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aligner_sw_driver.h
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aligner_sw_driver.h
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/*
* Copyright 2011, Ben Langmead <[email protected]>
*
* 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_driver.h
*
* REDUNDANT SEED HITS
*
* We say that two seed hits are redundant if they trigger identical
* seed-extend dynamic programming problems. Put another way, they both lie on
* the same diagonal of the overall read/reference dynamic programming matrix.
* Detecting redundant seed hits is simple when the seed hits are ungapped. We
* do this after offset resolution but before the offset is converted to genome
* coordinates (see uses of the seenDiags1_/seenDiags2_ fields for examples).
*
* REDUNDANT ALIGNMENTS
*
* In an unpaired context, we say that two alignments are redundant if they
* share any cells in the global DP table. Roughly speaking, this is like
* saying that two alignments are redundant if any read character aligns to the
* same reference character (same reference sequence, same strand, same offset)
* in both alignments.
*
* In a paired-end context, we say that two paired-end alignments are redundant
* if the mate #1s are redundant and the mate #2s are redundant.
*
* How do we enforce this? In the unpaired context, this is relatively simple:
* the cells from each alignment are checked against a set containing all cells
* from all previous alignments. Given a new alignment, for each cell in the
* new alignment we check whether it is in the set. If there is any overlap,
* the new alignment is rejected as redundant. Otherwise, the new alignment is
* accepted and its cells are added to the set.
*
* Enforcement in a paired context is a little trickier. Consider the
* following approaches:
*
* 1. Skip anchors that are redundant with any previous anchor or opposite
* alignment. This is sufficient to ensure no two concordant alignments
* found are redundant.
*
* 2. Same as scheme 1, but with a "transitive closure" scheme for finding all
* concordant pairs in the vicinity of an anchor. Consider the AB/AC
* scenario from the previous paragraph. If B is the anchor alignment, we
* will find AB but not AC. But under this scheme, once we find AB we then
* let B be a new anchor and immediately look for its opposites. Likewise,
* if we find any opposite, we make them anchors and continue searching. We
* don't stop searching until every opposite is used as an anchor.
*
* 3. Skip anchors that are redundant with any previous anchor alignment (but
* allow anchors that are redundant with previous opposite alignments).
* This isn't sufficient to avoid redundant concordant alignments. To avoid
* redundant concordants, we need an additional procedure that checks each
* new concordant alignment one-by-one against a list of previous concordant
* alignments to see if it is redundant.
*
* We take approach 1.
*/
#ifndef ALIGNER_SW_DRIVER_H_
#define ALIGNER_SW_DRIVER_H_
#include <iostream>
// -- BTL remove --
#include <stdlib.h>
#include <sys/time.h>
// -- --
#include <utility>
#include "ds.h"
#include "aligner_seed.h"
#include "aligner_sw.h"
#include "aligner_cache.h"
#include "reference.h"
#include "group_walk.h"
#include "bt2_idx.h"
#include "mem_ids.h"
#include "aln_sink.h"
#include "pe.h"
#include "ival_list.h"
#include "simple_func.h"
#include "random_util.h"
#include "dp_framer.h"
using namespace std;
template <typename index_t>
struct SeedPos {
SeedPos() : fw(false), offidx(0), rdoff(0), seedlen(0) { }
SeedPos(
bool fw_,
index_t offidx_,
index_t rdoff_,
index_t seedlen_)
{
init(fw_, offidx_, rdoff_, seedlen_);
}
void init(
bool fw_,
index_t offidx_,
index_t rdoff_,
index_t seedlen_)
{
fw = fw_;
offidx = offidx_;
rdoff = rdoff_;
seedlen = seedlen_;
}
bool operator<(const SeedPos& o) const {
if(offidx < o.offidx) return true;
if(offidx > o.offidx) return false;
if(rdoff < o.rdoff) return true;
if(rdoff > o.rdoff) return false;
if(seedlen < o.seedlen) return true;
if(seedlen > o.seedlen) return false;
if(fw && !o.fw) return true;
if(!fw && o.fw) return false;
return false;
}
bool operator>(const SeedPos& o) const {
if(offidx < o.offidx) return false;
if(offidx > o.offidx) return true;
if(rdoff < o.rdoff) return false;
if(rdoff > o.rdoff) return true;
if(seedlen < o.seedlen) return false;
if(seedlen > o.seedlen) return true;
if(fw && !o.fw) return false;
if(!fw && o.fw) return true;
return false;
}
bool operator==(const SeedPos& o) const {
return fw == o.fw && offidx == o.offidx &&
rdoff == o.rdoff && seedlen == o.seedlen;
}
bool fw;
index_t offidx;
index_t rdoff;
index_t seedlen;
};
/**
* An SATuple along with the associated seed position.
