https://github.com/infphilo/hisat2
Tip revision: 6f497ea117e49b4e477a538e4cd0e218e81a3476 authored by leejj82 on 05 July 2018, 21:16:53 UTC
Memory computation is improved. Resident memory size and repeat group memory size are computed
Memory computation is improved. Resident memory size and repeat group memory size are computed
Tip revision: 6f497ea
aln_sink.h
/*
* 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>
#include "alt.h"
#include "splice_site.h"
// Forward decl
template <typename index_t>
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, bool getLock = false) {
ThreadSafe ts(&mutex_m, getLock);
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 kseeds_,
THitInt mhits_,
THitInt pengap_,
bool msample_,
bool discord_,
bool mixed_,
bool secondary_,
bool localAlign_,
int bowtie2_dp_,
bool repeat_)
{
init(
khits_,
kseeds_,
mhits_,
pengap_,
msample_,
discord_,
mixed_,
secondary_,
localAlign_,
bowtie2_dp_,
repeat_);
}
void init(
THitInt khits_,
THitInt kseeds_,
THitInt mhits_,
THitInt pengap_,
bool msample_,
bool discord_,
bool mixed_,
bool secondary_,
bool localAlign_,
int bowtie2_dp_,
bool repeat_)
{
khits = khits_; // -k (or high if -a)
kseeds = kseeds_;
mhits = ((mhits_ == 0) ? std::numeric_limits<THitInt>::max() : mhits_);
pengap = pengap_;
msample = msample_;
discord = discord_;
mixed = mixed_;
secondary = secondary_;
localAlign = localAlign_;
bowtie2_dp = bowtie2_dp_;
repeat = repeat_;
}
#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;
// Number of seeds allowed to extend
THitInt kseeds;
// 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;
// true iff we allow secondary alignments to be output (secondary alignments
// have lower scores)
bool secondary;
// true iff we allow local alignment (not implemented yet)
bool localAlign;
// true iff we allow dynamic alignment
int bowtie2_dp;
// true iff we output alignments to repeat sequences
bool repeat;
};
/**
* 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.
*/
template <typename index_t>
class AlnSink {
typedef EList<std::string> StrList;
public:
explicit AlnSink(
OutputQueue& oq,
const StrList& refnames,
const StrList& repnames,
bool quiet,
ALTDB<index_t>* altdb = NULL,
SpliceSiteDB* ssdb = NULL) :
oq_(oq),
refnames_(refnames),
repnames_(repnames),
quiet_(quiet),
altdb_(altdb),
spliceSiteDB_(ssdb)
{ }
/**
* Destroy HitSinkobject;
*/
virtual ~AlnSink() { }
/**
* Called when the AlnSink is wrapped by a new AlnSinkWrap. This helps us
* keep track of whether the main lock or any of the per-stream locks will
* be contended by multiple threads.
*/
void addWrapper() { numWrappers_++; }
/**
* 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 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 5
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, true);
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);
}
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 1-4
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(
ostream& out,
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 newSummary, // alignment summary in a new style
bool hadoopOut); // output Hadoop counters?
/**
* Called when all alignments are complete. It is assumed that no
* synchronization is necessary.
*/
void finish(
ostream& out,
size_t repThresh,
bool discord,
bool mixed,
bool newSummary,
bool hadoopOut)
{
// Close output streams
if(!quiet_) {
printAlSumm(
out,
met_,
repThresh,
discord,
mixed,
newSummary,
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<index_t>& 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, bool getLock = true) {
met_.merge(met, getLock);
}
/**
* Return mutable reference to the shared OutputQueue.
*/
OutputQueue& outq() {
return oq_;
}
protected:
OutputQueue& oq_; // output queue
int numWrappers_; // # threads owning a wrapper for this HitSink
const StrList& refnames_; // reference names
const StrList& repnames_; // repeat names
bool quiet_; // true -> don't print alignment stats at the end
ReportingMetrics met_; // global repository of reporting metrics
ALTDB<index_t>* altdb_;
SpliceSiteDB* spliceSiteDB_; //
};
/**
* 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.
*
*
*/
template <typename index_t>
class AlnSinkWrap {
public:
AlnSinkWrap(
AlnSink<index_t>& g, // AlnSink being wrapped
const ReportingParams& rp, // Parameters governing reporting
Mapq& mapq, // Mapq calculator
size_t threadId, // Thread ID
bool secondary = false, // Secondary alignments
const SpliceSiteDB* ssdb = NULL, // splice sites
uint64_t threads_rids_mindist = 0) : // synchronization
g_(g),
rp_(rp),
threadid_(threadId),
mapq_(mapq),
secondary_(secondary),
ssdb_(ssdb),
threads_rids_mindist_(threads_rids_mindist),
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()),
bestSplicedPair_(0),
best2SplicedPair_(0),
bestSplicedUnp1_(0),
best2SplicedUnp1_(0),
bestSplicedUnp2_(0),
best2SplicedUnp2_(0),
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<index_t> *sr1, // seed alignment results for mate 1
const SeedResults<index_t> *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?
