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aligner_seed.cpp
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aligner_seed.cpp
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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/>.
*/
#include "aligner_cache.h"
#include "aligner_seed.h"
#include "search_globals.h"
#include "bt2_idx.h"
using namespace std;
/**
* Construct a constraint with no edits of any kind allowed.
*/
Constraint Constraint::exact() {
Constraint c;
c.edits = c.mms = c.ins = c.dels = c.penalty = 0;
return c;
}
/**
* Construct a constraint where the only constraint is a total
* penalty constraint.
*/
Constraint Constraint::penaltyBased(int pen) {
Constraint c;
c.penalty = pen;
return c;
}
/**
* Construct a constraint where the only constraint is a total
* penalty constraint related to the length of the read.
*/
Constraint Constraint::penaltyFuncBased(const SimpleFunc& f) {
Constraint c;
c.penFunc = f;
return c;
}
/**
* Construct a constraint where the only constraint is a total
* penalty constraint.
*/
Constraint Constraint::mmBased(int mms) {
Constraint c;
c.mms = mms;
c.edits = c.dels = c.ins = 0;
return c;
}
/**
* Construct a constraint where the only constraint is a total
* penalty constraint.
*/
Constraint Constraint::editBased(int edits) {
Constraint c;
c.edits = edits;
c.dels = c.ins = c.mms = 0;
return c;
}
//
// Some static methods for constructing some standard SeedPolicies
//
/**
* Given a read, depth and orientation, extract a seed data structure
* from the read and fill in the steps & zones arrays. The Seed
* contains the sequence and quality values.
*/
bool
Seed::instantiate(
const Read& read,
const BTDnaString& seq, // seed read sequence
const BTString& qual, // seed quality sequence
const Scoring& pens,
int depth,
int seedoffidx,
int seedtypeidx,
bool fw,
InstantiatedSeed& is) const
{
assert(overall != NULL);
int seedlen = len;
if((int)read.length() < seedlen) {
// Shrink seed length to fit read if necessary
seedlen = (int)read.length();
}
assert_gt(seedlen, 0);
is.steps.resize(seedlen);
is.zones.resize(seedlen);
// Fill in 'steps' and 'zones'
//
// The 'steps' list indicates which read character should be
// incorporated at each step of the search process. Often we will
// simply proceed from one end to the other, in which case the
// 'steps' list is ascending or descending. In some cases (e.g.
// the 2mm case), we might want to switch directions at least once
// during the search, in which case 'steps' will jump in the
// middle. When an element of the 'steps' list is negative, this
// indicates that the next
//
// The 'zones' list indicates which zone constraint is active at
// each step. Each element of the 'zones' list is a pair; the
// first pair element indicates the applicable zone when
// considering either mismatch or delete (ref gap) events, while
// the second pair element indicates the applicable zone when
// considering insertion (read gap) events. When either pair
// element is a negative number, that indicates that we are about
// to leave the zone for good, at which point we may need to
// evaluate whether we have reached the zone's budget.
