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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033
|
/*
* Copyright 2014, Daehwan Kim <infphilo@gmail.com>
*
* This file is part of HISAT.
*
* HISAT 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.
*
* HISAT 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 HISAT. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef HI_ALIGNER_H_
#define HI_ALIGNER_H_
#include <iostream>
#include <utility>
#include <limits>
#include "qual.h"
#include "ds.h"
#include "sstring.h"
#include "alphabet.h"
#include "edit.h"
#include "read.h"
// Threading is necessary to synchronize the classes that dump
// intermediate alignment results to files. Otherwise, all data herein
// is constant and shared, or per-thread.
#include "threading.h"
#include "aligner_result.h"
#include "scoring.h"
#include "mem_ids.h"
#include "simple_func.h"
#include "group_walk.h"
/**
* Hit types for BWTHit class below
* Three hit types to anchor a read on the genome
*
*/
enum {
CANDIDATE_HIT = 1,
PSEUDOGENE_HIT,
ANCHOR_HIT,
};
/**
* Simple struct for holding a partial alignment for the read
* The alignment locations are represented by FM offsets [top, bot),
* and later genomic offsets are calculated when necessary
*/
template <typename index_t>
struct BWTHit {
BWTHit() { reset(); }
void reset() {
_top = _bot = 0;
_fw = true;
_bwoff = (index_t)OFF_MASK;
_len = 0;
_coords.clear();
_anchor_examined = false;
_hit_type = CANDIDATE_HIT;
}
void init(
index_t top,
index_t bot,
bool fw,
uint32_t bwoff,
uint32_t len,
index_t hit_type = CANDIDATE_HIT)
{
_top = top;
_bot = bot;
_fw = fw;
_bwoff = bwoff;
_len = len;
_coords.clear();
_anchor_examined = false;
_hit_type = hit_type;
}
bool hasGenomeCoords() const { return !_coords.empty(); }
/**
* Return true iff there is no hit.
*/
bool empty() const {
return _bot <= _top;
}
/**
* Higher score = higher priority.
*/
bool operator<(const BWTHit& o) const {
return _len > o._len;
}
/**
* Return the size of the alignments SA ranges.
*/
index_t size() const {
assert_leq(_top, _bot);
return _bot - _top;
}
index_t len() const {
// assert_gt(_len, 0);
return _len;
}
#ifndef NDEBUG
/**
* Check that hit is sane w/r/t read.
*/
bool repOk(const Read& rd) const {
assert_gt(_bot, _top);
assert_neq(_bwoff, (index_t)OFF_MASK);
assert_gt(_len, 0);
return true;
}
#endif
index_t _top; // start of the range in the FM index
index_t _bot; // end of the range in the FM index
bool _fw; // whether read is forward or reverse complemented
index_t _bwoff; // current base of a read to search from the right end
index_t _len; // read length
EList<Coord> _coords; // genomic offsets corresponding to [_top, _bot)
bool _anchor_examined; // whether or not this hit is examined
index_t _hit_type; // hit type (anchor hit, pseudogene hit, or candidate hit)
};
/**
* Simple struct for holding alignments for the read
* The alignments are represented by chains of BWTHits
*/
template <typename index_t>
struct ReadBWTHit {
ReadBWTHit() { reset(); }
void reset() {
_fw = true;
_len = 0;
_cur = 0;
_done = false;
_numPartialSearch = 0;
_numUniqueSearch = 0;
_partialHits.clear();
}
void init(
bool fw,
index_t len)
{
_fw = fw;
assert_gt(len, 0);
_len = len;
_cur = 0;
_done = false;
_numPartialSearch = 0;
_numUniqueSearch = 0;
_partialHits.clear();
}
bool done() {
#ifndef NDEBUG
assert_gt(_len, 0);
if(_cur >= _len) {
assert(_done);
}
#endif
return _done;
}
void done(bool done) {
// assert(!_done);
assert(done);
_done = done;
}
index_t len() const { return _len; }
index_t cur() const { return _cur; }
size_t offsetSize() { return _partialHits.size(); }
size_t numPartialSearch() { return _numPartialSearch; }
