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/*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Bowtie 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef ALN_SINK_H_
#define ALN_SINK_H_
#include <limits>
#include "read.h"
#include "unique.h"
#include "sam.h"
#include "ds.h"
#include "simple_func.h"
#include "outq.h"
#include <utility>
// Forward decl
class SeedResults;
enum {
OUTPUT_SAM = 1
};
/**
* Metrics summarizing the work done by the reporter and summarizing
* the number of reads that align, that fail to align, and that align
* non-uniquely.
*/
struct ReportingMetrics {
ReportingMetrics():mutex_m() {
reset();
}
void reset() {
init(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0);
}
void init(
uint64_t nread_,
uint64_t npaired_,
uint64_t nunpaired_,
uint64_t nconcord_uni_,
uint64_t nconcord_uni1_,
uint64_t nconcord_uni2_,
uint64_t nconcord_rep_,
uint64_t nconcord_0_,
uint64_t ndiscord_,
uint64_t nunp_0_uni_,
uint64_t nunp_0_uni1_,
uint64_t nunp_0_uni2_,
uint64_t nunp_0_rep_,
uint64_t nunp_0_0_,
uint64_t nunp_rep_uni_,
uint64_t nunp_rep_uni1_,
uint64_t nunp_rep_uni2_,
uint64_t nunp_rep_rep_,
uint64_t nunp_rep_0_,
uint64_t nunp_uni_,
uint64_t nunp_uni1_,
uint64_t nunp_uni2_,
uint64_t nunp_rep_,
uint64_t nunp_0_,
uint64_t sum_best1_,
uint64_t sum_best2_,
uint64_t sum_best_)
{
nread = nread_;
npaired = npaired_;
nunpaired = nunpaired_;
nconcord_uni = nconcord_uni_;
nconcord_uni1 = nconcord_uni1_;
nconcord_uni2 = nconcord_uni2_;
nconcord_rep = nconcord_rep_;
nconcord_0 = nconcord_0_;
ndiscord = ndiscord_;
nunp_0_uni = nunp_0_uni_;
nunp_0_uni1 = nunp_0_uni1_;
nunp_0_uni2 = nunp_0_uni2_;
nunp_0_rep = nunp_0_rep_;
nunp_0_0 = nunp_0_0_;
nunp_rep_uni = nunp_rep_uni_;
nunp_rep_uni1 = nunp_rep_uni1_;
nunp_rep_uni2 = nunp_rep_uni2_;
nunp_rep_rep = nunp_rep_rep_;
nunp_rep_0 = nunp_rep_0_;
nunp_uni = nunp_uni_;
nunp_uni1 = nunp_uni1_;
nunp_uni2 = nunp_uni2_;
nunp_rep = nunp_rep_;
nunp_0 = nunp_0_;
sum_best1 = sum_best1_;
sum_best2 = sum_best2_;
sum_best = sum_best_;
}
/**
* Merge (add) the counters in the given ReportingMetrics object
* into this object. This is the only safe way to update a
* ReportingMetrics shared by multiple threads.
*/
void merge(const ReportingMetrics& met) {
ThreadSafe ts(mutex_m);
nread += met.nread;
npaired += met.npaired;
nunpaired += met.nunpaired;
nconcord_uni += met.nconcord_uni;
nconcord_uni1 += met.nconcord_uni1;
nconcord_uni2 += met.nconcord_uni2;
nconcord_rep += met.nconcord_rep;
nconcord_0 += met.nconcord_0;
ndiscord += met.ndiscord;
nunp_0_uni += met.nunp_0_uni;
nunp_0_uni1 += met.nunp_0_uni1;
nunp_0_uni2 += met.nunp_0_uni2;
nunp_0_rep += met.nunp_0_rep;
nunp_0_0 += met.nunp_0_0;
nunp_rep_uni += met.nunp_rep_uni;
nunp_rep_uni1 += met.nunp_rep_uni1;
nunp_rep_uni2 += met.nunp_rep_uni2;
nunp_rep_rep += met.nunp_rep_rep;
nunp_rep_0 += met.nunp_rep_0;
nunp_uni += met.nunp_uni;
nunp_uni1 += met.nunp_uni1;
nunp_uni2 += met.nunp_uni2;
nunp_rep += met.nunp_rep;
nunp_0 += met.nunp_0;
sum_best1 += met.sum_best1;
sum_best2 += met.sum_best2;
sum_best += met.sum_best;
}
uint64_t nread; // # reads
uint64_t npaired; // # pairs
uint64_t nunpaired; // # unpaired reads
// Paired
// Concordant
uint64_t nconcord_uni; // # pairs with unique concordant alns
uint64_t nconcord_uni1; // # pairs with exactly 1 concordant alns
uint64_t nconcord_uni2; // # pairs with >1 concordant aln, still unique
uint64_t nconcord_rep; // # pairs with repetitive concordant alns
uint64_t nconcord_0; // # pairs with 0 concordant alns
// Discordant
uint64_t ndiscord; // # pairs with 1 discordant aln
// Unpaired from failed pairs
uint64_t nunp_0_uni; // # unique from nconcord_0_ - ndiscord_
uint64_t nunp_0_uni1; // # pairs with exactly 1 concordant alns
uint64_t nunp_0_uni2; // # pairs with >1 concordant aln, still unique
uint64_t nunp_0_rep; // # repetitive from
uint64_t nunp_0_0; // # with 0 alignments
// Unpaired from repetitive pairs
uint64_t nunp_rep_uni; // # pairs with unique concordant alns
uint64_t nunp_rep_uni1; // # pairs with exactly 1 concordant alns
uint64_t nunp_rep_uni2; // # pairs with >1 concordant aln, still unique
uint64_t nunp_rep_rep; // # pairs with repetitive concordant alns
uint64_t nunp_rep_0; // # pairs with 0 concordant alns
// Unpaired
uint64_t nunp_uni; // # unique from nconcord_0_ - ndiscord_
uint64_t nunp_uni1; // # pairs with exactly 1 concordant alns
uint64_t nunp_uni2; // # pairs with >1 concordant aln, still unique
uint64_t nunp_rep; // # repetitive from
uint64_t nunp_0; // # with 0 alignments
uint64_t sum_best1; // Sum of all the best alignment scores
uint64_t sum_best2; // Sum of all the second-best alignment scores
uint64_t sum_best; // Sum of all the best and second-best
MUTEX_T mutex_m;
};
// Type for expression numbers of hits
typedef int64_t THitInt;
/**
* Parameters affecting reporting of alignments, specifically -k & -a,
* -m & -M.