//
switch(type) {
case SEED_TYPE_EXACT: {
for(int k = 0; k < seedlen; k++) {
is.steps[k] = -(seedlen - k);
// Zone 0 all the way
is.zones[k].first = is.zones[k].second = 0;
}
break;
}
case SEED_TYPE_LEFT_TO_RIGHT: {
for(int k = 0; k < seedlen; k++) {
is.steps[k] = k+1;
// Zone 0 from 0 up to ceil(len/2), then 1
is.zones[k].first = is.zones[k].second = ((k < (seedlen+1)/2) ? 0 : 1);
}
// Zone 1 ends at the RHS
is.zones[seedlen-1].first = is.zones[seedlen-1].second = -1;
break;
}
case SEED_TYPE_RIGHT_TO_LEFT: {
for(int k = 0; k < seedlen; k++) {
is.steps[k] = -(seedlen - k);
// Zone 0 from 0 up to floor(len/2), then 1
is.zones[k].first = ((k < seedlen/2) ? 0 : 1);
// Inserts: Zone 0 from 0 up to ceil(len/2)-1, then 1
is.zones[k].second = ((k < (seedlen+1)/2+1) ? 0 : 1);
}
is.zones[seedlen-1].first = is.zones[seedlen-1].second = -1;
break;
}
case SEED_TYPE_INSIDE_OUT: {
// Zone 0 from ceil(N/4) up to N-floor(N/4)
int step = 0;
for(int k = (seedlen+3)/4; k < seedlen - (seedlen/4); k++) {
is.zones[step].first = is.zones[step].second = 0;
is.steps[step++] = k+1;
}
// Zone 1 from N-floor(N/4) up
for(int k = seedlen - (seedlen/4); k < seedlen; k++) {
is.zones[step].first = is.zones[step].second = 1;
is.steps[step++] = k+1;
}
// No Zone 1 if seedlen is short (like 2)
//assert_eq(1, is.zones[step-1].first);
is.zones[step-1].first = is.zones[step-1].second = -1;
// Zone 2 from ((seedlen+3)/4)-1 down to 0
for(int k = ((seedlen+3)/4)-1; k >= 0; k--) {
is.zones[step].first = is.zones[step].second = 2;
is.steps[step++] = -(k+1);
}
assert_eq(2, is.zones[step-1].first);
is.zones[step-1].first = is.zones[step-1].second = -2;
assert_eq(seedlen, step);
break;
}
default:
throw 1;
}
// Instantiate constraints
for(int i = 0; i < 3; i++) {
is.cons[i] = zones[i];
is.cons[i].instantiate(read.length());
}
is.overall = *overall;
is.overall.instantiate(read.length());
// Take a sweep through the seed sequence. Consider where the Ns
// occur and how zones are laid out. Calculate the maximum number
// of positions we can jump over initially (e.g. with the ftab) and
// perhaps set this function's return value to false, indicating
// that the arrangements of Ns prevents the seed from aligning.
bool streak = true;
is.maxjump = 0;
bool ret = true;
bool ltr = (is.steps[0] > 0); // true -> left-to-right
for(size_t i = 0; i < is.steps.size(); i++) {
assert_neq(0, is.steps[i]);
int off = is.steps[i];
off = abs(off)-1;
Constraint& cons = is.cons[abs(is.zones[i].first)];
int c = seq[off]; assert_range(0, 4, c);
int q = qual[off];
if(ltr != (is.steps[i] > 0) || // changed direction
is.zones[i].first != 0 || // changed zone
is.zones[i].second != 0) // changed zone
{
streak = false;
}
if(c == 4) {
// Induced mismatch
if(cons.canN(q, pens)) {
cons.chargeN(q, pens);
} else {
// Seed disqualified due to arrangement of Ns
return false;
}
}
if(streak) is.maxjump++;
}
is.seedoff = depth;
is.seedoffidx = seedoffidx;
is.fw = fw;
is.s = *this;
return ret;
}
/**
* Return a set consisting of 1 seed encapsulating an exact matching
* strategy.
*/
void
Seed::zeroMmSeeds(int ln, EList<Seed>& pols, Constraint& oall) {
oall.init();
// Seed policy 1: left-to-right search
pols.expand();
pols.back().len = ln;
pols.back().type = SEED_TYPE_EXACT;
pols.back().zones[0] = Constraint::exact();
pols.back().zones[1] = Constraint::exact();
pols.back().zones[2] = Constraint::exact();
pols.back().overall = &oall;
}
/**
* Return a set of 2 seeds encapsulating a half-and-half 1mm strategy.
*/
void
Seed::oneMmSeeds(int ln, EList<Seed>& pols, Constraint& oall) {
oall.init();
// Seed policy 1: left-to-right search
pols.expand();
pols.back().len = ln;
pols.back().type = SEED_TYPE_LEFT_TO_RIGHT;
pols.back().zones[0] = Constraint::exact();
pols.back().zones[1] = Constraint::mmBased(1);
pols.back().zones[2] = Constraint::exact(); // not used
pols.back().overall = &oall;
// Seed policy 2: right-to-left search
pols.expand();
pols.back().len = ln;
pols.back().type = SEED_TYPE_RIGHT_TO_LEFT;
pols.back().zones[0] = Constraint::exact();
pols.back().zones[1] = Constraint::mmBased(1);
pols.back().zones[1].mmsCeil = 0;
pols.back().zones[2] = Constraint::exact(); // not used
pols.back().overall = &oall;
}
/**
* Return a set of 3 seeds encapsulating search roots for:
*
* 1. Starting from the left-hand side and searching toward the
* right-hand side allowing 2 mismatches in the right half.