size_t numActualPartialSearch()
{
assert_leq(_numUniqueSearch, _numPartialSearch);
return _numPartialSearch - _numUniqueSearch;
}
bool width(index_t offset_) {
assert_lt(offset_, _partialHits.size());
return _partialHits[offset_].size();
}
bool hasGenomeCoords(index_t offset_) {
assert_lt(offset_, _partialHits.size());
index_t width_ = width(offset_);
if(width_ == 0) {
return true;
} else {
return _partialHits[offset_].hasGenomeCoords();
}
}
bool hasAllGenomeCoords() {
if(_cur < _len) return false;
if(_partialHits.size() <= 0) return false;
for(size_t oi = 0; oi < _partialHits.size(); oi++) {
if(!_partialHits[oi].hasGenomeCoords())
return false;
}
return true;
}
/**
*
*/
index_t minWidth(index_t& offset) const {
index_t minWidth_ = (index_t)OFF_MASK;
index_t minWidthLen_ = 0;
for(size_t oi = 0; oi < _partialHits.size(); oi++) {
const BWTHit<index_t>& hit = _partialHits[oi];
if(hit.empty()) continue;
// if(!hit.hasGenomeCoords()) continue;
assert_gt(hit.size(), 0);
if((minWidth_ > hit.size()) ||
(minWidth_ == hit.size() && minWidthLen_ < hit.len())) {
minWidth_ = hit.size();
minWidthLen_ = hit.len();
offset = (index_t)oi;
}
}
return minWidth_;
}
// add policy for calculating a search score
int64_t searchScore(index_t minK) {
int64_t score = 0;
const int64_t penaltyPerOffset = minK * minK;
for(size_t i = 0; i < _partialHits.size(); i++) {
index_t len = _partialHits[i]._len;
score += (len * len);
}
assert_geq(_numPartialSearch, _partialHits.size());
index_t actualPartialSearch = numActualPartialSearch();
score -= (actualPartialSearch * penaltyPerOffset);
score -= (1 << (actualPartialSearch << 1));
return score;
}
BWTHit<index_t>& getPartialHit(index_t offset_) {
assert_lt(offset_, _partialHits.size());
return _partialHits[offset_];
}
bool adjustOffset(index_t minK) {
assert_gt(_partialHits.size(), 0);
const BWTHit<index_t>& hit = _partialHits.back();
if(hit.len() >= minK + 3) {
return false;
}
assert_geq(_cur, hit.len());
index_t origCur = _cur - hit.len();
_cur = origCur + max(hit.len(), minK + 1) - minK;
_partialHits.pop_back();
return true;
}
void setOffset(index_t offset) {
//assert_lt(offset, _len); //FIXME: assertion fails as offset == _len
_cur = offset;
}
#ifndef NDEBUG
/**
*/
bool repOk() const {
for(size_t i = 0; i < _partialHits.size(); i++) {
if(i == 0) {
assert_geq(_partialHits[i]._bwoff, 0);
}
if(i + 1 < _partialHits.size()) {
assert_leq(_partialHits[i]._bwoff + _partialHits[i]._len, _partialHits[i+1]._bwoff);
} else {
assert_eq(i+1, _partialHits.size());
assert_eq(_partialHits[i]._bwoff + _partialHits[i]._len, _cur);
}
}
return true;
}
#endif
bool _fw;
index_t _len;
index_t _cur;
bool _done;
index_t _numPartialSearch;
index_t _numUniqueSearch;
index_t _cur_local;
EList<BWTHit<index_t> > _partialHits;
};
/**
* this is per-thread data, which are shared by GenomeHit classes
* the main purpose of this struct is to avoid extensive use of memory related functions
* such as new and delete - those are really slow and lock based
*/
template <typename index_t>
struct SharedTempVars {
SStringExpandable<char> raw_refbuf;
SStringExpandable<char> raw_refbuf2;
EList<int64_t> temp_scores;
EList<int64_t> temp_scores2;
ASSERT_ONLY(SStringExpandable<uint32_t> destU32);
ASSERT_ONLY(BTDnaString editstr);
ASSERT_ONLY(BTDnaString partialseq);
ASSERT_ONLY(BTDnaString refstr);
ASSERT_ONLY(EList<index_t> reflens);
ASSERT_ONLY(EList<index_t> refoffs);
LinkedEList<EList<Edit> > raw_edits;
};
/**
* GenomeHit represents read alignment or alignment of a part of a read
* Two GenomeHits that represents alignments of different parts of a read
* can be combined together. Also, GenomeHit can be extended in both directions.
