare a row so we can use it to store masks.
*/
void resetRow(size_t i) {
assert(!reset_[i]);
masks_[i].resizeNoCopy(ncol_);
masks_[i].fillZero();
reset_[i] = true;
}
bool inited_; // initialized?
size_t nrow_; // # rows
size_t ncol_; // # columns
size_t nvecrow_; // # vector rows (<= nrow_)
size_t nveccol_; // # vector columns (<= ncol_)
size_t wperv_; // # words per vector
size_t vecshift_; // # bits to shift to divide by words per vec
size_t nvecPerCol_; // # vectors per column
size_t nvecPerCell_; // # vectors per matrix cell (4)
size_t colstride_; // # vectors b/t adjacent cells in same row
size_t rowstride_; // # vectors b/t adjacent cells in same col
EList_m128i matbuf_; // buffer for holding vectors
ELList<uint16_t> masks_; // buffer for masks/backtracking flags
EList<bool> reset_; // true iff row in masks_ has been reset
};
/**
* All the data associated with the query profile and other data needed for SSE
* alignment of a query.
*/
struct SSEData {
SSEData(int cat = 0) : profbuf_(cat), mat_(cat) { }
EList_m128i profbuf_; // buffer for query profile & temp vecs
EList_m128i vecbuf_; // buffer for 2 column vectors (not using mat_)
size_t qprofStride_; // stride for query profile
size_t gbarStride_; // gap barrier for query profile
SSEMatrix mat_; // SSE matrix for holding all E, F, H vectors
size_t maxPen_; // biggest penalty of all
size_t maxBonus_; // biggest bonus of all
size_t lastIter_; // which 128-bit striped word has final row?
size_t lastWord_; // which word within 128-word has final row?
int bias_; // all scores shifted up by this for unsigned
};
/**
* Return true iff the H mask has been set with a previous call to hMaskSet.
*/
inline bool SSEMatrix::isHMaskSet(
size_t row, // current row
size_t col) const // current column
{
return (masks_[row][col] & (1 << 1)) != 0;
}
/**
* Set the given cell's H mask. This is the mask of remaining legal ways to
* backtrack from the H cell at this coordinate. It's 5 bits long and has
* offset=2 into the 16-bit field.
*/
inline void SSEMatrix::hMaskSet(
size_t row, // current row
size_t col, // current column
int mask)
{
assert_lt(mask, 32);
masks_[row][col] &= ~(31 << 1);
masks_[row][col] |= (1 << 1 | mask << 2);
}
/**
* Return true iff the E mask has been set with a previous call to eMaskSet.
*/
inline bool SSEMatrix::isEMaskSet(
size_t row, // current row
size_t col) const // current column
{
return (masks_[row][col] & (1 << 7)) != 0;
}
/**
* Set the given cell's E mask. This is the mask of remaining legal ways to
* backtrack from the E cell at this coordinate. It's 2 bits long and has
* offset=8 into the 16-bit field.
*/
inline void SSEMatrix::eMaskSet(
size_t row, // current row
size_t col, // current column
int mask)
{
assert_lt(mask, 4);
masks_[row][col] &= ~(7 << 7);
masks_[row][col] |= (1 << 7 | mask << 8);
}
/**
* Return true iff the F mask has been set with a previous call to fMaskSet.
*/
inline bool SSEMatrix::isFMaskSet(
size_t row, // current row
size_t col) const // current column
{
return (masks_[row][col] & (1 << 10)) != 0;
}
/**
* Set the given cell's F mask. This is the mask of remaining legal ways to
* backtrack from the F cell at this coordinate. It's 2 bits long and has
* offset=11 into the 16-bit field.
*/
inline void SSEMatrix::fMaskSet(
size_t row, // current row
size_t col, // current column
int mask)
{
assert_lt(mask, 4);
masks_[row][col] &= ~(7 << 10);
masks_[row][col] |= (1 << 10 | mask << 11);
}
#define ROWSTRIDE_2COL 4
#define ROWSTRIDE 4
#endif /*ndef ALIGNER_SWSSE_H_*/
|