* 2. Starting from the right-hand side and searching toward the
* left-hand side allowing 2 mismatches in the left half.
* 3. Starting (effectively) from the center and searching out toward
* both the left and right-hand sides, allowing one mismatch on
* either side.
*
* This is not exhaustive. There are 2 mismatch cases mised; if you
* imagine the seed as divided into four successive quarters A, B, C
* and D, the cases we miss are when mismatches occur in A and C or B
* and D.
*/
void
Seed::twoMmSeeds(int ln, EList<Seed>& pols, Constraint& oall) {
oall.init();
// Seed policy 1: left-to-right search
pols.expand();
pols.back().len = ln;
pols.back().type = SEED_TYPE_LEFT_TO_RIGHT;
pols.back().zones[0] = Constraint::exact();
pols.back().zones[1] = Constraint::mmBased(2);
pols.back().zones[2] = Constraint::exact(); // not used
pols.back().overall = &oall;
// Seed policy 2: right-to-left search
pols.expand();
pols.back().len = ln;
pols.back().type = SEED_TYPE_RIGHT_TO_LEFT;
pols.back().zones[0] = Constraint::exact();
pols.back().zones[1] = Constraint::mmBased(2);
pols.back().zones[1].mmsCeil = 1; // Must have used at least 1 mismatch
pols.back().zones[2] = Constraint::exact(); // not used
pols.back().overall = &oall;
// Seed policy 3: inside-out search
pols.expand();
pols.back().len = ln;
pols.back().type = SEED_TYPE_INSIDE_OUT;
pols.back().zones[0] = Constraint::exact();
pols.back().zones[1] = Constraint::mmBased(1);
pols.back().zones[1].mmsCeil = 0; // Must have used at least 1 mismatch
pols.back().zones[2] = Constraint::mmBased(1);
pols.back().zones[2].mmsCeil = 0; // Must have used at least 1 mismatch
pols.back().overall = &oall;
}
/**
* Types of actions that can be taken by the SeedAligner.
*/
enum {
SA_ACTION_TYPE_RESET = 1,
SA_ACTION_TYPE_SEARCH_SEED, // 2
SA_ACTION_TYPE_FTAB, // 3
SA_ACTION_TYPE_FCHR, // 4
SA_ACTION_TYPE_MATCH, // 5
SA_ACTION_TYPE_EDIT // 6
};
/**
* Given a read and a few coordinates that describe a substring of the read (or
* its reverse complement), fill in 'seq' and 'qual' objects with the seed
* sequence and qualities.
*
* The seq field is filled with the sequence as it would align to the Watson
* reference strand. I.e. if fw is false, then the sequence that appears in
* 'seq' is the reverse complement of the raw read substring.
*/
void
SeedAligner::instantiateSeq(
const Read& read, // input read
BTDnaString& seq, // output sequence
BTString& qual, // output qualities
int len, // seed length
int depth, // seed's 0-based offset from 5' end
bool fw) const // seed's orientation
{
// Fill in 'seq' and 'qual'
int seedlen = len;
if((int)read.length() < seedlen) seedlen = (int)read.length();
seq.resize(len);
qual.resize(len);
// If fw is false, we take characters starting at the 3' end of the
// reverse complement of the read.
for(int i = 0; i < len; i++) {
seq.set(read.patFw.windowGetDna(i, fw, depth, len), i);
qual.set(read.qual.windowGet(i, fw, depth, len), i);
}
}
/**
* We assume that all seeds are the same length.
*
* For each seed, instantiate the seed, retracting if necessary.