bool sortByScore, // prioritize alignments by score
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 templateLenAdjustment = true);
/**
* 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,
bool alignMate = false);
#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_; }
const ReportingParams& reportingParams() { return rp_;}
/**
* 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_;
}
index_t bestSplicedPair() const {
return bestSplicedPair_;
}
index_t best2SplicedPair() const {
return best2SplicedPair_;
}
index_t bestSplicedUnp1() const {
return bestSplicedUnp1_;
}
index_t best2SplicedUnp1() const {
return best2SplicedUnp1_;
}
index_t bestSplicedUnp2() const {
return bestSplicedUnp2_;
}
index_t best2SplicedUnp2() const {
return best2SplicedUnp2_;
}
bool secondary() const {
return secondary_;
}
/**
*
*/
void getUnp1(const EList<AlnRes>*& rs) const { rs = &rs1u_; }
void getUnp2(const EList<AlnRes>*& rs) const { rs = &rs2u_; }
void getPair(const EList<AlnRes>*& rs1, const EList<AlnRes>*& rs2) const { rs1 = &rs1_; rs2 = &rs2_; }
index_t numUnp1() const { return rs1u_.size(); }
index_t numUnp2() const { return rs2u_.size(); }
index_t numPair() const { assert_eq(rs1_.size(), rs2_.size()); return rs1_.size(); }
pair<index_t, index_t> numBestUnp(index_t rdi) const {
index_t numGenome = 0, numRepeat = 0;
TAlScore maxScore = numeric_limits<TAlScore>::min();
const EList<AlnRes>& rs = (rdi == 0 ? rs1u_ : rs2u_);
for(size_t i = 0; i < rs.size(); i++) {
TAlScore curScore = rs[i].score().score();
if(curScore > maxScore) {
numGenome = numRepeat = 0;
maxScore = curScore;
}
if(curScore >= maxScore) {
if(rs[i].repeat()) {
numRepeat++;
} else {
numGenome++;
}
}
}
return pair<index_t, index_t>(numGenome, numRepeat);
}
pair<index_t, index_t> numBestPair() const {
index_t numGenome = 0, numRepeat = 0;
TAlScore maxScore = numeric_limits<TAlScore>::min();
assert_eq(rs1_.size(), rs2_.size());
for(size_t i = 0; i < rs1_.size(); i++) {
TAlScore curScore = rs1_[i].score().score() + rs2_[i].score().score();
if(curScore > maxScore) {
numGenome = numRepeat = 0;
maxScore = curScore;
}
if(curScore >= maxScore) {
if(rs1_[i].repeat() || rs2_[i].repeat()) {
assert(rs1_[i].repeat() && rs2_[i].repeat());
numRepeat++;
} else {
numGenome++;
}
}
}
return pair<index_t, index_t>(numGenome, numRepeat);
}
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
RandomSource& rnd)
const;
AlnSink<index_t>& g_; // global alignment sink
ReportingParams rp_; // reporting parameters: khits, mhits etc
size_t threadid_; // thread ID
Mapq& mapq_; // mapq calculator
bool secondary_; // allow for secondary alignments
const SpliceSiteDB* ssdb_; // splice sites
uint64_t threads_rids_mindist_; // synchronization
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
index_t bestSplicedPair_;
index_t best2SplicedPair_;
index_t bestSplicedUnp1_;
index_t best2SplicedUnp1_;
index_t bestSplicedUnp2_;
index_t best2SplicedUnp2_;
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<TAlScore, size_t> > selectBuf_;
BTString obuf_;
StackedAln staln_;
EList<SpliceSite> spliceSites_;
};
/**
* 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.
*/
template <typename index_t>
class AlnSinkSam : public AlnSink<index_t> {
typedef EList<std::string> StrList;
public:
AlnSinkSam(
OutputQueue& oq, // output queue
const SamConfig<index_t>& samc, // settings & routines for SAM output
const StrList& refnames, // reference names
const StrList& repnames, // repeat names
bool quiet, // don't print alignment summary at end
ALTDB<index_t>* altdb = NULL,
SpliceSiteDB* ssdb = NULL) :
AlnSink<index_t>(
oq,
refnames,
repnames,
quiet,
altdb,
ssdb),
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(rs1 != NULL && rs1->spliced() && this->spliceSiteDB_ != NULL) {
this->spliceSiteDB_->addSpliceSite(*rd1, *rs1);
}
}
if(rd2 != NULL && report2) {
assert(flags2 != NULL);
appendMate(o, staln, *rd2, rd1, rdid, rs2, rs1, summ, ssm2, ssm1,
*flags2, prm, mapq, sc);
if(rs2 != NULL && rs2->spliced() && this->spliceSiteDB_ != NULL) {
this->spliceSiteDB_->addSpliceSite(*rd2, *rs2);
}
}
}
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<index_t>& samc_; // settings & routines for SAM output
BTDnaString dseq_; // buffer for decoded read sequence
BTString dqual_; // buffer for decoded quality sequence
};
static inline std::ostream& printPct(
std::ostream& os,
uint64_t num,
uint64_t denom)
{
double pct = 0.0f;
if(denom != 0) { pct = 100.0 * (double)num / (double)denom; }
os << fixed << setprecision(2) << pct << '%';
return os;
}
/**
* Print a friendly summary of:
*
* 1. How many reads were aligned and had one or more alignments
* reported
* 2. How many reads exceeded the -m or -M ceiling and therefore had
* their alignments suppressed or sampled
* 3. How many reads failed to align entirely
*
* Optionally print a series of Hadoop streaming-style counter updates
* with similar information.
*/
template <typename index_t>
void AlnSink<index_t>::printAlSumm(
ostream& out,
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 newSummary, // alignment summary in a new style
bool hadoopOut) // output Hadoop counters?