*/
struct ReportingParams {
explicit ReportingParams(
THitInt khits_,
THitInt mhits_,
THitInt pengap_,
bool msample_,
bool discord_,
bool mixed_)
{
init(khits_, mhits_, pengap_, msample_, discord_, mixed_);
}
void init(
THitInt khits_,
THitInt mhits_,
THitInt pengap_,
bool msample_,
bool discord_,
bool mixed_)
{
khits = khits_; // -k (or high if -a)
mhits = ((mhits_ == 0) ? std::numeric_limits<THitInt>::max() : mhits_);
pengap = pengap_;
msample = msample_;
discord = discord_;
mixed = mixed_;
}
#ifndef NDEBUG
/**
* Check that reporting parameters are internally consistent.
*/
bool repOk() const {
assert_geq(khits, 1);
assert_geq(mhits, 1);
return true;
}
#endif
/**
* Return true iff a -m or -M limit was set by the user.
*/
inline bool mhitsSet() const {
return mhits < std::numeric_limits<THitInt>::max();
}
/**
* Return a multiplier that indicates how many alignments we might look for
* (max). We can use this to boost parameters like ROWM and POSF
* appropriately.
*/
inline THitInt mult() const {
if(mhitsSet()) {
return mhits+1;
}
return khits;
}
/**
* Given ROWM, POSF thresholds, boost them according to mult().
*/
void boostThreshold(SimpleFunc& func) {
THitInt mul = mult();
assert_gt(mul, 0);
if(mul == std::numeric_limits<THitInt>::max()) {
func.setMin(std::numeric_limits<double>::max());
} else if(mul > 1) {
func.mult(mul);
}
}
/**
* Return true iff we are reporting all hits.
*/
bool allHits() const {
return khits == std::numeric_limits<THitInt>::max();
}
// Number of alignments to report
THitInt khits;
// Read is non-unique if mhits-1 next-best alignments are within
// pengap of the best alignment
THitInt mhits, pengap;
// true if -M is specified, meaning that if the -M ceiling is
// exceeded, we should report 'khits' alignments chosen at random
// from those found
bool msample;
// true iff we should seek and report discordant paired-end alignments for
// paired-end reads.
bool discord;
// true iff we should seek and report unpaired mate alignments when there
// are paired-end alignments for a paired-end read, or if the number of
// paired-end alignments exceeds the -m ceiling.
bool mixed;
};
/**
* A state machine keeping track of the number and type of alignments found so
* far. Its purpose is to inform the caller as to what stage the alignment is
* in and what categories of alignment are still of interest. This information
* should allow the caller to short-circuit some alignment work. Another
* purpose is to tell the AlnSinkWrap how many and what type of alignment to
* report.
*
* TODO: This class does not keep accurate information about what
* short-circuiting took place. If a read is identical to a previous read,
* there should be a way to query this object to determine what work, if any,
* has to be re-done for the new read.
*/
class ReportingState {
public:
enum {
NO_READ = 1, // haven't got a read yet
CONCORDANT_PAIRS, // looking for concordant pairs
DISCORDANT_PAIRS, // looking for discordant pairs
UNPAIRED, // looking for unpaired
DONE // finished looking
};
// Flags for different ways we can finish out a category of potential
// alignments.
enum {
EXIT_DID_NOT_EXIT = 1, // haven't finished
EXIT_DID_NOT_ENTER, // never tried search
EXIT_SHORT_CIRCUIT_k, // -k exceeded
EXIT_SHORT_CIRCUIT_M, // -M exceeded
EXIT_SHORT_CIRCUIT_TRUMPED, // made irrelevant
EXIT_CONVERTED_TO_DISCORDANT, // unpair became discord
EXIT_NO_ALIGNMENTS, // none found
EXIT_WITH_ALIGNMENTS // some found
};
ReportingState(const ReportingParams& p) : p_(p) { reset(); }
/**
* Set all state to uninitialized defaults.
*/
void reset() {
state_ = ReportingState::NO_READ;
paired_ = false;
nconcord_ = 0;
ndiscord_ = 0;
nunpair1_ = 0;
nunpair2_ = 0;
doneConcord_ = false;
doneDiscord_ = false;
doneUnpair_ = false;
doneUnpair1_ = false;
doneUnpair2_ = false;
exitConcord_ = ReportingState::EXIT_DID_NOT_ENTER;
exitDiscord_ = ReportingState::EXIT_DID_NOT_ENTER;
exitUnpair1_ = ReportingState::EXIT_DID_NOT_ENTER;
exitUnpair2_ = ReportingState::EXIT_DID_NOT_ENTER;
done_ = false;
}
/**
* Return true iff this ReportingState has been initialized with a call to
* nextRead() since the last time reset() was called.
*/
bool inited() const { return state_ != ReportingState::NO_READ; }
/**
* Initialize state machine with a new read. The state we start in depends
* on whether it's paired-end or unpaired.