*/
template <typename index_t>
struct SATupleAndPos {
SATuple<index_t> sat; // result for this seed hit
SeedPos<index_t> pos; // seed position that yielded the range this was taken from
index_t origSz; // size of range this was taken from
index_t nlex; // # position we can extend seed hit to left w/o edit
index_t nrex; // # position we can extend seed hit to right w/o edit
bool operator<(const SATupleAndPos& o) const {
if(sat < o.sat) return true;
if(sat > o.sat) return false;
return pos < o.pos;
}
bool operator==(const SATupleAndPos& o) const {
return sat == o.sat && pos == o.pos;
}
};
/**
* Encapsulates the weighted random sampling scheme we want to use to pick
* which seed hit range to sample a row from.
*/
template <typename index_t>
class RowSampler {
public:
RowSampler(int cat = 0) : elim_(cat), masses_(cat) {
mass_ = 0.0f;
}
/**
* Initialze sampler with respect to a range of elements in a list of
* SATupleAndPos's.
*/
void init(
const EList<SATupleAndPos<index_t>, 16>& salist,
index_t sai,
index_t saf,
bool lensq, // whether to square the numerator, which = extended length
bool szsq) // whether to square denominator, which =
{
assert_gt(saf, sai);
elim_.resize(saf - sai);
elim_.fill(false);
// Initialize mass
mass_ = 0.0f;
masses_.resize(saf - sai);
for(index_t i = sai; i < saf; i++) {
index_t len = salist[i].nlex + salist[i].nrex + 1; // + salist[i].sat.key.len;
double num = (double)len;
if(lensq) {
num *= num;
}
double denom = (double)salist[i].sat.size();
if(szsq) {
denom *= denom;
}
masses_[i - sai] = num / denom;
mass_ += masses_[i - sai];
}
}
/**
* Caller is indicating that the bin at index i is exhausted and we should
* exclude it from our sampling from now on.
*/
void finishedRange(index_t i) {
assert_lt(i, masses_.size());
elim_[i] = true;
mass_ -= masses_[i];
}
/**
* Sample randomly from the mass.
*/
size_t next(RandomSource& rnd) {
// Throw the dart
double rd = rnd.nextFloat() * mass_;
double mass_sofar = 0.0f;
size_t sz = masses_.size();
size_t last_unelim = std::numeric_limits<size_t>::max();
for(size_t i = 0; i < sz; i++) {
if(!elim_[i]) {
last_unelim = i;
mass_sofar += masses_[i];
if(rd < mass_sofar) {
// This is the one we hit
return i;
}
}
}
assert_neq(std::numeric_limits<size_t>::max(), last_unelim);
return last_unelim;
}
protected:
double mass_; // total probability mass to throw darts at
EList<bool> elim_; // whether the range is eliminated
EList<double> masses_; // mass of each range
};
/**
* Return values from extendSeeds and extendSeedsPaired.
*/
enum {
// All end-to-end and seed hits were examined
// The policy does not need us to look any further
EXTEND_EXHAUSTED_CANDIDATES = 1,
EXTEND_POLICY_FULFILLED,
// We stopped because we reached a point where the only remaining
// alignments of interest have perfect scores, but we already investigated
// perfect alignments
EXTEND_PERFECT_SCORE,
// We stopped because we ran up against a limit on how much work we should
// do for one set of seed ranges, e.g. the limit on number of consecutive
// unproductive DP extensions
EXTEND_EXCEEDED_SOFT_LIMIT,
// We stopped because we ran up against a limit on how much work we should
// do for overall before giving up on a mate
EXTEND_EXCEEDED_HARD_LIMIT
};
/**
* Data structure encapsulating a range that's been extended out in two
* directions.
*/
struct ExtendRange {
void init(size_t off_, size_t len_, size_t sz_) {
off = off_; len = len_; sz = sz_;
}
size_t off; // offset of extended region
size_t len; // length between extremes of extended region
size_t sz; // # of elements in SA range
};
template <typename index_t>
class SwDriver {
typedef PList<index_t, CACHE_PAGE_SZ> TSAList;
public:
SwDriver(size_t bytes) :
satups_(DP_CAT),
gws_(DP_CAT),
seenDiags1_(DP_CAT),
seenDiags2_(DP_CAT),
redAnchor_(DP_CAT),
redMate1_(DP_CAT),
redMate2_(DP_CAT),
pool_(bytes, CACHE_PAGE_SZ, DP_CAT),
salistEe_(DP_CAT),
gwstate_(GW_CAT) { }
/**
* Given a collection of SeedHits for a single read, extend seed alignments
* into full alignments. Where possible, try to avoid redundant offset
* lookups and dynamic programming problems. Optionally report alignments
* to a AlnSinkWrap object as they are discovered.