*/
template <typename index_t>
struct GenomeHit {
GenomeHit() :
_fw(false),
_rdoff((index_t)OFF_MASK),
_len((index_t)OFF_MASK),
_trim5(0),
_trim3(0),
_tidx((index_t)OFF_MASK),
_toff((index_t)OFF_MASK),
_edits(NULL),
_score(MIN_I64),
_hitcount(1),
_edits_node(NULL),
_sharedVars(NULL)
{
}
GenomeHit(const GenomeHit& otherHit) :
_fw(false),
_rdoff((index_t)OFF_MASK),
_len((index_t)OFF_MASK),
_trim5(0),
_trim3(0),
_tidx((index_t)OFF_MASK),
_toff((index_t)OFF_MASK),
_edits(NULL),
_score(MIN_I64),
_hitcount(1),
_edits_node(NULL),
_sharedVars(NULL)
{
init(otherHit._fw,
otherHit._rdoff,
otherHit._len,
otherHit._trim5,
otherHit._trim3,
otherHit._tidx,
otherHit._toff,
*(otherHit._sharedVars),
otherHit._edits,
otherHit._score,
otherHit._splicescore);
}
GenomeHit<index_t>& operator=(const GenomeHit<index_t>& otherHit) {
if(this == &otherHit) return *this;
init(otherHit._fw,
otherHit._rdoff,
otherHit._len,
otherHit._trim5,
otherHit._trim3,
otherHit._tidx,
otherHit._toff,
*(otherHit._sharedVars),
otherHit._edits,
otherHit._score,
otherHit._splicescore);
return *this;
}
~GenomeHit() {
if(_edits_node != NULL) {
assert(_edits != NULL);
assert(_sharedVars != NULL);
_sharedVars->raw_edits.delete_node(_edits_node);
_edits = NULL;
_edits_node = NULL;
_sharedVars = NULL;
}
}
void init(
bool fw,
index_t rdoff,
index_t len,
index_t trim5,
index_t trim3,
index_t tidx,
index_t toff,
SharedTempVars<index_t>& sharedVars,
EList<Edit>* edits = NULL,
int64_t score = 0,
double splicescore = 0.0)
{
_fw = fw;
_rdoff = rdoff;
_len = len;
_trim5 = trim5;
_trim3 = trim3;
_tidx = tidx;
_toff = toff;
_score = score;
_splicescore = splicescore;
assert(_sharedVars == NULL || _sharedVars == &sharedVars);
_sharedVars = &sharedVars;
if(_edits == NULL) {
assert(_edits_node == NULL);
_edits_node = _sharedVars->raw_edits.new_node();
assert(_edits_node != NULL);
_edits = &(_edits_node->payload);
}
assert(_edits != NULL);
_edits->clear();
if(edits != NULL) *_edits = *edits;
_hitcount = 1;
}
bool inited() const {
return _len >= 0 && _len < (index_t)OFF_MASK;
}
index_t rdoff() const { return _rdoff; }
index_t len() const { return _len; }
index_t trim5() const { return _trim5; }
index_t trim3() const { return _trim3; }
void trim5(index_t trim5) { _trim5 = trim5; }
void trim3(index_t trim3) { _trim3 = trim3; }
index_t ref() const { return _tidx; }
index_t refoff() const { return _toff; }
index_t fw() const { return _fw; }
index_t hitcount() const { return _hitcount; }
/**
* Leftmost coordinate
*/
Coord coord() const {
return Coord(_tidx, _toff, _fw);
}
const EList<Edit>& edits() const { return *_edits; }
bool operator== (const GenomeHit<index_t>& other) const {
if(_fw != other._fw ||
_rdoff != other._rdoff ||
_len != other._len ||
_tidx != other._tidx ||
_toff != other._toff ||
_trim5 != other._trim5 ||
_trim3 != other._trim3) {
return false;
}
if(_edits->size() != other._edits->size()) return false;
for(index_t i = 0; i < _edits->size(); i++) {
if(!((*_edits)[i] == (*other._edits)[i])) return false;
}
// daehwan - this may not be true when some splice sites are provided from outside
// assert_eq(_score, other._score);
return true;
}
bool contains(const GenomeHit<index_t>& other) const {
return (*this) == other;
}
#ifndef NDEBUG
/**
* Check that hit is sane w/r/t read.