*/
void nextRead(bool paired);
/**
* Caller uses this member function to indicate that one additional
* concordant alignment has been found.
*/
bool foundConcordant();
/**
* Caller uses this member function to indicate that one additional
* discordant alignment has been found.
*/
bool foundUnpaired(bool mate1);
/**
* Called to indicate that the aligner has finished searching for
* alignments. This gives us a chance to finalize our state.
*
* TODO: Keep track of short-circuiting information.
*/
void finish();
/**
* Populate given counters with the number of various kinds of alignments
* to report for this read. Concordant alignments are preferable to (and
* mutually exclusive with) discordant alignments, and paired-end
* alignments are preferable to unpaired alignments.
*
* The caller also needs some additional information for the case where a
* pair or unpaired read aligns repetitively. If the read is paired-end
* and the paired-end has repetitive concordant alignments, that should be
* reported, and 'pairMax' is set to true to indicate this. If the read is
* paired-end, does not have any conordant alignments, but does have
* repetitive alignments for one or both mates, then that should be
* reported, and 'unpair1Max' and 'unpair2Max' are set accordingly.
*
* Note that it's possible in the case of a paired-end read for the read to
* have repetitive concordant alignments, but for one mate to have a unique
* unpaired alignment.
*/
void getReport(
uint64_t& nconcordAln, // # concordant alignments to report
uint64_t& ndiscordAln, // # discordant alignments to report
uint64_t& nunpair1Aln, // # unpaired alignments for mate #1 to report
uint64_t& nunpair2Aln, // # unpaired alignments for mate #2 to report
bool& pairMax, // repetitive concordant alignments
bool& unpair1Max, // repetitive alignments for mate #1
bool& unpair2Max) // repetitive alignments for mate #2
const;
/**
* Return an integer representing the alignment state we're in.
*/
inline int state() const { return state_; }
/**
* If false, there's no need to solve any more dynamic programming problems
* for finding opposite mates.
*/
inline bool doneConcordant() const { return doneConcord_; }
/**
* If false, there's no need to seek any more discordant alignment.
*/
inline bool doneDiscordant() const { return doneDiscord_; }
/**
* If false, there's no need to seek any more unpaired alignments for the
* specified mate. Note: this doesn't necessarily mean we can stop looking
* for alignments for the mate, since this might be necessary for finding
* concordant and discordant alignments.
*/
inline bool doneUnpaired(bool mate1) const {
return mate1 ? doneUnpair1_ : doneUnpair2_;
}
/**
* If false, no further consideration of the given mate is necessary. It's
* not needed for *any* class of alignment: concordant, discordant or
* unpaired.
*/
inline bool doneWithMate(bool mate1) const {
bool doneUnpair = mate1 ? doneUnpair1_ : doneUnpair2_;
uint64_t nun = mate1 ? nunpair1_ : nunpair2_;
if(!doneUnpair || !doneConcord_) {
return false; // still needed for future concordant/unpaired alns
}
if(!doneDiscord_ && nun == 0) {
return false; // still needed for future discordant alignments
}
return true; // done
}
/**
* Return true iff there's no need to seek any more unpaired alignments.
*/
inline bool doneUnpaired() const { return doneUnpair_; }
/**
* Return true iff all alignment stages have been exited.
*/
inline bool done() const { return done_; }
inline uint64_t numConcordant() const { return nconcord_; }
inline uint64_t numDiscordant() const { return ndiscord_; }
inline uint64_t numUnpaired1() const { return nunpair1_; }
inline uint64_t numUnpaired2() const { return nunpair2_; }
inline int exitConcordant() const { return exitConcord_; }
inline int exitDiscordant() const { return exitDiscord_; }
inline int exitUnpaired1() const { return exitUnpair1_; }
inline int exitUnpaired2() const { return exitUnpair2_; }
#ifndef NDEBUG
/**
* Check that ReportingState is internally consistent.
*/
bool repOk() const {
assert(p_.discord || doneDiscord_);
assert(p_.mixed || !paired_ || doneUnpair_);
assert(doneUnpair_ || !doneUnpair1_ || !doneUnpair2_);
if(p_.mhitsSet()) {
assert_leq(numConcordant(), (uint64_t)p_.mhits+1);
assert_leq(numDiscordant(), (uint64_t)p_.mhits+1);
assert(paired_ || numUnpaired1() <= (uint64_t)p_.mhits+1);
assert(paired_ || numUnpaired2() <= (uint64_t)p_.mhits+1);
}
assert(done() || !doneWithMate(true) || !doneWithMate(false));
return true;
}
#endif
/**
* Return ReportingParams object governing this ReportingState.
*/
const ReportingParams& params() const {
return p_;
}
protected:
/**
* Update state to reflect situation after converting two unique unpaired
* alignments, one for mate 1 and one for mate 2, into a single discordant
* alignment.
*/
void convertUnpairedToDiscordant() {
assert_eq(1, numUnpaired1());
assert_eq(1, numUnpaired2());
assert_eq(0, numDiscordant());
exitUnpair1_ = exitUnpair2_ = ReportingState::EXIT_CONVERTED_TO_DISCORDANT;
nunpair1_ = nunpair2_ = 0;
ndiscord_ = 1;
assert_eq(1, numDiscordant());
}
/**
* Given the number of alignments in a category, check whether we
* short-circuited out of the category. Set the done and exit arguments to
* indicate whether and how we short-circuited.
*/
inline void areDone(
uint64_t cnt, // # alignments in category
bool& done, // out: whether we short-circuited out of category
int& exit) const; // out: if done, how we short-circuited (-k? -m? etc)
/**
* Update done_ field to reflect whether we're totally done now.