*/
pair<int, int> SeedAligner::instantiateSeeds(
const EList<Seed>& seeds, // search seeds
size_t off, // offset into read to start extracting
int per, // interval between seeds
const Read& read, // read to align
const Scoring& pens, // scoring scheme
bool nofw, // don't align forward read
bool norc, // don't align revcomp read
AlignmentCacheIface& cache,// holds some seed hits from previous reads
SeedResults& sr, // holds all the seed hits
SeedSearchMetrics& met, // metrics
pair<int, int>& instFw,
pair<int, int>& instRc)
{
assert(!seeds.empty());
assert_gt(read.length(), 0);
// Check whether read has too many Ns
offIdx2off_.clear();
int len = seeds[0].len; // assume they're all the same length
#ifndef NDEBUG
for(size_t i = 1; i < seeds.size(); i++) {
assert_eq(len, seeds[i].len);
}
#endif
// Calc # seeds within read interval
int nseeds = 1;
if((int)read.length() - (int)off > len) {
nseeds += ((int)read.length() - (int)off - len) / per;
}
for(int i = 0; i < nseeds; i++) {
offIdx2off_.push_back(per * i + (int)off);
}
pair<int, int> ret;
ret.first = 0; // # seeds that require alignment
ret.second = 0; // # seeds that hit in cache with non-empty results
sr.reset(read, offIdx2off_, nseeds);
assert(sr.repOk(&cache.current(), true)); // require that SeedResult be initialized
// For each seed position
for(int fwi = 0; fwi < 2; fwi++) {
bool fw = (fwi == 0);
if((fw && nofw) || (!fw && norc)) {
// Skip this orientation b/c user specified --nofw or --norc
continue;
}
// For each seed position
for(int i = 0; i < nseeds; i++) {
int depth = i * per + (int)off;
int seedlen = seeds[0].len;
// Extract the seed sequence at this offset
// If fw == true, we extract the characters from i*per to
// i*(per-1) (exclusive). If fw == false,
instantiateSeq(
read,
sr.seqs(fw)[i],
sr.quals(fw)[i],
std::min<int>((int)seedlen, (int)read.length()),
depth,
fw);
QKey qk(sr.seqs(fw)[i] ASSERT_ONLY(, tmpdnastr_));
// For each search strategy
EList<InstantiatedSeed>& iss = sr.instantiatedSeeds(fw, i);
for(int j = 0; j < (int)seeds.size(); j++) {
iss.expand();
assert_eq(seedlen, seeds[j].len);
InstantiatedSeed* is = &iss.back();
if(seeds[j].instantiate(
read,
sr.seqs(fw)[i],
sr.quals(fw)[i],
pens,
depth,
i,
j,
fw,
*is))
{
// Can we fill this seed hit in from the cache?
ret.first++;
if(fwi == 0) { instFw.first++; } else { instRc.first++; }
} else {
// Seed may fail to instantiate if there are Ns
// that prevent it from matching
met.filteredseed++;
iss.pop_back();
}
}
}
}
return ret;
}
/**
* We assume that all seeds are the same length.
*
* For each seed:
*
* 1. Instantiate all seeds, retracting them if necessary.
* 2. Calculate zone boundaries for each seed
*/
void SeedAligner::searchAllSeeds(
const EList<Seed>& seeds, // search seeds
const Ebwt* ebwtFw, // BWT index
const Ebwt* ebwtBw, // BWT' index
const Read& read, // read to align
const Scoring& pens, // scoring scheme
AlignmentCacheIface& cache, // local cache for seed alignments
SeedResults& sr, // holds all the seed hits
SeedSearchMetrics& met, // metrics
PerReadMetrics& prm) // per-read metrics
{
assert(!seeds.empty());
assert(ebwtFw != NULL);
assert(ebwtFw->isInMemory());
assert(sr.repOk(&cache.current()));
ebwtFw_ = ebwtFw;
ebwtBw_ = ebwtBw;
sc_ = &pens;
read_ = &read;
ca_ = &cache;
bwops_ = bwedits_ = 0;
uint64_t possearches = 0, seedsearches = 0, intrahits = 0, interhits = 0, ooms = 0;
// For each instantiated seed
for(int i = 0; i < (int)sr.numOffs(); i++) {
size_t off = sr.idx2off(i);
for(int fwi = 0; fwi < 2; fwi++) {
bool fw = (fwi == 0);
assert(sr.repOk(&cache.current()));
EList<InstantiatedSeed>& iss = sr.instantiatedSeeds(fw, i);
if(iss.empty()) {
// Cache hit in an across-read cache
continue;
}
QVal qv;
seq_ = &sr.seqs(fw)[i]; // seed sequence
qual_ = &sr.quals(fw)[i]; // seed qualities
off_ = off; // seed offset (from 5')
fw_ = fw; // seed orientation
// Tell the cache that we've started aligning, so the cache can
// expect a series of on-the-fly updates
int ret = cache.beginAlign(*seq_, *qual_, qv);
ASSERT_ONLY(hits_.clear());
if(ret == -1) {
// Out of memory when we tried to add key to map
ooms++;
continue;
}
bool abort = false;
if(ret == 0) {
// Not already in cache
assert(cache.aligning());
possearches++;
for(size_t j = 0; j < iss.size(); j++) {
// Set seq_ and qual_ appropriately, using the seed sequences
// and qualities already installed in SeedResults
assert_eq(fw, iss[j].fw);
assert_eq(i, (int)iss[j].seedoffidx);
s_ = &iss[j];
// Do the search with respect to seq_, qual_ and s_.