*/
bool repOk(const Read& rd, const BitPairReference& ref);
#endif
public:
bool _fw;
index_t _rdoff;
index_t _len;
index_t _trim5;
index_t _trim3;
index_t _tidx;
index_t _toff;
EList<Edit>* _edits;
int64_t _score;
double _splicescore;
index_t _hitcount; // for selection purposes
LinkedEListNode<EList<Edit> >* _edits_node;
SharedTempVars<index_t>* _sharedVars;
};
#ifndef NDEBUG
/**
* Check that hit is sane w/r/t read.
*/
template <typename index_t>
bool GenomeHit<index_t>::repOk(const Read& rd, const BitPairReference& ref)
{
assert(_sharedVars != NULL);
SStringExpandable<char>& raw_refbuf = _sharedVars->raw_refbuf;
SStringExpandable<uint32_t>& destU32 = _sharedVars->destU32;
BTDnaString& editstr = _sharedVars->editstr;
BTDnaString& partialseq = _sharedVars->partialseq;
BTDnaString& refstr = _sharedVars->refstr;
EList<index_t>& reflens = _sharedVars->reflens;
EList<index_t>& refoffs = _sharedVars->refoffs;
editstr.clear(); partialseq.clear(); refstr.clear();
reflens.clear(); refoffs.clear();
const BTDnaString& seq = _fw ? rd.patFw : rd.patRc;
partialseq.install(seq.buf() + this->_rdoff, (size_t)this->_len);
Edit::toRef(partialseq, *_edits, editstr);
index_t refallen = 0;
int64_t reflen = 0;
int64_t refoff = this->_toff;
refoffs.push_back(refoff);
size_t eidx = 0;
for(size_t i = 0; i < _len; i++, reflen++, refoff++) {
while(eidx < _edits->size() && (*_edits)[eidx].pos == i) {
const Edit& edit = (*_edits)[eidx];
if(edit.isReadGap()) {
reflen++;
refoff++;
} else if(edit.isRefGap()) {
reflen--;
refoff--;
}
if(edit.isSpliced()) {
assert_gt(reflen, 0);
refallen += reflen;
reflens.push_back((index_t)reflen);
reflen = 0;
refoff += edit.splLen;
assert_gt(refoff, 0);
refoffs.push_back((index_t)refoff);
}
eidx++;
}
}
assert_gt(reflen, 0);
refallen += (index_t)reflen;
reflens.push_back(reflen);
assert_gt(reflens.size(), 0);
assert_gt(refoffs.size(), 0);
assert_eq(reflens.size(), refoffs.size());
refstr.clear();
for(index_t i = 0; i < reflens.size(); i++) {
assert_gt(reflens[i], 0);
if(i > 0) {
assert_gt(refoffs[i], refoffs[i-1]);
}
raw_refbuf.resize(reflens[i] + 16);
raw_refbuf.clear();
int off = ref.getStretch(
reinterpret_cast<uint32_t*>(raw_refbuf.wbuf()),
(size_t)this->_tidx,
(size_t)max<TRefOff>(refoffs[i], 0),
reflens[i],
destU32);
assert_leq(off, 16);
for(index_t j = 0; j < reflens[i]; j++) {
char rfc = *(raw_refbuf.buf()+off+j);
refstr.append(rfc);
}
}
if(refstr != editstr) {
cerr << "Decoded nucleotides and edits don't match reference:" << endl;
//cerr << " score: " << score.score()
//<< " (" << gaps << " gaps)" << endl;
cerr << " edits: ";
Edit::print(cerr, *_edits);
cerr << endl;
cerr << " decoded nucs: " << partialseq << endl;
cerr << " edited nucs: " << editstr << endl;
cerr << " reference nucs: " << refstr << endl;
assert(0);
}
return true;
}
#endif
/**
* Encapsulates counters that measure how much work has been done by
* hierarchical indexing
*/
struct HIMetrics {
HIMetrics() : mutex_m() {
reset();
}
void reset() {
anchoratts = 0;
localatts = 0;
localindexatts = 0;
localextatts = 0;
localsearchrecur = 0;
globalgenomecoords = 0;
localgenomecoords = 0;
}
void init(
uint64_t localatts_,
uint64_t anchoratts_,
uint64_t localindexatts_,
uint64_t localextatts_,
uint64_t localsearchrecur_,
uint64_t globalgenomecoords_,
uint64_t localgenomecoords_)
{
localatts = localatts_;
anchoratts = anchoratts_;
localindexatts = localindexatts_;
localextatts = localextatts_;
localsearchrecur = localsearchrecur_;
globalgenomecoords = globalgenomecoords_;
localgenomecoords = localgenomecoords_;
}
/**
* Merge (add) the counters in the given HIMetrics object into this
* object. This is the only safe way to update a HIMetrics shared
* by multiple threads.