*/
inline void updateDone() {
doneUnpair_ = doneUnpair1_ && doneUnpair2_;
done_ = doneUnpair_ && doneDiscord_ && doneConcord_;
}
const ReportingParams& p_; // reporting parameters
int state_; // state we're currently in
bool paired_; // true iff read we're currently handling is paired
uint64_t nconcord_; // # concordants found so far
uint64_t ndiscord_; // # discordants found so far
uint64_t nunpair1_; // # unpaired alignments found so far for mate 1
uint64_t nunpair2_; // # unpaired alignments found so far for mate 2
bool doneConcord_; // true iff we're no longner interested in concordants
bool doneDiscord_; // true iff we're no longner interested in discordants
bool doneUnpair_; // no longner interested in unpaired alns
bool doneUnpair1_; // no longner interested in unpaired alns for mate 1
bool doneUnpair2_; // no longner interested in unpaired alns for mate 2
int exitConcord_; // flag indicating how we exited concordant state
int exitDiscord_; // flag indicating how we exited discordant state
int exitUnpair1_; // flag indicating how we exited unpaired 1 state
int exitUnpair2_; // flag indicating how we exited unpaired 2 state
bool done_; // done with all alignments
};
/**
* Global hit sink for hits from the MultiSeed aligner. Encapsulates
* all aspects of the MultiSeed aligner hitsink that are global to all
* threads. This includes aspects relating to:
*
* (a) synchronized access to the output stream
* (b) the policy to be enforced by the per-thread wrapper
*
* TODO: Implement splitting up of alignments into separate files
* according to genomic coordinate.
*/
class AlnSink {
typedef EList<std::string> StrList;
public:
explicit AlnSink(
OutputQueue& oq,
const StrList& refnames,
bool quiet) :
oq_(oq),
refnames_(refnames),
quiet_(quiet)
{ }
/**
* Destroy HitSinkobject;
*/
virtual ~AlnSink() { }
/**
* Append a single hit to the given output stream. If
* synchronization is required, append() assumes the caller has
* already grabbed the appropriate lock.
*/
virtual void append(
BTString& o,
StackedAln& staln,
size_t threadId,
const Read *rd1,
const Read *rd2,
const TReadId rdid,
AlnRes *rs1,
AlnRes *rs2,
const AlnSetSumm& summ,
const SeedAlSumm& ssm1,
const SeedAlSumm& ssm2,
const AlnFlags* flags1,
const AlnFlags* flags2,
const PerReadMetrics& prm,
const Mapq& mapq,
const Scoring& sc,
bool report2) = 0;
/**
* Report a given batch of hits for the given read or read pair.
* Should be called just once per read pair. Assumes all the
* alignments are paired, split between rs1 and rs2.
*
* The caller hasn't decided which alignments get reported as primary
* or secondary; that's up to the routine. Because the caller might
* want to know this, we use the pri1 and pri2 out arguments to
* convey this.
*/
virtual void reportHits(
BTString& o, // write to this buffer
StackedAln& staln, // StackedAln to write stacked alignment
size_t threadId, // which thread am I?
const Read *rd1, // mate #1
const Read *rd2, // mate #2
const TReadId rdid, // read ID
const EList<size_t>& select1, // random subset of rd1s
const EList<size_t>* select2, // random subset of rd2s
EList<AlnRes> *rs1, // alignments for mate #1
EList<AlnRes> *rs2, // alignments for mate #2
bool maxed, // true iff -m/-M exceeded
const AlnSetSumm& summ, // summary
const SeedAlSumm& ssm1, // seed alignment summ
const SeedAlSumm& ssm2, // seed alignment summ
const AlnFlags* flags1, // flags for mate #1
const AlnFlags* flags2, // flags for mate #2
const PerReadMetrics& prm, // per-read metrics
const Mapq& mapq, // MAPQ generator
const Scoring& sc, // scoring scheme
bool reportBoth,
bool getLock = true) // true iff lock held by caller
{
// There are a few scenarios:
// 1. Read is unpaired, in which case rd2 is NULL
// 2. Read is paired-end and we're reporting concordant alignments
// 3. Read is paired-end and we're reporting discordant alignments
// 4. Read is paired-end and we're reporting unpaired alignments for
// both mates
// 5. Read is paired-end and we're reporting an unpaired alignments for
// just one mate or the other
assert(rd1 != NULL || rd2 != NULL);
assert(rs1 != NULL || rs2 != NULL);
AlnFlags flagscp1, flagscp2;
if(flags1 != NULL) {
flagscp1 = *flags1;
flags1 = &flagscp1;
flagscp1.setPrimary(true);
}
if(flags2 != NULL) {
flagscp2 = *flags2;
flags2 = &flagscp2;
flagscp2.setPrimary(true);
}
if(select2 != NULL) {
// Handle case 4
assert(rd1 != NULL); assert(flags1 != NULL);
assert(rd2 != NULL); assert(flags2 != NULL);
assert_gt(select1.size(), 0);
assert_gt(select2->size(), 0);
AlnRes* r1pri = ((rs1 != NULL) ? &rs1->get(select1[0]) : NULL);
AlnRes* r2pri = ((rs2 != NULL) ? &rs2->get((*select2)[0]) : NULL);
append(o, staln, threadId, rd1, rd2, rdid, r1pri, r2pri, summ,
ssm1, ssm2, flags1, flags2, prm, mapq, sc, false);
flagscp1.setPrimary(false);
flagscp2.setPrimary(false);
for(size_t i = 1; i < select1.size(); i++) {
AlnRes* r1 = ((rs1 != NULL) ? &rs1->get(select1[i]) : NULL);
append(o, staln, threadId, rd1, rd2, rdid, r1, r2pri, summ,
ssm1, ssm2, flags1, flags2, prm, mapq, sc, false);
}
if(reportBoth) {
for(size_t i = 1; i < select2->size(); i++) {
AlnRes* r2 = ((rs2 != NULL) ? &rs2->get((*select2)[i]) : NULL);
append(o, staln, threadId, rd2, rd1, rdid, r2, r1pri, summ,
ssm2, ssm1, flags2, flags1, prm, mapq, sc, false);
}
}
} else {
// Handle cases 1-3 and 5
for(size_t i = 0; i < select1.size(); i++) {
AlnRes* r1 = ((rs1 != NULL) ? &rs1->get(select1[i]) : NULL);
AlnRes* r2 = ((rs2 != NULL) ? &rs2->get(select1[i]) : NULL);
append(o, staln, threadId, rd1, rd2, rdid, r1, r2, summ,
ssm1, ssm2, flags1, flags2, prm, mapq, sc, true);
if(flags1 != NULL) {
flagscp1.setPrimary(false);
}
if(flags2 != NULL) {
flagscp2.setPrimary(false);
}
}
}
}
/**
* Report an unaligned read. Typically we do nothing, but we might
* want to print a placeholder when output is chained.