if(!searchSeedBi()) {
// Memory exhausted during search
ooms++;
abort = true;
break;
}
seedsearches++;
assert(cache.aligning());
}
if(!abort) {
qv = cache.finishAlign();
}
} else {
// Already in cache
assert_eq(1, ret);
assert(qv.valid());
intrahits++;
}
assert(abort || !cache.aligning());
if(qv.valid()) {
sr.add(
qv, // range of ranges in cache
cache.current(), // cache
i, // seed index (from 5' end)
fw); // whether seed is from forward read
}
}
}
prm.nSeedRanges = sr.numRanges();
prm.nSeedElts = sr.numElts();
prm.nSeedRangesFw = sr.numRangesFw();
prm.nSeedRangesRc = sr.numRangesRc();
prm.nSeedEltsFw = sr.numEltsFw();
prm.nSeedEltsRc = sr.numEltsRc();
prm.seedMedian = (uint64_t)(sr.medianHitsPerSeed() + 0.5);
prm.seedMean = (uint64_t)sr.averageHitsPerSeed();
prm.nSdFmops += bwops_;
met.seedsearch += seedsearches;
met.nrange += sr.numRanges();
met.nelt += sr.numElts();
met.possearch += possearches;
met.intrahit += intrahits;
met.interhit += interhits;
met.ooms += ooms;
met.bwops += bwops_;
met.bweds += bwedits_;
}
bool SeedAligner::sanityPartial(
const Ebwt* ebwtFw, // BWT index
const Ebwt* ebwtBw, // BWT' index
const BTDnaString& seq,
size_t dep,
size_t len,
bool do1mm,
TIndexOffU topfw,
TIndexOffU botfw,
TIndexOffU topbw,
TIndexOffU botbw)
{
tmpdnastr_.clear();
for(size_t i = dep; i < len; i++) {
tmpdnastr_.append(seq[i]);
}
TIndexOffU top_fw = 0, bot_fw = 0;
ebwtFw->contains(tmpdnastr_, &top_fw, &bot_fw);
assert_eq(top_fw, topfw);
assert_eq(bot_fw, botfw);
if(do1mm && ebwtBw != NULL) {
tmpdnastr_.reverse();
TIndexOffU top_bw = 0, bot_bw = 0;
ebwtBw->contains(tmpdnastr_, &top_bw, &bot_bw);
assert_eq(top_bw, topbw);
assert_eq(bot_bw, botbw);
}
return true;
}
/**
* 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.
*/
size_t SeedAligner::exactSweep(
const Ebwt& ebwt, // BWT index
const Read& read, // read to align
const Scoring& sc, // scoring scheme
bool nofw, // don't align forward read
bool norc, // don't align revcomp 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
bool repex, // report 0mm hits?