*
* If 'reportImmediately' is true, returns true iff a call to
* mhs->report() returned true (indicating that the reporting
* policy is satisfied and we can stop). Otherwise, returns false.
*/
int extendSeeds(
Read& rd, // read to align
bool mate1, // true iff rd is mate #1
SeedResults<index_t>& sh, // seed hits to extend into full alignments
const Ebwt<index_t>& ebwtFw, // BWT
const Ebwt<index_t>* ebwtBw, // BWT'
const BitPairReference& ref, // Reference strings
SwAligner& swa, // dynamic programming aligner
const Scoring& sc, // scoring scheme
int seedmms, // # mismatches allowed in seed
int seedlen, // length of seed
int seedival, // interval between seeds
TAlScore& minsc, // minimum score for anchor
int nceil, // maximum # Ns permitted in ref portion
size_t maxhalf, // maximum width on one side of DP table
bool doUngapped, // do ungapped alignment
size_t maxIters, // stop after this many seed-extend loop iters
size_t maxUg, // max # ungapped extends
size_t maxDp, // max # DPs
size_t maxUgStreak, // stop after streak of this many ungap fails
size_t maxDpStreak, // stop after streak of this many dp fails
bool doExtend, // do seed extension
bool enable8, // use 8-bit SSE where possible
size_t cminlen, // use checkpointer if read longer than this
size_t cpow2, // interval between diagonals to checkpoint
bool doTri, // triangular mini-fills
int tighten, // -M score tightening mode
AlignmentCacheIface<index_t>& ca, // alignment cache for seed hits
RandomSource& rnd, // pseudo-random source
WalkMetrics& wlm, // group walk left metrics
SwMetrics& swmSeed, // DP metrics for seed-extend
PerReadMetrics& prm, // per-read metrics
AlnSinkWrap<index_t>* mhs, // HitSink for multiseed-style aligner
bool reportImmediately, // whether to report hits immediately to mhs
bool& exhaustive);
/**
* Given a collection of SeedHits for a read pair, extend seed
* alignments into full alignments and then look for the opposite
* mate using dynamic programming. Where possible, try to avoid
* redundant offset lookups. Optionally report alignments to a
* AlnSinkWrap object as they are discovered.
*
* If 'reportImmediately' is true, returns true iff a call to
* mhs->report() returned true (indicating that the reporting
* policy is satisfied and we can stop). Otherwise, returns false.
*/
int extendSeedsPaired(
Read& rd, // mate to align as anchor
Read& ord, // mate to align as opposite
bool anchor1, // true iff anchor mate is mate1
bool oppFilt, // true iff opposite mate was filtered out
SeedResults<index_t>& sh, // seed hits for anchor
const Ebwt<index_t>& ebwtFw, // BWT
const Ebwt<index_t>* ebwtBw, // BWT'
const BitPairReference& ref, // Reference strings
SwAligner& swa, // dyn programming aligner for anchor
SwAligner& swao, // dyn programming aligner for opposite
const Scoring& sc, // scoring scheme
const PairedEndPolicy& pepol,// paired-end policy
int seedmms, // # mismatches allowed in seed
int seedlen, // length of seed
int seedival, // interval between seeds
TAlScore& minsc, // minimum score for anchor
TAlScore& ominsc, // minimum score for opposite
int nceil, // max # Ns permitted in ref for anchor
int onceil, // max # Ns permitted in ref for opposite
bool nofw, // don't align forward read
bool norc, // don't align revcomp read
size_t maxhalf, // maximum width on one side of DP table
bool doUngapped, // do ungapped alignment
size_t maxIters, // stop after this many seed-extend loop iters
size_t maxUg, // max # ungapped extends
size_t maxDp, // max # DPs
size_t maxEeStreak, // stop after streak of this many end-to-end fails
size_t maxUgStreak, // stop after streak of this many ungap fails
size_t maxDpStreak, // stop after streak of this many dp fails
size_t maxMateStreak, // stop seed range after N mate-find fails
bool doExtend, // do seed extension
bool enable8, // use 8-bit SSE where possible
size_t cminlen, // use checkpointer if read longer than this
size_t cpow2, // interval between diagonals to checkpoint
bool doTri, // triangular mini-fills
int tighten, // -M score tightening mode
AlignmentCacheIface<index_t>& cs, // alignment cache for seed hits
RandomSource& rnd, // pseudo-random source
WalkMetrics& wlm, // group walk left metrics
SwMetrics& swmSeed, // DP metrics for seed-extend
SwMetrics& swmMate, // DP metrics for mate finidng
PerReadMetrics& prm, // per-read metrics for anchor
AlnSinkWrap<index_t>* msink, // AlnSink wrapper for multiseed-style aligner
bool swMateImmediately, // whether to look for mate immediately
bool reportImmediately, // whether to report hits immediately to msink
bool discord, // look for discordant alignments?