*/
virtual void reportUnaligned(
BTString& o, // write to this string
StackedAln& staln, // StackedAln to write stacked alignment
size_t threadId, // which thread am I?
const Read *rd1, // mate #1
const Read *rd2, // mate #2
const TReadId rdid, // read ID
const AlnSetSumm& summ, // summary
const SeedAlSumm& ssm1, // seed alignment summary
const SeedAlSumm& ssm2, // seed alignment summary
const AlnFlags* flags1, // flags for mate #1
const AlnFlags* flags2, // flags for mate #2
const PerReadMetrics& prm, // per-read metrics
const Mapq& mapq, // MAPQ calculator
const Scoring& sc, // scoring scheme
bool report2, // report alns for both mates?
bool getLock = true) // true iff lock held by caller
{
append(o, staln, threadId, rd1, rd2, rdid, NULL, NULL, summ,
ssm1, ssm2, flags1, flags2, prm, mapq, sc, report2);
}
/**
* Print summary of how many reads aligned, failed to align and aligned
* repetitively. Write it to stderr. Optionally write Hadoop counter
* updates.
*/
void printAlSumm(
const ReportingMetrics& met,
size_t repThresh, // threshold for uniqueness, or max if no thresh
bool discord, // looked for discordant alignments
bool mixed, // looked for unpaired alignments where paired failed?
bool hadoopOut); // output Hadoop counters?
/**
* Called when all alignments are complete. It is assumed that no
* synchronization is necessary.
*/
void finish(
size_t repThresh,
bool discord,
bool mixed,
bool hadoopOut)
{
// Close output streams
if(!quiet_) {
printAlSumm(
met_,
repThresh,
discord,
mixed,
hadoopOut);
}
}
#ifndef NDEBUG
/**
* Check that hit sink is internally consistent.
*/
bool repOk() const { return true; }
#endif
//
// Related to reporting seed hits
//
/**
* Given a Read and associated, filled-in SeedResults objects,
* print a record summarizing the seed hits.
*/
void reportSeedSummary(
BTString& o,
const Read& rd,
TReadId rdid,
size_t threadId,
const SeedResults& rs,
bool getLock = true);
/**
* Given a Read, print an empty record (all 0s).
*/
void reportEmptySeedSummary(
BTString& o,
const Read& rd,
TReadId rdid,
size_t threadId,
bool getLock = true);
/**
* Append a batch of unresolved seed alignment results (i.e. seed
* alignments where all we know is the reference sequence aligned
* to and its SA range, not where it falls in the reference
* sequence) to the given output stream in Bowtie's seed-alignment
* verbose-mode format.
*/
virtual void appendSeedSummary(
BTString& o,
const Read& rd,
const TReadId rdid,
size_t seedsTried,
size_t nonzero,
size_t ranges,
size_t elts,
size_t seedsTriedFw,
size_t nonzeroFw,
size_t rangesFw,
size_t eltsFw,
size_t seedsTriedRc,
size_t nonzeroRc,
size_t rangesRc,
size_t eltsRc);
/**
* Merge given metrics in with ours by summing all individual metrics.
*/
void mergeMetrics(const ReportingMetrics& met) {
met_.merge(met);
}
/**
* Return mutable reference to the shared OutputQueue.
*/
OutputQueue& outq() {
return oq_;
}
protected:
OutputQueue& oq_; // output queue
const StrList& refnames_; // reference names
bool quiet_; // true -> don't print alignment stats at the end
ReportingMetrics met_; // global repository of reporting metrics
};
/**
* Per-thread hit sink "wrapper" for the MultiSeed aligner. Encapsulates
* aspects of the MultiSeed aligner hit sink that are per-thread. This
* includes aspects relating to:
*
* (a) Enforcement of the reporting policy
* (b) Tallying of results
* (c) Storing of results for the previous read in case this allows us to
* short-circuit some work for the next read (i.e. if it's identical)
*
* PHASED ALIGNMENT ASSUMPTION
*
* We make some assumptions about how alignment proceeds when we try to
* short-circuit work for identical reads. Specifically, we assume that for
* each read the aligner proceeds in a series of stages (or perhaps just one
* stage). In each stage, the aligner either:
*
* (a) Finds no alignments, or
* (b) Finds some alignments and short circuits out of the stage with some
* random reporting involved (e.g. in -k and/or -M modes), or
* (c) Finds all of the alignments in the stage
*
* In the event of (a), the aligner proceeds to the next stage and keeps
* trying; we can skip the stage entirely for the next read if it's identical.