{
// NOTE: there's a filtering step at the very beginning, so everything
// being reported here is post filtering
bool canRep = repThresh != MAX_SIZE_T;
if(hadoopOut) {
out << "reporter:counter:HISAT2,Reads processed," << met.nread << endl;
}
uint64_t totread = met.nread;
uint64_t totpair = met.npaired;
uint64_t totunpair = met.nunpaired;
uint64_t tot_al_cand = totunpair + totpair*2;
uint64_t tot_al = (met.nconcord_uni + met.nconcord_rep) * 2 + (met.ndiscord) * 2 + met.nunp_0_uni + met.nunp_0_rep + met.nunp_uni + met.nunp_rep;
assert_leq(tot_al, tot_al_cand);
if(newSummary) {
out << "HISAT2 summary stats:" << endl;
if(totpair > 0) {
uint64_t ncondiscord_0 = met.nconcord_0 - met.ndiscord;
out << "\tTotal pairs: " << totpair << endl;
out << "\t\tAligned concordantly or discordantly 0 time: " << ncondiscord_0 << " ("; printPct(out, ncondiscord_0, met.npaired); out << ")" << endl;
out << "\t\tAligned concordantly 1 time: " << met.nconcord_uni1 << " ("; printPct(out, met.nconcord_uni1, met.npaired); out << ")" << endl;
out << "\t\tAligned concordantly >1 times: " << met.nconcord_uni2 << " ("; printPct(out, met.nconcord_uni2, met.npaired); out << ")" << endl;
out << "\t\tAligned discordantly 1 time: " << met.ndiscord << " ("; printPct(out, met.ndiscord, met.npaired); out << ")" << endl;
out << "\tTotal unpaired reads: " << ncondiscord_0 * 2 << endl;
out << "\t\tAligned 0 time: " << met.nunp_0_0 << " ("; printPct(out, met.nunp_0_0, ncondiscord_0 * 2); out << ")" << endl;
out << "\t\tAligned 1 time: " << met.nunp_0_uni1 << " ("; printPct(out, met.nunp_0_uni1, ncondiscord_0 * 2); out << ")" << endl;
out << "\t\tAligned >1 times: " << met.nunp_0_uni2 << " ("; printPct(out, met.nunp_0_uni2, ncondiscord_0 * 2); out << ")" << endl;
} else {
out << "\tTotal reads: " << totread << endl;
out << "\t\tAligned 0 time: " << met.nunp_0 << " ("; printPct(out, met.nunp_0, met.nunpaired); out << ")" << endl;
out << "\t\tAligned 1 time: " << met.nunp_uni1 << " ("; printPct(out, met.nunp_uni1, met.nunpaired); out << ")" << endl;
out << "\t\tAligned >1 times: " << met.nunp_uni2 << " ("; printPct(out, met.nunp_uni2, met.nunpaired); out << ")" << endl;
}
out << "\tOverall alignment rate: "; printPct(out, tot_al, tot_al_cand); out << endl;
} else {
if(totread > 0) {
out << "" << totread << " reads; of these:" << endl;
} else {
assert_eq(0, met.npaired);
assert_eq(0, met.nunpaired);
out << "" << totread << " reads" << endl;
}
if(totpair > 0) {
// Paired output
out << " " << totpair << " (";
printPct(out, totpair, totread);
out << ") were paired; of these:" << endl;
// Concordants
out << " " << met.nconcord_0 << " (";
printPct(out, met.nconcord_0, met.npaired);
out << ") aligned concordantly 0 times" << endl;
if(canRep) {
// Print the number that aligned concordantly exactly once
assert_eq(met.nconcord_uni, met.nconcord_uni1+met.nconcord_uni2);
out << " " << met.nconcord_uni1 << " (";
printPct(out, met.nconcord_uni1, met.npaired);
out << ") aligned concordantly exactly 1 time" << endl;
// Print the number that aligned concordantly more than once but
// fewer times than the limit
out << " " << met.nconcord_uni2+met.nconcord_rep << " (";
printPct(out, met.nconcord_uni2+met.nconcord_rep, met.npaired);
out << ") aligned concordantly >1 times" << endl;
} else {
// Print the number that aligned concordantly exactly once
assert_eq(met.nconcord_uni, met.nconcord_uni1+met.nconcord_uni2);
out << " " << met.nconcord_uni1 << " (";
printPct(out, met.nconcord_uni1, met.npaired);
out << ") aligned concordantly exactly 1 time" << endl;
// Print the number that aligned concordantly more than once
out << " " << met.nconcord_uni2 << " (";
printPct(out, met.nconcord_uni2, met.npaired);
out << ") aligned concordantly >1 times" << endl;
}
if(discord) {
// TODO: what about discoardant and on separate chromosomes?
// Bring out the unaligned pair total so we can subtract discordants
out << " ----" << endl;
out << " " << met.nconcord_0
<< " pairs aligned concordantly 0 times; of these:" << endl;
// Discordants
out << " " << met.ndiscord << " (";
printPct(out, met.ndiscord, met.nconcord_0);
out << ") aligned discordantly 1 time" << endl;
}
uint64_t ncondiscord_0 = met.nconcord_0 - met.ndiscord;
if(mixed) {
// Bring out the unaligned pair total so we can subtract discordants
out << " ----" << endl;
out << " " << ncondiscord_0
<< " pairs aligned 0 times concordantly or discordantly; of these:" << endl;
out << " " << (ncondiscord_0 * 2) << " mates make up the pairs; of these:" << endl;
out << " " << met.nunp_0_0 << " " << "(";
printPct(out, met.nunp_0_0, ncondiscord_0 * 2);
out << ") aligned 0 times" << endl;
if(canRep) {
// Print the number that aligned exactly once
assert_eq(met.nunp_0_uni, met.nunp_0_uni1+met.nunp_0_uni2);