*/
void merge(const HIMetrics& r, bool getLock = false) {
ThreadSafe ts(&mutex_m, getLock);
localatts += r.localatts;
anchoratts += r.anchoratts;
localindexatts += r.localindexatts;
localextatts += r.localextatts;
localsearchrecur += r.localsearchrecur;
globalgenomecoords += r.globalgenomecoords;
localgenomecoords += r.localgenomecoords;
}
uint64_t localatts; // # attempts of local search
uint64_t anchoratts; // # attempts of anchor search
uint64_t localindexatts; // # attempts of local index search
uint64_t localextatts; // # attempts of extension search
uint64_t localsearchrecur;
uint64_t globalgenomecoords;
uint64_t localgenomecoords;
MUTEX_T mutex_m;
};
/**
* With a hierarchical indexing, SplicedAligner provides several alignment strategies
* , which enable effective alignment of RNA-seq reads
*/
template <typename index_t, typename local_index_t>
class HI_Aligner {
public:
/**
* Initialize with index.
*/
HI_Aligner(
const Ebwt<index_t>& ebwt,
bool secondary = false,
bool local = false,
uint64_t threads_rids_mindist = 0,
bool no_spliced_alignment = false) :
_secondary(secondary),
_local(local),
_gwstate(GW_CAT),
_gwstate_local(GW_CAT),
_thread_rids_mindist(threads_rids_mindist),
_no_spliced_alignment(no_spliced_alignment)
{
index_t genomeLen = ebwt.eh().len();
_minK = 0;
while(genomeLen > 0) {
genomeLen >>= 2;
_minK++;
}
_minK_local = 8;
}
HI_Aligner() {
}
/**
*/
void initRead(Read *rd, bool nofw, bool norc, TAlScore minsc, TAlScore maxpen, bool rightendonly = false) {
assert(rd != NULL);
_rds[0] = rd;
_rds[1] = NULL;
_paired = false;
_rightendonly = rightendonly;
_nofw[0] = nofw;
_nofw[1] = true;
_norc[0] = norc;
_norc[1] = true;
_minsc[0] = minsc;
_minsc[1] = OFF_MASK;
_maxpen[0] = maxpen;
_maxpen[1] = OFF_MASK;
for(size_t fwi = 0; fwi < 2; fwi++) {
bool fw = (fwi == 0);
_hits[0][fwi].init(fw, _rds[0]->length());
}
_genomeHits.clear();
_concordantPairs.clear();
_hits_searched[0].clear();
assert(!_paired);
}
/**
*/
void initReads(Read *rds[2], bool nofw[2], bool norc[2], TAlScore minsc[2], TAlScore maxpen[2]) {
assert(rds[0] != NULL && rds[1] != NULL);
_paired = true;
_rightendonly = false;
for(size_t rdi = 0; rdi < 2; rdi++) {
_rds[rdi] = rds[rdi];
_nofw[rdi] = nofw[rdi];
_norc[rdi] = norc[rdi];
_minsc[rdi] = minsc[rdi];
_maxpen[rdi] = maxpen[rdi];
for(size_t fwi = 0; fwi < 2; fwi++) {
bool fw = (fwi == 0);
_hits[rdi][fwi].init(fw, _rds[rdi]->length());
}
_hits_searched[rdi].clear();
}
_genomeHits.clear();
_concordantPairs.clear();
assert(_paired);
assert(!_rightendonly);
}
/**
* Aligns a read or a pair
* This funcion is called per read or pair
*/
virtual
int go(
const Scoring& sc,
const Ebwt<index_t>& ebwtFw,
const Ebwt<index_t>& ebwtBw,
const BitPairReference& ref,
WalkMetrics& wlm,
PerReadMetrics& prm,
HIMetrics& him,
SpeciesMetrics& spm,
RandomSource& rnd,
AlnSinkWrap<index_t>& sink) = 0;