* In the event of (b), or (c), the aligner stops and does not proceed to
* further stages. In the event of (b1), if the next read is identical we
* would like to tell the aligner to start again at the beginning of the stage
* that was short-circuited.
*
* In any event, the rs1_/rs2_/rs1u_/rs2u_ fields contain the alignments found
* in the last alignment stage attempted.
*
* HANDLING REPORTING LIMITS
*
* The user can specify reporting limits, like -k (specifies number of
* alignments to report out of those found) and -M (specifies a ceiling s.t. if
* there are more alignments than the ceiling, read is called repetitive and
* best found is reported). Enforcing these limits is straightforward for
* unpaired alignments: if a new alignment causes us to exceed the -M ceiling,
* we can stop looking.
*
* The case where both paired-end and unpaired alignments are possible is
* trickier. Once we have a number of unpaired alignments that exceeds the
* ceiling, we can stop looking *for unpaired alignments* - but we can't
* necessarily stop looking for paired-end alignments, since there may yet be
* more to find. However, if the input read is not a pair, then we can stop at
* this point. If the input read is a pair and we have a number of paired
* aligments that exceeds the -M ceiling, we can stop looking.
*
* CONCORDANT & DISCORDANT, PAIRED & UNPAIRED
*
* A note on paired-end alignment: Clearly, if an input read is
* paired-end and we find either concordant or discordant paired-end
* alignments for the read, then we would like to tally and report
* those alignments as such (and not as groups of 2 unpaired
* alignments). And if we fail to find any paired-end alignments, but
* we do find some unpaired alignments for one mate or the other, then
* we should clearly tally and report those alignments as unpaired
* alignments (if the user so desires).
*
* The situation is murkier when there are no paired-end alignments,
* but there are unpaired alignments for *both* mates. In this case,
* we might want to pick out zero or more pairs of mates and classify
* those pairs as discordant paired-end alignments. And we might want
* to classify the remaining alignments as unpaired. But how do we
* pick which pairs if any to call discordant?
*
* Because the most obvious use for discordant pairs is for identifying
* large-scale variation, like rearrangements or large indels, we would
* usually like to be conservative about what we call a discordant
* alignment. If there's a good chance that one or the other of the
* two mates has a good alignment to another place on the genome, this
* compromises the evidence for the large-scale variant. For this
* reason, Bowtie 2's policy is: if there are no paired-end alignments
* and there is *exactly one alignment each* for both mates, then the
* two alignments are paired and treated as a discordant paired-end
* alignment. Otherwise, all alignments are treated as unpaired
* alignments.
*
* When both paired and unpaired alignments are discovered by the
* aligner, only the paired alignments are reported by default. This
* is sensible considering relative likelihoods: if a good paired-end
* alignment is found, it is much more likely that the placement of
* the two mates implied by that paired alignment is correct than any
* placement implied by an unpaired alignment.
*
*
*/
class AlnSinkWrap {
public:
AlnSinkWrap(
AlnSink& g, // AlnSink being wrapped
const ReportingParams& rp, // Parameters governing reporting
Mapq& mapq, // Mapq calculator
size_t threadId) : // Thread ID
g_(g),
rp_(rp),
threadid_(threadId),
mapq_(mapq),
init_(false),
maxed1_(false), // read is pair and we maxed out mate 1 unp alns
maxed2_(false), // read is pair and we maxed out mate 2 unp alns
maxedOverall_(false), // alignments found so far exceed -m/-M ceiling
bestPair_(std::numeric_limits<TAlScore>::min()),
best2Pair_(std::numeric_limits<TAlScore>::min()),
bestUnp1_(std::numeric_limits<TAlScore>::min()),
best2Unp1_(std::numeric_limits<TAlScore>::min()),
bestUnp2_(std::numeric_limits<TAlScore>::min()),
best2Unp2_(std::numeric_limits<TAlScore>::min()),
rd1_(NULL), // mate 1
rd2_(NULL), // mate 2
rdid_(std::numeric_limits<TReadId>::max()), // read id
rs1_(), // mate 1 alignments for paired-end alignments
rs2_(), // mate 2 alignments for paired-end alignments
rs1u_(), // mate 1 unpaired alignments
rs2u_(), // mate 2 unpaired alignments
select1_(), // for selecting random subsets for mate 1
select2_(), // for selecting random subsets for mate 2
st_(rp) // reporting state - what's left to do?
{
assert(rp_.repOk());
}
/**
* Initialize the wrapper with a new read pair and return an
* integer >= -1 indicating which stage the aligner should start
* at. If -1 is returned, the aligner can skip the read entirely.
* at. If . Checks if the new read pair is identical to the
* previous pair. If it is, then we return the id of the first
* stage to run.
*/
int nextRead(
// One of the other of rd1, rd2 will = NULL if read is unpaired
const Read* rd1, // new mate #1
const Read* rd2, // new mate #2
TReadId rdid, // read ID for new pair
bool qualitiesMatter);// aln policy distinguishes b/t quals?
/**
* Inform global, shared AlnSink object that we're finished with
* this read. The global AlnSink is responsible for updating
* counters, creating the output record, and delivering the record
* to the appropriate output stream.
*/
void finishRead(
const SeedResults *sr1, // seed alignment results for mate 1
const SeedResults *sr2, // seed alignment results for mate 2
bool exhaust1, // mate 1 exhausted?
bool exhaust2, // mate 2 exhausted?
bool nfilt1, // mate 1 N-filtered?
bool nfilt2, // mate 2 N-filtered?
bool scfilt1, // mate 1 score-filtered?
bool scfilt2, // mate 2 score-filtered?
bool lenfilt1, // mate 1 length-filtered?
bool lenfilt2, // mate 2 length-filtered?
bool qcfilt1, // mate 1 qc-filtered?
bool qcfilt2, // mate 2 qc-filtered?