bool mixed, // look for unpaired as well as paired alns?
bool& exhaustive);
/**
* Prepare for a new read.
*/
void nextRead(bool paired, size_t mate1len, size_t mate2len) {
redAnchor_.reset();
seenDiags1_.reset();
seenDiags2_.reset();
seedExRangeFw_[0].clear(); // mate 1 fw
seedExRangeFw_[1].clear(); // mate 2 fw
seedExRangeRc_[0].clear(); // mate 1 rc
seedExRangeRc_[1].clear(); // mate 2 rc
size_t maxlen = mate1len;
if(paired) {
redMate1_.reset();
redMate1_.init(mate1len);
redMate2_.reset();
redMate2_.init(mate2len);
if(mate2len > maxlen) {
maxlen = mate2len;
}
}
redAnchor_.init(maxlen);
}
protected:
bool eeSaTups(
const Read& rd, // read
SeedResults<index_t>& sh, // seed hits to extend into full alignments
const Ebwt<index_t>& ebwt, // BWT
const BitPairReference& ref, // Reference strings
RandomSource& rnd, // pseudo-random generator
WalkMetrics& wlm, // group walk left metrics
SwMetrics& swmSeed, // metrics for seed extensions
index_t& nelt_out, // out: # elements total
index_t maxelts, // max # elts to report
bool all); // report all hits?
void extend(
const Read& rd, // read
const Ebwt<index_t>& ebwtFw, // Forward Bowtie index
const Ebwt<index_t>* ebwtBw, // Backward Bowtie index
index_t topf, // top in fw index
index_t botf, // bot in fw index
index_t topb, // top in bw index
index_t botb, // bot in bw index
bool fw, // seed orientation
index_t off, // seed offset from 5' end
index_t len, // seed length
PerReadMetrics& prm, // per-read metrics
index_t& nlex, // # positions we can extend to left w/o edit
index_t& nrex); // # positions we can extend to right w/o edit
void prioritizeSATups(
const Read& rd, // read
SeedResults<index_t>& sh, // seed hits to extend into full alignments
const Ebwt<index_t>& ebwtFw, // BWT
const Ebwt<index_t>* ebwtBw, // BWT'
const BitPairReference& ref, // Reference strings
int seedmms, // # seed mismatches allowed
index_t maxelt, // max elts we'll consider
bool doExtend, // extend out seeds
bool lensq, // square extended length
bool szsq, // square SA range size
index_t nsm, // if range as <= nsm elts, it's "small"
AlignmentCacheIface<index_t>& ca, // alignment cache for seed hits
RandomSource& rnd, // pseudo-random generator
WalkMetrics& wlm, // group walk left metrics
PerReadMetrics& prm, // per-read metrics
index_t& nelt_out, // out: # elements total
bool all); // report all hits?
Random1toN rand_; // random number generators
EList<Random1toN, 16> rands_; // random number generators
EList<Random1toN, 16> rands2_; // random number generators
EList<EEHit<index_t>, 16> eehits_; // holds end-to-end hits
EList<SATupleAndPos<index_t>, 16> satpos_; // holds SATuple, SeedPos pairs
EList<SATupleAndPos<index_t>, 16> satpos2_; // holds SATuple, SeedPos pairs
EList<SATuple<index_t>, 16> satups_; // holds SATuples to explore elements from
EList<GroupWalk2S<index_t, TSlice, 16> > gws_; // list of GroupWalks; no particular order
EList<size_t> mateStreaks_; // mate-find fail streaks
RowSampler<index_t> rowsamp_; // row sampler
// Ranges that we've extended through when extending seed hits
EList<ExtendRange> seedExRangeFw_[2];
EList<ExtendRange> seedExRangeRc_[2];
// Data structures encapsulating the diagonals that have already been used
// to seed alignment for mate 1 and mate 2.