SeedResults& hits, // holds all the seed hits (and exact hit)
SeedSearchMetrics& met) // metrics
{
assert_gt(mineMax, 0);
TIndexOffU top = 0, bot = 0;
SideLocus tloc, bloc;
const size_t len = read.length();
size_t nelt = 0;
for(int fwi = 0; fwi < 2; fwi++) {
bool fw = (fwi == 0);
if( fw && nofw) continue;
if(!fw && norc) continue;
const BTDnaString& seq = fw ? read.patFw : read.patRc;
assert(!seq.empty());
int ftabLen = ebwt.eh().ftabChars();
size_t dep = 0;
size_t nedit = 0;
bool done = false;
while(dep < len && !done) {
top = bot = 0;
size_t left = len - dep;
assert_gt(left, 0);
bool doFtab = ftabLen > 1 && left >= (size_t)ftabLen;
if(doFtab) {
// Does N interfere with use of Ftab?
for(size_t i = 0; i < (size_t)ftabLen; i++) {
int c = seq[len-dep-1-i];
if(c > 3) {
doFtab = false;
break;
}
}
}
if(doFtab) {
// Use ftab
ebwt.ftabLoHi(seq, len - dep - ftabLen, false, top, bot);
dep += (size_t)ftabLen;
} else {
// Use fchr
int c = seq[len-dep-1];
if(c < 4) {
top = ebwt.fchr()[c];
bot = ebwt.fchr()[c+1];
}
dep++;
}
if(bot <= top) {
nedit++;
if(nedit >= mineMax) {
if(fw) { mineFw = nedit; } else { mineRc = nedit; }
break;
}
continue;
}
INIT_LOCS(top, bot, tloc, bloc, ebwt);
// Keep going
while(dep < len) {
int c = seq[len-dep-1];
if(c > 3) {
top = bot = 0;
} else {
if(bloc.valid()) {
bwops_ += 2;
top = ebwt.mapLF(tloc, c);
bot = ebwt.mapLF(bloc, c);
} else {
bwops_++;
top = ebwt.mapLF1(top, tloc, c);
if(top == OFF_MASK) {
top = bot = 0;
} else {
bot = top+1;
}
}
}
if(bot <= top) {
nedit++;
if(nedit >= mineMax) {
if(fw) { mineFw = nedit; } else { mineRc = nedit; }
done = true;
}
break;
}
INIT_LOCS(top, bot, tloc, bloc, ebwt);
dep++;
}
if(done) {
break;
}
if(dep == len) {
// Set the minimum # edits
if(fw) { mineFw = nedit; } else { mineRc = nedit; }
// Done
if(nedit == 0 && bot > top) {
if(repex) {
// This is an exact hit
int64_t score = len * sc.match();
if(fw) {
hits.addExactEeFw(top, bot, NULL, NULL, fw, score);
assert(ebwt.contains(seq, NULL, NULL));
} else {
hits.addExactEeRc(top, bot, NULL, NULL, fw, score);
assert(ebwt.contains(seq, NULL, NULL));
}
}
nelt += (bot - top);
}
break;
}
dep++;
}
}
return nelt;
}
/**
* Search for end-to-end exact hit for read. Return true iff one is found.
*/
bool SeedAligner::oneMmSearch(
const Ebwt* ebwtFw, // BWT index
const Ebwt* ebwtBw, // BWT' index
const Read& read, // read to align
const Scoring& sc, // scoring
int64_t minsc, // minimum score
bool nofw, // don't align forward read
bool norc, // don't align revcomp read
bool local, // 1mm hits must be legal local alignments
bool repex, // report 0mm hits?
bool rep1mm, // report 1mm hits?