RandomSource& rnd, // pseudo-random generator
ReportingMetrics& met, // reporting metrics
const PerReadMetrics& prm, // per-read metrics
const Scoring& sc, // scoring scheme
bool suppressSeedSummary = true,
bool suppressAlignments = false,
bool scUnMapped = false,
bool xeq = false);
/**
* Called by the aligner when a new unpaired or paired alignment is
* discovered in the given stage. This function checks whether the
* addition of this alignment causes the reporting policy to be
* violated (by meeting or exceeding the limits set by -k, -m, -M),
* in which case true is returned immediately and the aligner is
* short circuited. Otherwise, the alignment is tallied and false
* is returned.
*/
bool report(
int stage,
const AlnRes* rs1,
const AlnRes* rs2);
#ifndef NDEBUG
/**
* Check that hit sink wrapper is internally consistent.
*/
bool repOk() const {
assert_eq(rs2_.size(), rs1_.size());
if(rp_.mhitsSet()) {
assert_gt(rp_.mhits, 0);
assert_leq((int)rs1_.size(), rp_.mhits+1);
assert_leq((int)rs2_.size(), rp_.mhits+1);
assert(readIsPair() || (int)rs1u_.size() <= rp_.mhits+1);
assert(readIsPair() || (int)rs2u_.size() <= rp_.mhits+1);
}
if(init_) {
assert(rd1_ != NULL);
assert_neq(std::numeric_limits<TReadId>::max(), rdid_);
}
assert_eq(st_.numConcordant() + st_.numDiscordant(), rs1_.size());
//assert_eq(st_.numUnpaired1(), rs1u_.size());
//assert_eq(st_.numUnpaired2(), rs2u_.size());
assert(st_.repOk());
return true;
}
#endif
/**
* Return true iff no alignments have been reported to this wrapper
* since the last call to nextRead().
*/
bool empty() const {
return rs1_.empty() && rs1u_.empty() && rs2u_.empty();
}
/**
* Return true iff we have already encountered a number of alignments that
* exceeds the -m/-M ceiling. TODO: how does this distinguish between
* pairs and mates?
*/
bool maxed() const {
return maxedOverall_;
}
/**
* Return true if the current read is paired.
*/
bool readIsPair() const {
return rd1_ != NULL && rd2_ != NULL;
}
/**
* Return true iff nextRead() has been called since the last time
* finishRead() was called.
*/
bool inited() const { return init_; }
/**
* Return a const ref to the ReportingState object associated with the
* AlnSinkWrap.
*/
const ReportingState& state() const { return st_; }
/**
* Return true iff we're in -M mode.
*/
bool Mmode() const {
return rp_.mhitsSet();
}
/**
* Return true iff the policy is to report all hits.
*/
bool allHits() const {
return rp_.allHits();
}
/**
* Return true iff at least two alignments have been reported so far for an
* unpaired read or mate 1.
*/
bool hasSecondBestUnp1() const {
return best2Unp1_ != std::numeric_limits<TAlScore>::min();
}
/**
* Return true iff at least two alignments have been reported so far for
* mate 2.
*/
bool hasSecondBestUnp2() const {
return best2Unp2_ != std::numeric_limits<TAlScore>::min();
}
/**
* Return true iff at least two paired-end alignments have been reported so
* far.
*/
bool hasSecondBestPair() const {
return best2Pair_ != std::numeric_limits<TAlScore>::min();
}
/**
* Get best score observed so far for an unpaired read or mate 1.
*/
TAlScore bestUnp1() const {
return bestUnp1_;
}
/**
* Get second-best score observed so far for an unpaired read or mate 1.
*/
TAlScore secondBestUnp1() const {
return best2Unp1_;
}
/**
* Get best score observed so far for mate 2.
*/
TAlScore bestUnp2() const {
return bestUnp2_;
}
/**
* Get second-best score observed so far for mate 2.
*/
TAlScore secondBestUnp2() const {
return best2Unp2_;
}
/**
* Get best score observed so far for paired-end read.
*/
TAlScore bestPair() const {
return bestPair_;
}
/**
* Get second-best score observed so far for paired-end read.
*/
TAlScore secondBestPair() const {
return best2Pair_;
}
protected:
/**
* Return true iff the read in rd1/rd2 matches the last read handled, which
* should still be in rd1_/rd2_.
*/
bool sameRead(
const Read* rd1,
const Read* rd2,
bool qualitiesMatter);
/**
* If there is a configuration of unpaired alignments that fits our
* criteria for there being one or more discordant alignments, then
* shift the discordant alignments over to the rs1_/rs2_ lists, clear the
* rs1u_/rs2u_ lists and return true. Otherwise, return false.
*/
bool prepareDiscordants();
/**
* Given that rs is already populated with alignments, consider the
* alignment policy and make random selections where necessary. E.g. if we
* found 10 alignments and the policy is -k 2 -m 20, select 2 alignments at
* random. We "select" an alignment by setting the parallel entry in the
* 'select' list to true.
*/
size_t selectAlnsToReport(
const EList<AlnRes>& rs, // alignments to select from
uint64_t num, // number of alignments to select
EList<size_t>& select, // list to put results in
RandomSource& rnd)
const;
/**
* rs1 (possibly together with rs2 if reads are paired) are populated with
* alignments. Here we prioritize them according to alignment score, and
* some randomness to break ties. Priorities are returned in the 'select'
* list.