out << " " << met.nunp_0_uni1 << " (";
printPct(out, met.nunp_0_uni1, ncondiscord_0 * 2);
out << ") aligned exactly 1 time" << endl;
// Print the number that aligned more than once but fewer times
// than the limit
out << " " << met.nunp_0_uni2+met.nunp_0_rep << " (";
printPct(out, met.nunp_0_uni2+met.nunp_0_rep, ncondiscord_0 * 2);
out << ") aligned >1 times" << endl;
} else {
// Print the number that aligned exactly once
assert_eq(met.nunp_0_uni, met.nunp_0_uni1+met.nunp_0_uni2);
out << " " << met.nunp_0_uni1 << " (";
printPct(out, met.nunp_0_uni1, ncondiscord_0 * 2);
out << ") aligned exactly 1 time" << endl;
// Print the number that aligned more than once but fewer times
// than the limit
out << " " << met.nunp_0_uni2 << " (";
printPct(out, met.nunp_0_uni2, ncondiscord_0 * 2);
out << ") aligned >1 times" << endl;
}
}
}
if(totunpair > 0) {
// Unpaired output
out << " " << totunpair << " (";
printPct(out, totunpair, totread);
out << ") were unpaired; of these:" << endl;
out << " " << met.nunp_0 << " (";
printPct(out, met.nunp_0, met.nunpaired);
out << ") aligned 0 times" << endl;
if(hadoopOut) {
out << "reporter:counter:HISAT 2,Unpaired reads with 0 alignments,"
<< met.nunpaired << endl;
}
if(canRep) {
// Print the number that aligned exactly once
assert_eq(met.nunp_uni, met.nunp_uni1+met.nunp_uni2);
out << " " << met.nunp_uni1 << " (";
printPct(out, met.nunp_uni1, met.nunpaired);
out << ") aligned exactly 1 time" << endl;
// Print the number that aligned more than once but fewer times
// than the limit
out << " " << met.nunp_uni2+met.nunp_rep << " (";
printPct(out, met.nunp_uni2+met.nunp_rep, met.nunpaired);
out << ") aligned >1 times" << endl;
} else {
// Print the number that aligned exactly once
assert_eq(met.nunp_uni, met.nunp_uni1+met.nunp_uni2);
out << " " << met.nunp_uni1 << " (";
printPct(out, met.nunp_uni1, met.nunpaired);
out << ") aligned exactly 1 time" << endl;
// Print the number that aligned more than once
out << " " << met.nunp_uni2 << " (";
printPct(out, met.nunp_uni2, met.nunpaired);
out << ") aligned >1 times" << endl;
}
}
printPct(out, tot_al, tot_al_cand);
out << " overall alignment rate" << endl;
}
}
/**
* Return true iff the read in rd1/rd2 matches the last read handled, which
* should still be in rd1_/rd2_.
*/
template <typename index_t>
bool AlnSinkWrap<index_t>::sameRead(
// 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
bool qualitiesMatter) // aln policy distinguishes b/t quals?
{
bool same = false;
if(rd1_ != NULL || rd2_ != NULL) {
// This is not the first time the sink was initialized with
// a read. Check if new read/pair is identical to previous
// read/pair
if((rd1_ == NULL) == (rd1 == NULL) &&
(rd2_ == NULL) == (rd2 == NULL))
{
bool m1same = (rd1 == NULL && rd1_ == NULL);
if(!m1same) {
assert(rd1 != NULL);
assert(rd1_ != NULL);
m1same = Read::same(
rd1->patFw, // new seq
rd1->qual, // new quals
rd1_->patFw, // old seq
rd1_->qual, // old quals
qualitiesMatter);
}
if(m1same) {
bool m2same = (rd2 == NULL && rd2_ == NULL);
if(!m2same) {
m2same = Read::same(
rd2->patFw, // new seq
rd2->qual, // new quals
rd2_->patFw, // old seq
rd2_->qual, // old quals
qualitiesMatter);
}
same = m2same;
}
}
}
return same;
}
/**
* 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. 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.
*/
template <typename index_t>
int AlnSinkWrap<index_t>::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?
{
assert(!init_);
assert(rd1 != NULL || rd2 != NULL);
init_ = true;
// Keep copy of new read, so that we can compare it with the
// next one
if(rd1 != NULL) {
rd1_ = rd1;
} else rd1_ = NULL;
if(rd2 != NULL) {
rd2_ = rd2;
} else rd2_ = NULL;
rdid_ = rdid;
// Caller must now align the read
maxed1_ = false;
maxed2_ = false;
maxedOverall_ = false;
bestPair_ = best2Pair_ =
bestUnp1_ = best2Unp1_ =
bestUnp2_ = best2Unp2_ = std::numeric_limits<THitInt>::min();
bestSplicedPair_ = best2SplicedPair_ =
bestSplicedUnp1_ = best2SplicedUnp1_ =
bestSplicedUnp2_ = best2SplicedUnp2_ = 0;
rs1_.clear(); // clear out paired-end alignments
rs2_.clear(); // clear out paired-end alignments
rs1u_.clear(); // clear out unpaired alignments for mate #1
rs2u_.clear(); // clear out unpaired alignments for mate #2
st_.nextRead(readIsPair()); // reset state
assert(empty());
assert(!maxed());
// Start from the first stage
return 0;
}
/**
* 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.
*
* What gets reported for a paired-end alignment?
*
* 1. If there are reportable concordant alignments, report those and stop
* 2. If there are reportable discordant alignments, report those and stop
* 3. If unpaired alignments can be reported:
* 3a. Report
#
* Update metrics. Only ambiguity is: what if a pair aligns repetitively and
* one of its mates aligns uniquely?