SeedResults& hits, // holds all the seed hits (and exact hit)
SeedSearchMetrics& met) // metrics
{
assert(!rep1mm || ebwtBw != NULL);
const size_t len = read.length();
int nceil = sc.nCeil.f<int>((double)len);
size_t ns = read.ns();
if(ns > 1) {
// Can't align this with <= 1 mismatches
return false;
} else if(ns == 1 && !rep1mm) {
// Can't align this with 0 mismatches
return false;
}
assert_geq(len, 2);
assert(!rep1mm || ebwtBw->eh().ftabChars() == ebwtFw->eh().ftabChars());
#ifndef NDEBUG
if(ebwtBw != NULL) {
for(int i = 0; i < 4; i++) {
assert_eq(ebwtBw->fchr()[i], ebwtFw->fchr()[i]);
}
}
#endif
size_t halfFw = len >> 1;
size_t halfBw = len >> 1;
if((len & 1) != 0) {
halfBw++;
}
assert_geq(halfFw, 1);
assert_geq(halfBw, 1);
SideLocus tloc, bloc;
TIndexOffU t[4], b[4]; // dest BW ranges for BWT
t[0] = t[1] = t[2] = t[3] = 0;
b[0] = b[1] = b[2] = b[3] = 0;
TIndexOffU tp[4], bp[4]; // dest BW ranges for BWT'
tp[0] = tp[1] = tp[2] = tp[3] = 0;
bp[0] = bp[1] = bp[2] = bp[3] = 0;
TIndexOffU top = 0, bot = 0, topp = 0, botp = 0;
// Align fw read / rc read
bool results = false;
for(int fwi = 0; fwi < 2; fwi++) {
bool fw = (fwi == 0);
if( fw && nofw) continue;
if(!fw && norc) continue;
// Align going right-to-left, left-to-right
int lim = rep1mm ? 2 : 1;
for(int ebwtfwi = 0; ebwtfwi < lim; ebwtfwi++) {
bool ebwtfw = (ebwtfwi == 0);
const Ebwt* ebwt = (ebwtfw ? ebwtFw : ebwtBw);
const Ebwt* ebwtp = (ebwtfw ? ebwtBw : ebwtFw);
assert(rep1mm || ebwt->fw());
const BTDnaString& seq =
(fw ? (ebwtfw ? read.patFw : read.patFwRev) :
(ebwtfw ? read.patRc : read.patRcRev));
assert(!seq.empty());
const BTString& qual =
(fw ? (ebwtfw ? read.qual : read.qualRev) :
(ebwtfw ? read.qualRev : read.qual));
int ftabLen = ebwt->eh().ftabChars();
size_t nea = ebwtfw ? halfFw : halfBw;
// Check if there's an N in the near portion
bool skip = false;
for(size_t dep = 0; dep < nea; dep++) {
if(seq[len-dep-1] > 3) {
skip = true;
break;
}
}
if(skip) {
continue;
}
size_t dep = 0;
// Align near half
if(ftabLen > 1 && (size_t)ftabLen <= nea) {
// Use ftab to jump partway into near half
bool rev = !ebwtfw;
ebwt->ftabLoHi(seq, len - ftabLen, rev, top, bot);
if(rep1mm) {
ebwtp->ftabLoHi(seq, len - ftabLen, rev, topp, botp);
assert_eq(bot - top, botp - topp);
}
if(bot - top == 0) {
continue;
}
int c = seq[len - ftabLen];
t[c] = top; b[c] = bot;
tp[c] = topp; bp[c] = botp;
dep = ftabLen;
// initialize tloc, bloc??
} else {
// Use fchr to jump in by 1 pos
int c = seq[len-1];
assert_range(0, 3, c);
top = topp = tp[c] = ebwt->fchr()[c];
bot = botp = bp[c] = ebwt->fchr()[c+1];
if(bot - top == 0) {
continue;
}
dep = 1;
// initialize tloc, bloc??
}
INIT_LOCS(top, bot, tloc, bloc, *ebwt);
assert(sanityPartial(ebwt, ebwtp, seq, len-dep, len, rep1mm, top, bot, topp, botp));
bool do_continue = false;
for(; dep < nea; dep++) {
assert_lt(dep, len);
int rdc = seq[len - dep - 1];
tp[0] = tp[1] = tp[2] = tp[3] = topp;
bp[0] = bp[1] = bp[2] = bp[3] = botp;
if(bloc.valid()) {
bwops_++;
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);
top = t[rdc]; bot = b[rdc];
if(bot <= top) {
do_continue = true;
break;
}
topp = tp[rdc]; botp = bp[rdc];
assert(!rep1mm || bot - top == botp - topp);
} else {