*/
size_t selectByScore(
const EList<AlnRes>* rs1, // alignments to select from (mate 1)
const EList<AlnRes>* rs2, // alignments to select from (mate 2, or NULL)
uint64_t num, // number of alignments to select
EList<size_t>& select, // prioritized list to put results in
const EList<AlnRes>* rs1u, // alignments to select from (mate 1)
const EList<AlnRes>* rs2u, // alignments to select from (mate 2, or NULL)
AlnScore& bestUScore,
AlnScore& bestUDist,
AlnScore& bestP1Score,
AlnScore& bestP1Dist,
AlnScore& bestP2Score,
AlnScore& bestP2Dist,
AlnScore& bestCScore,
AlnScore& bestCDist,
AlnScore& bestUnchosenUScore,
AlnScore& bestUnchosenUDist,
AlnScore& bestUnchosenP1Score,
AlnScore& bestUnchosenP1Dist,
AlnScore& bestUnchosenP2Score,
AlnScore& bestUnchosenP2Dist,
AlnScore& bestUnchosenCScore,
AlnScore& bestUnchosenCDist,
RandomSource& rnd)
const;
AlnSink& g_; // global alignment sink
ReportingParams rp_; // reporting parameters: khits, mhits etc
size_t threadid_; // thread ID
Mapq& mapq_; // mapq calculator
bool init_; // whether we're initialized w/ read pair
bool maxed1_; // true iff # unpaired mate-1 alns reported so far exceeded -m/-M
bool maxed2_; // true iff # unpaired mate-2 alns reported so far exceeded -m/-M
bool maxedOverall_; // true iff # paired-end alns reported so far exceeded -m/-M
TAlScore bestPair_; // greatest score so far for paired-end
TAlScore best2Pair_; // second-greatest score so far for paired-end
TAlScore bestUnp1_; // greatest score so far for unpaired/mate1
TAlScore best2Unp1_; // second-greatest score so far for unpaired/mate1
TAlScore bestUnp2_; // greatest score so far for mate 2
TAlScore best2Unp2_; // second-greatest score so far for mate 2
const Read* rd1_; // mate #1
const Read* rd2_; // mate #2
TReadId rdid_; // read ID (potentially used for ordering)
EList<AlnRes> rs1_; // paired alignments for mate #1
EList<AlnRes> rs2_; // paired alignments for mate #2
EList<AlnRes> rs1u_; // unpaired alignments for mate #1
EList<AlnRes> rs2u_; // unpaired alignments for mate #2
EList<size_t> select1_; // parallel to rs1_/rs2_ - which to report
EList<size_t> select2_; // parallel to rs1_/rs2_ - which to report
ReportingState st_; // reporting state - what's left to do?
EList<std::pair<AlnScore, size_t> > selectBuf_;
BTString obuf_;
StackedAln staln_;
};
/**
* An AlnSink concrete subclass for printing SAM alignments. The user might
* want to customize SAM output in various ways. We encapsulate all these
* customizations, and some of the key printing routines, in the SamConfig
* class in sam.h/sam.cpp.
*/
class AlnSinkSam : public AlnSink {
typedef EList<std::string> StrList;
public:
AlnSinkSam(
OutputQueue& oq, // output queue
const SamConfig& samc, // settings & routines for SAM output
const StrList& refnames, // reference names
bool quiet) : // don't print alignment summary at end
AlnSink(
oq,
refnames,
quiet),
samc_(samc)
{ }
virtual ~AlnSinkSam() { }
/**
* Append a single alignment result, which might be paired or
* unpaired, to the given output stream in Bowtie's verbose-mode
* format. If the alignment is paired-end, print mate1's alignment
* then mate2's alignment.
*/
virtual void append(
BTString& o, // write output to this string
StackedAln& staln, // StackedAln to write stacked alignment
size_t threadId, // which thread am I?
const Read* rd1, // mate #1
const Read* rd2, // mate #2
const TReadId rdid, // read ID
AlnRes* rs1, // alignments for mate #1
AlnRes* rs2, // alignments for mate #2
const AlnSetSumm& summ, // summary
const SeedAlSumm& ssm1, // seed alignment summary
const SeedAlSumm& ssm2, // seed alignment summary
const AlnFlags* flags1, // flags for mate #1
const AlnFlags* flags2, // flags for mate #2
const PerReadMetrics& prm, // per-read metrics
const Mapq& mapq, // MAPQ calculator
const Scoring& sc, // scoring scheme
bool report2) // report alns for both mates
{
assert(rd1 != NULL || rd2 != NULL);
if(rd1 != NULL) {
assert(flags1 != NULL);
appendMate(o, staln, *rd1, rd2, rdid, rs1, rs2, summ, ssm1, ssm2,
*flags1, prm, mapq, sc);
}
if(rd2 != NULL && report2) {
assert(flags2 != NULL);
appendMate(o, staln, *rd2, rd1, rdid, rs2, rs1, summ, ssm2, ssm1,
*flags2, prm, mapq, sc);
}
}
protected:
/**
* Append a single per-mate alignment result to the given output
* stream. If the alignment is part of a pair, information about
* the opposite mate and its alignment are given in rdo/rso.
*/
void appendMate(
BTString& o,
StackedAln& staln,
const Read& rd,
const Read* rdo,
const TReadId rdid,
AlnRes* rs,
AlnRes* rso,
const AlnSetSumm& summ,
const SeedAlSumm& ssm,
const SeedAlSumm& ssmo,
const AlnFlags& flags,
const PerReadMetrics& prm, // per-read metrics
const Mapq& mapq, // MAPQ calculator
const Scoring& sc); // scoring scheme
const SamConfig& samc_; // settings & routines for SAM output
BTDnaString dseq_; // buffer for decoded read sequence
BTString dqual_; // buffer for decoded quality sequence
};
#endif /*ndef ALN_SINK_H_*/
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