*
* uint64_t al; // # mates w/ >= 1 reported alignment
* uint64_t unal; // # mates w/ 0 alignments
* uint64_t max; // # mates withheld for exceeding -M/-m ceiling
* uint64_t al_concord; // # pairs w/ >= 1 concordant alignment
* uint64_t al_discord; // # pairs w/ >= 1 discordant alignment
* uint64_t max_concord; // # pairs maxed out
* uint64_t unal_pair; // # pairs where neither mate aligned
*/
template <typename index_t>
void AlnSinkWrap<index_t>::finishRead(
const SeedResults<index_t> *sr1, // seed alignment results for mate 1
const SeedResults<index_t> *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?
bool sortByScore, // prioritize alignments by score
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 templateLenAdjustment) // = true
{
obuf_.clear();
OutputQueueMark qqm(g_.outq(), obuf_, rdid_, threadid_);
assert(init_);
if(!suppressSeedSummary) {
if(sr1 != NULL) {
assert(rd1_ != NULL);
// Mate exists and has non-empty SeedResults
g_.reportSeedSummary(obuf_, *rd1_, rdid_, threadid_, *sr1, true);
} else if(rd1_ != NULL) {
// Mate exists but has NULL SeedResults
g_.reportEmptySeedSummary(obuf_, *rd1_, rdid_, true);
}
if(sr2 != NULL) {
assert(rd2_ != NULL);
// Mate exists and has non-empty SeedResults
g_.reportSeedSummary(obuf_, *rd2_, rdid_, threadid_, *sr2, true);
} else if(rd2_ != NULL) {
// Mate exists but has NULL SeedResults
g_.reportEmptySeedSummary(obuf_, *rd2_, rdid_, true);
}
}
if(!suppressAlignments) {
// Ask the ReportingState what to report
st_.finish();
uint64_t nconcord = 0, ndiscord = 0, nunpair1 = 0, nunpair2 = 0;
bool pairMax = false, unpair1Max = false, unpair2Max = false;
st_.getReport(
nconcord,
ndiscord,
nunpair1,
nunpair2,
pairMax,
unpair1Max,
unpair2Max);
assert_leq(nconcord, rs1_.size());
assert_leq(nunpair1, rs1u_.size());
assert_leq(nunpair2, rs2u_.size());
assert_leq(ndiscord, 1);
assert_gt(rp_.khits, 0);
assert_gt(rp_.mhits, 0);
assert(!pairMax || rs1_.size() >= (uint64_t)rp_.mhits);
assert(!unpair1Max || rs1u_.size() >= (uint64_t)rp_.mhits);
assert(!unpair2Max || rs2u_.size() >= (uint64_t)rp_.mhits);
met.nread++;
if(readIsPair()) {
met.npaired++;
} else {
met.nunpaired++;
}
// Report concordant paired-end alignments if possible
if(nconcord > 0) {
AlnSetSumm concordSumm(
rd1_, rd2_, &rs1_, &rs2_, &rs1u_, &rs2u_,
exhaust1, exhaust2, -1, -1);
// Possibly select a random subset
size_t off;
if(sortByScore) {
// DK CONCORDANT - debugging purposes
nconcord = rs1_.size();
// Sort by score then pick from low to high
off = selectByScore(&rs1_, &rs2_, nconcord, select1_, rnd);
} else {
// Select subset randomly
off = selectAlnsToReport(rs1_, nconcord, select1_, rnd);
}
concordSumm.numAlnsPaired(select1_.size());
assert_lt(off, rs1_.size());
const AlnRes *rs1 = &rs1_[off];
const AlnRes *rs2 = &rs2_[off];
AlnFlags flags1(
ALN_FLAG_PAIR_CONCORD_MATE1,
st_.params().mhitsSet(),
unpair1Max,
pairMax,
nfilt1,
scfilt1,
lenfilt1,
qcfilt1,
st_.params().mixed,
true, // primary
true, // opp aligned
rs2->fw()); // opp fw
AlnFlags flags2(
ALN_FLAG_PAIR_CONCORD_MATE2,
st_.params().mhitsSet(),
unpair2Max,
pairMax,
nfilt2,
scfilt2,
lenfilt2,
qcfilt2,
st_.params().mixed,
false, // primary
true, // opp aligned
rs1->fw()); // opp fw
// Issue: we only set the flags once, but some of the flags might
// vary from pair to pair among the pairs we're reporting. For
// instance, whether a given mate aligns to the forward strand.
SeedAlSumm ssm1, ssm2;
if(sr1 != NULL && sr2 != NULL) {
sr1->toSeedAlSumm(ssm1);
sr2->toSeedAlSumm(ssm2);
}
for(size_t i = 0; i < rs1_.size(); i++) {
spliceSites_.clear();
if(templateLenAdjustment) {
rs1_[i].setMateParams(ALN_RES_TYPE_MATE1, &rs2_[i], flags1, ssdb_, threads_rids_mindist_, &spliceSites_);
rs2_[i].setMateParams(ALN_RES_TYPE_MATE2, &rs1_[i], flags2, ssdb_, threads_rids_mindist_, &spliceSites_);
} else {
rs1_[i].setMateParams(ALN_RES_TYPE_MATE1, &rs2_[i], flags1);
rs2_[i].setMateParams(ALN_RES_TYPE_MATE2, &rs1_[i], flags2);
}
assert_eq(abs(rs1_[i].fragmentLength()), abs(rs2_[i].fragmentLength()));
}
assert(!select1_.empty());
g_.reportHits(
obuf_,
staln_,
threadid_,
rd1_,
rd2_,
rdid_,
select1_,
NULL,
&rs1_,
&rs2_,
pairMax,
concordSumm,
ssm1,
ssm2,
&flags1,
&flags2,
prm,
mapq_,
sc);
if(pairMax) {
met.nconcord_rep++;
} else {
met.nconcord_uni++;
assert(!rs1_.empty());
if(select1_.size() == 1) {
met.nconcord_uni1++;
} else {
met.nconcord_uni2++;
}
}
init_ = false;
//g_.outq().finishRead(obuf_, rdid_, threadid_);
return;
}
// Report concordant paired-end alignments if possible
else if(ndiscord > 0) {
ASSERT_ONLY(bool ret =) prepareDiscordants();
assert(ret);
assert_eq(1, rs1_.size());
assert_eq(1, rs2_.size());
AlnSetSumm discordSumm(
rd1_, rd2_, &rs1_, &rs2_, &rs1u_, &rs2u_,
exhaust1, exhaust2, -1, -1);
const AlnRes *rs1 = &rs1_[0];
const AlnRes *rs2 = &rs2_[0];
AlnFlags flags1(
ALN_FLAG_PAIR_DISCORD_MATE1,
st_.params().mhitsSet(),
false,
pairMax,
nfilt1,
scfilt1,