EIvalMergeListBinned seenDiags1_;
EIvalMergeListBinned seenDiags2_;
// For weeding out redundant alignments
RedundantAlns redAnchor_; // database of cells used for anchor alignments
RedundantAlns redMate1_; // database of cells used for mate 1 alignments
RedundantAlns redMate2_; // database of cells used for mate 2 alignments
// For holding results for anchor (res_) and opposite (ores_) mates
SwResult resGap_; // temp holder for alignment result
SwResult oresGap_; // temp holder for alignment result, opp mate
SwResult resUngap_; // temp holder for ungapped alignment result
SwResult oresUngap_; // temp holder for ungap. aln. opp mate
SwResult resEe_; // temp holder for ungapped alignment result
SwResult oresEe_; // temp holder for ungap. aln. opp mate
Pool pool_; // memory pages for salistExact_
TSAList salistEe_; // PList for offsets for end-to-end hits
GroupWalkState<index_t> gwstate_; // some per-thread state shared by all GroupWalks
// For AlnRes::matchesRef:
ASSERT_ONLY(SStringExpandable<char> raw_refbuf_);
ASSERT_ONLY(SStringExpandable<uint32_t> raw_destU32_);
ASSERT_ONLY(EList<bool> raw_matches_);
ASSERT_ONLY(BTDnaString tmp_rf_);
ASSERT_ONLY(BTDnaString tmp_rdseq_);
ASSERT_ONLY(BTString tmp_qseq_);
ASSERT_ONLY(EList<index_t> tmp_reflens_);
ASSERT_ONLY(EList<index_t> tmp_refoffs_);
};
#define TIMER_START() \
struct timeval tv_i, tv_f; \
struct timezone tz_i, tz_f; \
size_t total_usecs; \
gettimeofday(&tv_i, &tz_i)
#define IF_TIMER_END() \
gettimeofday(&tv_f, &tz_f); \
total_usecs = \
(tv_f.tv_sec - tv_i.tv_sec) * 1000000 + (tv_f.tv_usec - tv_i.tv_usec); \
if(total_usecs > 300000)
/*
* aligner_sw_driver.cpp
*
* Routines that drive the alignment process given a collection of seed hits.
* This is generally done in a few stages: extendSeeds visits the set of
* seed-hit BW elements in some order; for each element visited it resolves its
* reference offset; once the reference offset is known, bounds for a dynamic
* programming subproblem are established; if these bounds are distinct from
* the bounds we've already tried, we solve the dynamic programming subproblem
* and report the hit; if the AlnSinkWrap indicates that we can stop, we
* return, otherwise we continue on to the next BW element.
*/
/**
* Given end-to-end alignment results stored in the SeedResults structure, set
* up all of our state for resolving and keeping track of reference offsets for
* hits. Order the list of ranges to examine such that all exact end-to-end
* alignments are examined before any 1mm end-to-end alignments.
*
* Note: there might be a lot of hits and a lot of wide ranges to look for
* here. We use 'maxelt'.
*/
template <typename index_t>
bool SwDriver<index_t>::eeSaTups(
const Read& rd, // read
SeedResults<index_t>& sh, // seed hits to extend into full alignments
const Ebwt<index_t>& ebwt, // BWT
const BitPairReference& ref, // Reference strings
RandomSource& rnd, // pseudo-random generator
WalkMetrics& wlm, // group walk left metrics
SwMetrics& swmSeed, // metrics for seed extensions
index_t& nelt_out, // out: # elements total
index_t maxelt, // max elts we'll consider
bool all) // report all hits?