/**
* Align a part of a read without any edits
*/
size_t partialSearch(
const Ebwt<index_t>& ebwt, // BWT index
const Read& read, // read to align
const Scoring& sc, // scoring scheme
bool fw, // don't align forward read
size_t mineMax, // don't care about edit bounds > this
size_t& mineFw, // minimum # edits for forward read
size_t& mineRc, // minimum # edits for revcomp read
ReadBWTHit<index_t>& hit, // holds all the seed hits (and exact hit)
RandomSource& rnd);
protected:
Read * _rds[2];
bool _paired;
bool _rightendonly;
bool _nofw[2];
bool _norc[2];
TAlScore _minsc[2];
TAlScore _maxpen[2];
bool _secondary; // allow secondary alignments
bool _local; // perform local alignments
ReadBWTHit<index_t> _hits[2][2];
EList<index_t, 16> _offs;
SARangeWithOffs<EListSlice<index_t, 16> > _sas;
GroupWalk2S<index_t, EListSlice<index_t, 16>, 16> _gws;
GroupWalkState<index_t> _gwstate;
EList<local_index_t, 16> _offs_local;
SARangeWithOffs<EListSlice<local_index_t, 16> > _sas_local;
GroupWalk2S<local_index_t, EListSlice<local_index_t, 16>, 16> _gws_local;
GroupWalkState<local_index_t> _gwstate_local;
// temporary and shared variables used for GenomeHit
// this should be defined before _genomeHits and _hits_searched
SharedTempVars<index_t> _sharedVars;
// temporary and shared variables for AlnRes
LinkedEList<EList<Edit> > _rawEdits;
// temporary
EList<GenomeHit<index_t> > _genomeHits;
EList<bool> _genomeHits_done;
ELList<Coord> _coords;
EList<pair<index_t, index_t> > _concordantPairs;
size_t _minK; // log4 of the size of a genome
size_t _minK_local; // log4 of the size of a local index (8)
ELList<GenomeHit<index_t> > _local_genomeHits;
EList<uint8_t> _anchors_added;
uint64_t max_localindexatts;
uint64_t bwops_; // Burrows-Wheeler operations
uint64_t bwedits_; // Burrows-Wheeler edits
//
EList<GenomeHit<index_t> > _hits_searched[2];
uint64_t _thread_rids_mindist;
bool _no_spliced_alignment;
// For AlnRes::matchesRef
ASSERT_ONLY(EList<bool> raw_matches_);
ASSERT_ONLY(BTDnaString tmp_rf_);
ASSERT_ONLY(BTDnaString tmp_rdseq_);
ASSERT_ONLY(BTString tmp_qseq_);
};
#define HIER_INIT_LOCS(top, bot, tloc, bloc, e) { \
if(bot - top == 1) { \
tloc.initFromRow(top, (e).eh(), (e).ebwt()); \
bloc.invalidate(); \
} else { \
SideLocus<index_t>::initFromTopBot(top, bot, (e).eh(), (e).ebwt(), tloc, bloc); \
assert(bloc.valid()); \
} \
}
#define HIER_SANITY_CHECK_4TUP(t, b, tp, bp) { \
ASSERT_ONLY(cur_index_t tot = (b[0]-t[0])+(b[1]-t[1])+(b[2]-t[2])+(b[3]-t[3])); \
ASSERT_ONLY(cur_index_t totp = (bp[0]-tp[0])+(bp[1]-tp[1])+(bp[2]-tp[2])+(bp[3]-tp[3])); \
assert_eq(tot, totp); \
}
/**
* Sweep right-to-left and left-to-right using exact matching. Remember all
* the SA ranges encountered along the way. Report exact matches if there are
* any. Calculate a lower bound on the number of edits in an end-to-end
* alignment.