lenfilt1,
qcfilt1,
st_.params().mixed,
true, // primary
true, // opp aligned
rs2->fw()); // opp fw
AlnFlags flags2(
ALN_FLAG_PAIR_DISCORD_MATE2,
st_.params().mhitsSet(),
false,
pairMax,
nfilt2,
scfilt2,
lenfilt2,
qcfilt2,
st_.params().mixed,
false, // primary
true, // opp aligned
rs1->fw()); // opp fw
SeedAlSumm ssm1, ssm2;
if(sr1 != NULL) sr1->toSeedAlSumm(ssm1);
if(sr2 != NULL) sr2->toSeedAlSumm(ssm2);
for(size_t i = 0; i < rs1_.size(); i++) {
rs1_[i].setMateParams(ALN_RES_TYPE_MATE1, &rs2_[i], flags1);
rs2_[i].setMateParams(ALN_RES_TYPE_MATE2, &rs1_[i], flags2);
assert(rs1_[i].isFraglenSet() == rs2_[i].isFraglenSet());
assert(!rs1_[i].isFraglenSet() || abs(rs1_[i].fragmentLength()) == abs(rs2_[i].fragmentLength()));
}
ASSERT_ONLY(size_t off);
if(sortByScore) {
// Sort by score then pick from low to high
ASSERT_ONLY(off =) selectByScore(&rs1_, &rs2_, ndiscord, select1_, rnd);
} else {
// Select subset randomly
ASSERT_ONLY(off =) selectAlnsToReport(rs1_, ndiscord, select1_, rnd);
}
assert_eq(0, off);
assert(!select1_.empty());
g_.reportHits(
obuf_,
staln_,
threadid_,
rd1_,
rd2_,
rdid_,
select1_,
NULL,
&rs1_,
&rs2_,
pairMax,
discordSumm,
ssm1,
ssm2,
&flags1,
&flags2,
prm,
mapq_,
sc);
met.nconcord_0++;
met.ndiscord++;
init_ = false;
//g_.outq().finishRead(obuf_, rdid_, threadid_);
return;
}
// If we're at this point, at least one mate failed to align.
// BTL: That's not true. It could be that there are no concordant
// alignments but both mates have unpaired alignments, with one of
// the mates having more than one.
//assert(nunpair1 == 0 || nunpair2 == 0);
assert(!pairMax);
const AlnRes *repRs1 = NULL, *repRs2 = NULL;
AlnSetSumm summ1, summ2;
AlnFlags flags1, flags2;
TRefId refid = -1; TRefOff refoff = -1;
bool rep1 = rd1_ != NULL && nunpair1 > 0;
bool rep2 = rd2_ != NULL && nunpair2 > 0;
// This is the preliminary if statement for mate 1 - here we're
// gathering some preliminary information, making it possible to call
// g_.reportHits(...) with information about both mates potentially
if(rep1) {
// Mate 1 aligned at least once
if(rep2) {
summ1.init(
rd1_, rd2_, NULL, NULL, &rs1u_, &rs2u_,
exhaust1, exhaust2, -1, -1);
} else {
summ1.init(
rd1_, NULL, NULL, NULL, &rs1u_, NULL,
exhaust1, exhaust2, -1, -1);
}
size_t off;
if(sortByScore) {
// Sort by score then pick from low to high
off = selectByScore(&rs1u_, NULL, nunpair1, select1_, rnd);
} else {
// Select subset randomly
off = selectAlnsToReport(rs1u_, nunpair1, select1_, rnd);
}
summ1.numAlns1(select1_.size());
summ2.numAlns1(select1_.size());
repRs1 = &rs1u_[off];
} else if(rd1_ != NULL) {
// Mate 1 failed to align - don't do anything yet. First we want
// to collect information on mate 2 in case that factors into the
// summary
assert(!unpair1Max);
}
if(rep2) {
if(rep1) {
summ2.init(
rd1_, rd2_, NULL, NULL, &rs1u_, &rs2u_,
exhaust1, exhaust2, -1, -1);
} else {
summ2.init(
NULL, rd2_, NULL, NULL, NULL, &rs2u_,
exhaust1, exhaust2, -1, -1);
}
size_t off;
if(sortByScore) {
// Sort by score then pick from low to high
off = selectByScore(&rs2u_, NULL, nunpair2, select2_, rnd);
} else {
// Select subset randomly
off = selectAlnsToReport(rs2u_, nunpair2, select2_, rnd);
}
repRs2 = &rs2u_[off];
summ1.numAlns2(select2_.size());
summ2.numAlns2(select2_.size());
} else if(rd2_ != NULL) {
// Mate 2 failed to align - don't do anything yet. First we want
// to collect information on mate 1 in case that factors into the
// summary
assert(!unpair2Max);
}
// Update counters given that one mate didn't align
if(readIsPair()) {
met.nconcord_0++;
}
if(rd1_ != NULL) {
if(nunpair1 > 0) {
// Update counters
if(readIsPair()) {
if(unpair1Max) met.nunp_0_rep++;
else {
met.nunp_0_uni++;
assert(!rs1u_.empty());
if(select1_.size() == 1) {
met.nunp_0_uni1++;
} else {
met.nunp_0_uni2++;
}
}
} else {
if(unpair1Max) met.nunp_rep++;
else {
met.nunp_uni++;
assert(!rs1u_.empty());
if(select1_.size() == 1) {
met.nunp_uni1++;
} else {
met.nunp_uni2++;
}
}
}
} else if(unpair1Max) {
// Update counters
if(readIsPair()) met.nunp_0_rep++;
else met.nunp_rep++;
} else {
// Update counters
if(readIsPair()) met.nunp_0_0++;
else met.nunp_0++;
}
}
if(rd2_ != NULL) {
if(nunpair2 > 0) {
// Update counters
if(readIsPair()) {
if(unpair2Max) met.nunp_0_rep++;
else {
assert(!rs2u_.empty());
met.nunp_0_uni++;
if(select2_.size() == 1) {
met.nunp_0_uni1++;
} else {
met.nunp_0_uni2++;
}
}
} else {
if(unpair2Max) met.nunp_rep++;
else {
assert(!rs2u_.empty());
met.nunp_uni++;
if(select2_.size() == 1) {
met.nunp_uni1++;
} else {
met.nunp_uni2++;
}
}
}
} else if(unpair2Max) {
// Update counters
if(readIsPair()) met.nunp_0_rep++;
else met.nunp_rep++;
} else {
// Update counters
if(readIsPair()) met.nunp_0_0++;
else met.nunp_0++;
}
}
// Now set up flags
if(rep1) {
// Initialize flags. Note: We want to have information about how
// the other mate aligned (if it did) at this point
flags1.init(
readIsPair() ?