{
assert_eq(0, nelt_out);
gws_.clear();
rands_.clear();
satpos_.clear();
eehits_.clear();
// First, count up the total number of satpos_, rands_, eehits_, and gws_
// we're going to tuse
index_t nobj = 0;
if(!sh.exactFwEEHit().empty()) nobj++;
if(!sh.exactRcEEHit().empty()) nobj++;
nobj += sh.mm1EEHits().size();
nobj = min(nobj, maxelt);
gws_.ensure(nobj);
rands_.ensure(nobj);
satpos_.ensure(nobj);
eehits_.ensure(nobj);
index_t tot = sh.exactFwEEHit().size() + sh.exactRcEEHit().size();
bool succ = false;
bool firstEe = true;
bool done = false;
if(tot > 0) {
bool fwFirst = true;
// Pick fw / rc to go first in a weighted random fashion
#ifdef BOWTIE_64BIT_INDEX
index_t rn64 = rnd.nextU64();
index_t rn = rn64 % (uint64_t)tot;
#else
index_t rn32 = rnd.nextU32();
index_t rn = rn32 % (uint32_t)tot;
#endif
if(rn >= sh.exactFwEEHit().size()) {
fwFirst = false;
}
for(int fwi = 0; fwi < 2 && !done; fwi++) {
bool fw = ((fwi == 0) == fwFirst);
EEHit<index_t> hit = fw ? sh.exactFwEEHit() : sh.exactRcEEHit();
if(hit.empty()) {
continue;
}
assert(hit.fw == fw);
if(hit.bot > hit.top) {
// Possibly adjust bot and width if we would have exceeded maxelt
index_t tops[2] = { hit.top, 0 };
index_t bots[2] = { hit.bot, 0 };
index_t width = hit.bot - hit.top;
if(nelt_out + width > maxelt) {
index_t trim = (index_t)((nelt_out + width) - maxelt);
#ifdef BOWTIE_64BIT_INDEX
index_t rn = rnd.nextU64() % width;
#else
index_t rn = rnd.nextU32() % width;
#endif
index_t newwidth = width - trim;
if(hit.top + rn + newwidth > hit.bot) {
// Two pieces
tops[0] = hit.top + rn;
bots[0] = hit.bot;
tops[1] = hit.top;
bots[1] = hit.top + newwidth - (bots[0] - tops[0]);
} else {
// One piece
tops[0] = hit.top + rn;
bots[0] = tops[0] + newwidth;
}
assert_leq(bots[0], hit.bot);
assert_leq(bots[1], hit.bot);
assert_geq(bots[0], tops[0]);
assert_geq(bots[1], tops[1]);
assert_eq(newwidth, (bots[0] - tops[0]) + (bots[1] - tops[1]));
}
for(int i = 0; i < 2 && !done; i++) {
if(bots[i] <= tops[i]) break;
index_t width = bots[i] - tops[i];
index_t top = tops[i];
// Clear list where resolved offsets are stored
swmSeed.exranges++;
swmSeed.exrows += width;
if(!succ) {
swmSeed.exsucc++;
succ = true;
}
if(firstEe) {
salistEe_.clear();
pool_.clear();
firstEe = false;
}
// We have to be careful not to allocate excessive amounts of memory here
TSlice o(salistEe_, (index_t)salistEe_.size(), width);
for(index_t i = 0; i < width; i++) {
if(!salistEe_.add(pool_, (index_t)OFF_MASK)) {
swmSeed.exooms++;
return false;
}
}
assert(!done);
eehits_.push_back(hit);
satpos_.expand();
satpos_.back().sat.init(SAKey(), top, (index_t)OFF_MASK, o);
satpos_.back().sat.key.seq = MAX_U64;
satpos_.back().sat.key.len = (index_t)rd.length();
satpos_.back().pos.init(fw, 0, 0, (index_t)rd.length());
satpos_.back().origSz = width;
rands_.expand();
rands_.back().init(width, all);
gws_.expand();
SARangeWithOffs<TSlice> sa;
sa.topf = satpos_.back().sat.topf;
sa.len = satpos_.back().sat.key.len;
sa.offs = satpos_.back().sat.offs;
gws_.back().init(
ebwt, // forward Bowtie index
ref, // reference sequences
sa, // SATuple
rnd, // pseudo-random generator
wlm); // metrics
assert(gws_.back().repOk(sa));
nelt_out += width;
if(nelt_out >= maxelt) {
done = true;
}
}
}
}
}
succ = false;
if(!done && !sh.mm1EEHits().empty()) {
sh.sort1mmEe(rnd);
index_t sz = sh.mm1EEHits().size();
for(index_t i = 0; i < sz && !done; i++) {
EEHit<index_t> hit = sh.mm1EEHits()[i];
assert(hit.repOk(rd));