*/
template <typename index_t, typename local_index_t>
size_t HI_Aligner<index_t, local_index_t>::partialSearch(
const Ebwt<index_t>& ebwt, // BWT index
const Read& read, // read to align
const Scoring& sc, // scoring scheme
bool fw,
size_t mineMax, // don't care about edit bounds > this
size_t& mineFw, // minimum # edits for forward read
size_t& mineRc, // minimum # edits for revcomp read
ReadBWTHit<index_t>& hit, // holds all the seed hits (and exact hit)
RandomSource& rnd) // pseudo-random source
{
const index_t ftabLen = ebwt.eh().ftabChars();
SideLocus<index_t> tloc, bloc;
const index_t len = (index_t)read.length();
const BTDnaString& seq = fw ? read.patFw : read.patRc;
assert(!seq.empty());
size_t nelt = 0;
EList<BWTHit<index_t> >& partialHits = hit._partialHits;
index_t& cur = hit._cur;
assert_lt(cur, hit._len);
hit._numPartialSearch++;
index_t offset = cur;
index_t dep = offset;
index_t top = 0, bot = 0;
index_t topTemp = 0, botTemp = 0;
index_t left = len - dep;
assert_gt(left, 0);
if(left < ftabLen) {
cur = hit._len;
partialHits.expand();
partialHits.back().init((index_t)OFF_MASK,
(index_t)OFF_MASK,
fw,
(uint32_t)offset,
(uint32_t)(cur - offset));
hit.done(true);
return 0;
}
// Does N interfere with use of Ftab?
for(index_t i = 0; i < ftabLen; i++) {
int c = seq[len-dep-1-i];
if(c > 3) {
cur += (i+1);
partialHits.expand();
partialHits.back().init((index_t)OFF_MASK,
(index_t)OFF_MASK,
fw,
(uint32_t)offset,
(uint32_t)(cur - offset));
if(cur >= hit._len) {
hit.done(true);
}
return 0;
}
}
// Use ftab
ebwt.ftabLoHi(seq, len - dep - ftabLen, false, top, bot);
dep += ftabLen;
if(bot <= top) {
cur = dep;
partialHits.expand();
partialHits.back().init((index_t)OFF_MASK,
(index_t)OFF_MASK,
fw,
(uint32_t)offset,
(uint32_t)(cur - offset));
if(cur >= hit._len) {
hit.done(true);
}
return 0;
}
HIER_INIT_LOCS(top, bot, tloc, bloc, ebwt);
// Keep going
while(dep < len) {
int c = seq[len-dep-1];
if(c > 3) {
topTemp = botTemp = 0;
} else {
if(bloc.valid()) {
bwops_ += 2;
topTemp = ebwt.mapLF(tloc, c);
botTemp = ebwt.mapLF(bloc, c);
} else {
bwops_++;
topTemp = ebwt.mapLF1(top, tloc, c);
if(topTemp == (index_t)OFF_MASK) {
topTemp = botTemp = 0;
} else {
botTemp = topTemp + 1;
}
}
}
if(botTemp <= topTemp) {
break;
}
top = topTemp;
bot = botTemp;
dep++;
HIER_INIT_LOCS(top, bot, tloc, bloc, ebwt);
}
// Done
if(bot > top) {
// This is an exact hit
assert_gt(dep, offset);
assert_leq(dep, len);
partialHits.expand();
index_t hit_type = CANDIDATE_HIT;
partialHits.back().init(top,
bot,
fw,
(uint32_t)offset,
(uint32_t)(dep - offset),
hit_type);
nelt += (bot - top);
cur = dep;
if(cur >= hit._len) {
if(hit_type == CANDIDATE_HIT) hit._numUniqueSearch++;
hit.done(true);
}
}
return nelt;
}
#endif /*HI_ALIGNER_H_*/
|