ALN_FLAG_PAIR_UNPAIRED_MATE1 :
ALN_FLAG_PAIR_UNPAIRED,
st_.params().mhitsSet(),
unpair1Max,
pairMax,
nfilt1,
scfilt1,
lenfilt1,
qcfilt1,
st_.params().mixed,
true, // primary
repRs2 != NULL, // opp aligned
repRs2 == NULL || repRs2->fw()); // opp fw
for(size_t i = 0; i < rs1u_.size(); i++) {
rs1u_[i].setMateParams(ALN_RES_TYPE_UNPAIRED_MATE1, NULL, flags1);
}
}
if(rep2) {
// Initialize flags. Note: We want to have information about how
// the other mate aligned (if it did) at this point
flags2.init(
readIsPair() ?
ALN_FLAG_PAIR_UNPAIRED_MATE2 :
ALN_FLAG_PAIR_UNPAIRED,
st_.params().mhitsSet(),
unpair2Max,
pairMax,
nfilt2,
scfilt2,
lenfilt2,
qcfilt2,
st_.params().mixed,
true, // primary
repRs1 != NULL, // opp aligned
repRs1 == NULL || repRs1->fw()); // opp fw
for(size_t i = 0; i < rs2u_.size(); i++) {
rs2u_[i].setMateParams(ALN_RES_TYPE_UNPAIRED_MATE2, NULL, flags2);
}
}
// Now report mate 1
if(rep1) {
SeedAlSumm ssm1, ssm2;
if(sr1 != NULL) sr1->toSeedAlSumm(ssm1);
if(sr2 != NULL) sr2->toSeedAlSumm(ssm2);
assert(!select1_.empty());
g_.reportHits(
obuf_,
staln_,
threadid_,
rd1_,
repRs2 != NULL ? rd2_ : NULL,
rdid_,
select1_,
repRs2 != NULL ? &select2_ : NULL,
&rs1u_,
repRs2 != NULL ? &rs2u_ : NULL,
unpair1Max,
summ1,
ssm1,
ssm2,
&flags1,
repRs2 != NULL ? &flags2 : NULL,
prm,
mapq_,
sc);
assert_lt(select1_[0], rs1u_.size());
refid = rs1u_[select1_[0]].refid();
refoff = rs1u_[select1_[0]].refoff();
}
// Now report mate 2
if(rep2 && !rep1) {
SeedAlSumm ssm1, ssm2;
if(sr1 != NULL) sr1->toSeedAlSumm(ssm1);
if(sr2 != NULL) sr2->toSeedAlSumm(ssm2);
assert(!select2_.empty());
g_.reportHits(
obuf_,
staln_,
threadid_,
rd2_,
repRs1 != NULL ? rd1_ : NULL,
rdid_,
select2_,
repRs1 != NULL ? &select1_ : NULL,
&rs2u_,
repRs1 != NULL ? &rs1u_ : NULL,
unpair2Max,
summ2,
ssm1,
ssm2,
&flags2,
repRs1 != NULL ? &flags1 : NULL,
prm,
mapq_,
sc);
assert_lt(select2_[0], rs2u_.size());
refid = rs2u_[select2_[0]].refid();
refoff = rs2u_[select2_[0]].refoff();
}
if(rd1_ != NULL && nunpair1 == 0) {
if(nunpair2 > 0) {
assert_neq(-1, refid);
summ1.init(
rd1_, NULL, NULL, NULL, NULL, NULL,
exhaust1, exhaust2, refid, refoff);
} else {
summ1.init(
rd1_, NULL, NULL, NULL, NULL, NULL,
exhaust1, exhaust2, -1, -1);
}
SeedAlSumm ssm1, ssm2;
if(sr1 != NULL) sr1->toSeedAlSumm(ssm1);
if(sr2 != NULL) sr2->toSeedAlSumm(ssm2);
flags1.init(
readIsPair() ?
ALN_FLAG_PAIR_UNPAIRED_MATE1 :
ALN_FLAG_PAIR_UNPAIRED,
st_.params().mhitsSet(),
false,
false,
nfilt1,
scfilt1,
lenfilt1,
qcfilt1,
st_.params().mixed,
true, // primary
repRs2 != NULL, // opp aligned
(repRs2 != NULL) ? repRs2->fw() : false); // opp fw
g_.reportUnaligned(
obuf_, // string to write output to
staln_,
threadid_,
rd1_, // read 1
NULL, // read 2
rdid_, // read id
summ1, // summ
ssm1, //
ssm2,
&flags1, // flags 1
NULL, // flags 2
prm, // per-read metrics
mapq_, // MAPQ calculator
sc, // scoring scheme
true); // get lock?