assert(!hit.empty());
// Possibly adjust bot and width if we would have exceeded maxelt
index_t tops[2] = { hit.top, 0 };
index_t bots[2] = { hit.bot, 0 };
index_t width = hit.bot - hit.top;
if(nelt_out + width > maxelt) {
index_t trim = (index_t)((nelt_out + width) - maxelt);
#ifdef BOWTIE_64BIT_INDEX
index_t rn = rnd.nextU64() % width;
#else
index_t rn = rnd.nextU32() % width;
#endif
index_t newwidth = width - trim;
if(hit.top + rn + newwidth > hit.bot) {
// Two pieces
tops[0] = hit.top + rn;
bots[0] = hit.bot;
tops[1] = hit.top;
bots[1] = hit.top + newwidth - (bots[0] - tops[0]);
} else {
// One piece
tops[0] = hit.top + rn;
bots[0] = tops[0] + newwidth;
}
assert_leq(bots[0], hit.bot);
assert_leq(bots[1], hit.bot);
assert_geq(bots[0], tops[0]);
assert_geq(bots[1], tops[1]);
assert_eq(newwidth, (bots[0] - tops[0]) + (bots[1] - tops[1]));
}
for(int i = 0; i < 2 && !done; i++) {
if(bots[i] <= tops[i]) break;
index_t width = bots[i] - tops[i];
index_t top = tops[i];
// Clear list where resolved offsets are stored
swmSeed.mm1ranges++;
swmSeed.mm1rows += width;
if(!succ) {
swmSeed.mm1succ++;
succ = true;
}
if(firstEe) {
salistEe_.clear();
pool_.clear();
firstEe = false;
}
TSlice o(salistEe_, (index_t)salistEe_.size(), width);
for(size_t i = 0; i < width; i++) {
if(!salistEe_.add(pool_, (index_t)OFF_MASK)) {
swmSeed.mm1ooms++;
return false;
}
}
eehits_.push_back(hit);
satpos_.expand();
satpos_.back().sat.init(SAKey(), top, (index_t)OFF_MASK, o);
satpos_.back().sat.key.seq = MAX_U64;
satpos_.back().sat.key.len = (index_t)rd.length();
satpos_.back().pos.init(hit.fw, 0, 0, (index_t)rd.length());
satpos_.back().origSz = width;
rands_.expand();
rands_.back().init(width, all);
gws_.expand();
SARangeWithOffs<TSlice> sa;
sa.topf = satpos_.back().sat.topf;
sa.len = satpos_.back().sat.key.len;
sa.offs = satpos_.back().sat.offs;
gws_.back().init(
ebwt, // forward Bowtie index
ref, // reference sequences
sa, // SATuple
rnd, // pseudo-random generator
wlm); // metrics
assert(gws_.back().repOk(sa));
nelt_out += width;
if(nelt_out >= maxelt) {
done = true;
}
}
}
}
return true;
}
/**
* Extend a seed hit out on either side. Requires that we know the seed hit's
* offset into the read and orientation. Also requires that we know top/bot
* for the seed hit in both the forward and (if we want to extend to the right)
* reverse index.
*/
template <typename index_t>
void SwDriver<index_t>::extend(
const Read& rd, // read
const Ebwt<index_t>& ebwtFw, // Forward Bowtie index
const Ebwt<index_t>* ebwtBw, // Backward Bowtie index
index_t topf, // top in fw index
index_t botf, // bot in fw index
index_t topb, // top in bw index
index_t botb, // bot in bw index
bool fw, // seed orientation
index_t off, // seed offset from 5' end
index_t len, // seed length
PerReadMetrics& prm, // per-read metrics
index_t& nlex, // # positions we can extend to left w/o edit
index_t& nrex) // # positions we can extend to right w/o edit
{
index_t t[4], b[4];
index_t tp[4], bp[4];
SideLocus<index_t> tloc, bloc;
index_t rdlen = (index_t)rd.length();
index_t lim = fw ? off : rdlen - len - off;
// We're about to add onto the beginning, so reverse it
#ifndef NDEBUG
if(false) {
// TODO: This will sometimes fail even when the extension is legitimate
// This is because contains() comes in from one extreme or the other,
// whereas we started from the inside and worked outwards. This
// affects which Ns are OK and which are not OK.