assert_eq(bot, top+1);
assert(!rep1mm || botp == topp+1);
bwops_++;
top = ebwt->mapLF1(top, tloc, rdc);
if(top == OFF_MASK) {
do_continue = true;
break;
}
bot = top + 1;
t[rdc] = top; b[rdc] = bot;
tp[rdc] = topp; bp[rdc] = botp;
assert(!rep1mm || b[rdc] - t[rdc] == bp[rdc] - tp[rdc]);
// topp/botp stay the same
}
INIT_LOCS(top, bot, tloc, bloc, *ebwt);
assert(sanityPartial(ebwt, ebwtp, seq, len - dep - 1, len, rep1mm, top, bot, topp, botp));
}
if(do_continue) {
continue;
}
// Align far half
for(; dep < len; dep++) {
int rdc = seq[len-dep-1];
int quc = qual[len-dep-1];
if(rdc > 3 && nceil == 0) {
break;
}
tp[0] = tp[1] = tp[2] = tp[3] = topp;
bp[0] = bp[1] = bp[2] = bp[3] = botp;
int clo = 0, chi = 3;
bool match = true;
if(bloc.valid()) {
bwops_++;
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);
match = rdc < 4;
top = t[rdc]; bot = b[rdc];
topp = tp[rdc]; botp = bp[rdc];
} else {
assert_eq(bot, top+1);
assert(!rep1mm || botp == topp+1);
bwops_++;
clo = ebwt->mapLF1(top, tloc);
match = (clo == rdc);
assert_range(-1, 3, clo);
if(clo < 0) {
break; // Hit the $
} else {
t[clo] = top;
b[clo] = bot = top + 1;
}
bp[clo] = botp;
tp[clo] = topp;
assert(!rep1mm || bot - top == botp - topp);
assert(!rep1mm || b[clo] - t[clo] == bp[clo] - tp[clo]);
chi = clo;
}
//assert(sanityPartial(ebwt, ebwtp, seq, len - dep - 1, len, rep1mm, top, bot, topp, botp));
if(rep1mm && (ns == 0 || rdc > 3)) {
for(int j = clo; j <= chi; j++) {
if(j == rdc || b[j] == t[j]) {
// Either matches read or isn't a possibility
continue;
}
// Potential mismatch - next, try
size_t depm = dep + 1;
TIndexOffU topm = t[j], botm = b[j];
TIndexOffU topmp = tp[j], botmp = bp[j];
assert_eq(botm - topm, botmp - topmp);
TIndexOffU tm[4], bm[4]; // dest BW ranges for BWT
tm[0] = t[0]; tm[1] = t[1];
tm[2] = t[2]; tm[3] = t[3];
bm[0] = b[0]; bm[1] = t[1];
bm[2] = b[2]; bm[3] = t[3];
TIndexOffU tmp[4], bmp[4]; // dest BW ranges for BWT'
tmp[0] = tp[0]; tmp[1] = tp[1];
tmp[2] = tp[2]; tmp[3] = tp[3];
bmp[0] = bp[0]; bmp[1] = tp[1];
bmp[2] = bp[2]; bmp[3] = tp[3];
SideLocus tlocm, blocm;
INIT_LOCS(topm, botm, tlocm, blocm, *ebwt);
for(; depm < len; depm++) {
int rdcm = seq[len - depm - 1];
tmp[0] = tmp[1] = tmp[2] = tmp[3] = topmp;
bmp[0] = bmp[1] = bmp[2] = bmp[3] = botmp;
if(blocm.valid()) {
bwops_++;
tm[0] = tm[1] = tm[2] = tm[3] =
bm[0] = bm[1] = bm[2] = bm[3] = 0;
ebwt->mapBiLFEx(tlocm, blocm, tm, bm, tmp, bmp);
SANITY_CHECK_4TUP(tm, bm, tmp, bmp);
topm = tm[rdcm]; botm = bm[rdcm];
topmp = tmp[rdcm]; botmp = bmp[rdcm];
if(botm <= topm) {
break;
}
} else {
assert_eq(botm, topm+1);
assert_eq(botmp, topmp+1);
bwops_++;
topm = ebwt->mapLF1(topm, tlocm, rdcm);
if(topm == OFF_MASK) {
break;
}
botm = topm + 1;
// topp/botp stay the same
}
INIT_LOCS(topm, botm, tlocm, blocm, *ebwt);
}
if(depm == len) {
// Success; this is a 1MM hit
size_t off5p = dep; // offset from 5' end of read
size_t offstr = dep; // offset into patFw/patRc
if(fw == ebwtfw) {
off5p = len - off5p - 1;
}
if(!ebwtfw) {
offstr = len - offstr - 1;
}
Edit e((uint32_t)off5p, j, rdc, EDIT_TYPE_MM, false);
results = true;
int64_t score = (len - 1) * sc.match();
// In --local mode, need to double-check that
// end-to-end alignment doesn't violate local