// Have to do both because whether we can get through an N depends on
// which direction we're coming in
bool fwContains = ebwtFw.contains(tmp_rdseq_);
tmp_rdseq_.reverse();
bool bwContains = ebwtBw != NULL && ebwtBw->contains(tmp_rdseq_);
tmp_rdseq_.reverse();
assert(fwContains || bwContains);
}
#endif
ASSERT_ONLY(tmp_rdseq_.reverse());
if(lim > 0) {
const Ebwt<index_t> *ebwt = &ebwtFw;
assert(ebwt != NULL);
// Extend left using forward index
const BTDnaString& seq = fw ? rd.patFw : rd.patRc;
// See what we get by extending
index_t top = topf, bot = botf;
t[0] = t[1] = t[2] = t[3] = 0;
b[0] = b[1] = b[2] = b[3] = 0;
tp[0] = tp[1] = tp[2] = tp[3] = topb;
bp[0] = bp[1] = bp[2] = bp[3] = botb;
SideLocus<index_t> tloc, bloc;
INIT_LOCS(top, bot, tloc, bloc, *ebwt);
for(index_t ii = 0; ii < lim; ii++) {
// Starting to left of seed (<off) and moving left
index_t i = 0;
if(fw) {
i = off - ii - 1;
} else {
i = rdlen - off - len - 1 - ii;
}
// Get char from read
int rdc = seq.get(i);
// See what we get by extending
if(bloc.valid()) {
prm.nSdFmops++;
t[0] = t[1] = t[2] = t[3] =
b[0] = b[1] = b[2] = b[3] = 0;
ebwt->mapBiLFEx(tloc, bloc, t, b, tp, bp);
SANITY_CHECK_4TUP(t, b, tp, bp);
int nonz = -1;
bool abort = false;
size_t origSz = bot - top;
for(int j = 0; j < 4; j++) {
if(b[j] > t[j]) {
if(nonz >= 0) {
abort = true;
break;
}
nonz = j;
top = t[j]; bot = b[j];
}
}
assert_leq(bot - top, origSz);
if(abort || (nonz != rdc && rdc <= 3) || bot - top < origSz) {
break;
}
} else {
assert_eq(bot, top+1);
prm.nSdFmops++;
int c = ebwt->mapLF1(top, tloc);
if(c != rdc && rdc <= 3) {
break;
}
bot = top + 1;
}
ASSERT_ONLY(tmp_rdseq_.append(rdc));
if(++nlex == 255) {
break;
}
INIT_LOCS(top, bot, tloc, bloc, *ebwt);
}
}
// We're about to add onto the end, so re-reverse
ASSERT_ONLY(tmp_rdseq_.reverse());
lim = fw ? rdlen - len - off : off;
if(lim > 0 && ebwtBw != NULL) {
const Ebwt<index_t> *ebwt = ebwtBw;
assert(ebwt != NULL);
// Extend right using backward index
const BTDnaString& seq = fw ? rd.patFw : rd.patRc;
// See what we get by extending
index_t top = topb, bot = botb;
t[0] = t[1] = t[2] = t[3] = 0;
b[0] = b[1] = b[2] = b[3] = 0;
tp[0] = tp[1] = tp[2] = tp[3] = topf;
bp[0] = bp[1] = bp[2] = bp[3] = botf;
INIT_LOCS(top, bot, tloc, bloc, *ebwt);
for(index_t ii = 0; ii < lim; ii++) {
// Starting to right of seed (<off) and moving right
index_t i;
if(fw) {
i = ii + len + off;
} else {
i = rdlen - off + ii;
}
// Get char from read
int rdc = seq.get(i);
// See what we get by extending
if(bloc.valid()) {
prm.nSdFmops++;
t[0] = t[1] = t[2] = t[3] =
b[0] = b[1] = b[2] = b[3] = 0;
ebwt->mapBiLFEx(tloc, bloc, t, b, tp, bp);
SANITY_CHECK_4TUP(t, b, tp, bp);
int nonz = -1;
bool abort = false;
size_t origSz = bot - top;
for(int j = 0; j < 4; j++) {
if(b[j] > t[j]) {
if(nonz >= 0) {
abort = true;
break;
}
nonz = j;
top = t[j]; bot = b[j];
}
}
assert_leq(bot - top, origSz);
if(abort || (nonz != rdc && rdc <= 3) || bot - top < origSz) {
break;
}
} else {
assert_eq(bot, top+1);
prm.nSdFmops++;
int c = ebwt->mapLF1(top, tloc);
if(c != rdc && rdc <= 3) {
break;
}
bot = top + 1;
}
ASSERT_ONLY(tmp_rdseq_.append(rdc));
if(++nrex == 255) {
break;
}
INIT_LOCS(top, bot, tloc, bloc, *ebwt);
}
}
#ifndef NDEBUG
if(false) {
// TODO: This will sometimes fail even when the extension is legitimate
// This is because contains() comes in from one extreme or the other,
// whereas we started from the inside and worked outwards. This
// affects which Ns are OK and which are not OK.
// Have to do both because whether we can get through an N depends on
// which direction we're coming in
bool fwContains = ebwtFw.contains(tmp_rdseq_);
tmp_rdseq_.reverse();
bool bwContains = ebwtBw != NULL && ebwtBw->contains(tmp_rdseq_);
tmp_rdseq_.reverse();
assert(fwContains || bwContains);