}
if(rd2_ != NULL && nunpair2 == 0) {
if(nunpair1 > 0) {
assert_neq(-1, refid);
summ2.init(
NULL, rd2_, NULL, NULL, NULL, NULL,
exhaust1, exhaust2, refid, refoff);
} else {
summ2.init(
NULL, rd2_, NULL, NULL, NULL, NULL,
exhaust1, exhaust2, -1, -1);
}
SeedAlSumm ssm1, ssm2;
if(sr1 != NULL) sr1->toSeedAlSumm(ssm1);
if(sr2 != NULL) sr2->toSeedAlSumm(ssm2);
flags2.init(
readIsPair() ?
ALN_FLAG_PAIR_UNPAIRED_MATE2 :
ALN_FLAG_PAIR_UNPAIRED,
st_.params().mhitsSet(),
false,
false,
nfilt2,
scfilt2,
lenfilt2,
qcfilt2,
st_.params().mixed,
true, // primary
repRs1 != NULL, // opp aligned
(repRs1 != NULL) ? repRs1->fw() : false); // opp fw
g_.reportUnaligned(
obuf_, // string to write output to
staln_,
threadid_,
rd2_, // read 1
NULL, // read 2
rdid_, // read id
summ2, // summ
ssm1,
ssm2,
&flags2, // flags 1
NULL, // flags 2
prm, // per-read metrics
mapq_, // MAPQ calculator
sc, // scoring scheme
true); // get lock?
}
} // if(suppress alignments)
init_ = false;
return;
}
/**
* 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.
*/
template <typename index_t>
bool AlnSinkWrap<index_t>::report(
int stage,
const AlnRes* rs1,
const AlnRes* rs2,
bool alignMate)
{
assert(init_);
assert(rs1 != NULL || rs2 != NULL);
assert(rs1 == NULL || !rs1->empty());
assert(rs2 == NULL || !rs2->empty());
assert(rs1 == NULL || rs1->repOk());
assert(rs2 == NULL || rs2->repOk());
bool paired = (rs1 != NULL && rs2 != NULL);
bool one = (rs1 != NULL);
const AlnRes* rsa = one ? rs1 : rs2;
const AlnRes* rsb = one ? rs2 : rs1;
// Tally overall alignment score
TAlScore score = rsa->score().score();
if(rsb != NULL) score += rsb->score().score();
index_t num_spliced = (index_t)rsa->num_spliced();
if(rsb != NULL) num_spliced += (index_t)rsb->num_spliced();
if(paired) {
assert(readIsPair());
st_.foundConcordant();
rs1_.push_back(*rs1);
rs2_.push_back(*rs2);
} else {
st_.foundUnpaired(one);
if(one) {
rs1u_.push_back(*rs1);
} else {
rs2u_.push_back(*rs2);
}
}
// Update best score so far
if(paired) {
if(score > bestPair_) {
best2Pair_ = bestPair_;
bestPair_ = score;
best2SplicedPair_ = bestSplicedPair_;
bestSplicedPair_ = num_spliced;
} else if(score > best2Pair_) {
best2Pair_ = score;
best2SplicedPair_ = num_spliced;
}
} else {
if(one) {
if(score > bestUnp1_) {
best2Unp1_ = bestUnp1_;
bestUnp1_ = score;
best2SplicedUnp1_ = bestSplicedUnp1_;
bestSplicedUnp1_ = num_spliced;
} else if(score > best2Unp1_) {
best2Unp1_ = score;
best2SplicedUnp1_ = num_spliced;
}
} else {
if(score > bestUnp2_) {
best2Unp2_ = bestUnp2_;
bestUnp2_ = score;
best2SplicedUnp2_ = bestSplicedUnp2_;
bestSplicedUnp2_ = num_spliced;
} else if(score > best2Unp2_) {
best2Unp2_ = score;
best2SplicedUnp1_ = num_spliced;
}
}
}
return st_.done();
}
/**
* 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.
*/
template <typename index_t>
bool AlnSinkWrap<index_t>::prepareDiscordants() {
if(rs1u_.size() == 1 && rs2u_.size() == 1) {
assert(rs1_.empty());
assert(rs2_.empty());
rs1_.push_back(rs1u_[0]);
rs2_.push_back(rs2u_[0]);
return true;
}
return false;
}
/**
* 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.
*/
template <typename index_t>
size_t AlnSinkWrap<index_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
RandomSource& rnd)
const
{
assert(init_);
assert(repOk());
assert_gt(num, 0);
assert(rs1 != NULL);
size_t sz = rs1->size(); // sz = # alignments found
assert_leq(num, sz);
if(sz < num) {
num = sz;
}
// num = # to select
if(sz < 1) {
return 0;
}
select.resize((size_t)num);
// Use 'selectBuf_' as a temporary list for sorting purposes
EList<std::pair<TAlScore, size_t> >& buf =
const_cast<EList<std::pair<TAlScore, size_t> >& >(selectBuf_);
buf.resize(sz);
// Sort by score. If reads are pairs, sort by sum of mate scores.
for(size_t i = 0; i < sz; i++) {
buf[i].first = (*rs1)[i].score().hisat2_score();
if(rs2 != NULL) {
buf[i].first += (*rs2)[i].score().hisat2_score();
}
buf[i].second = i; // original offset
}
buf.sort(); buf.reverse(); // sort in descending order by score
// Randomize streaks of alignments that are equal by score
size_t streak = 0;
for(size_t i = 1; i < buf.size(); i++) {
if(buf[i].first == buf[i-1].first) {
if(streak == 0) { streak = 1; }
streak++;
} else {
if(streak > 1) {
assert_geq(i, streak);
buf.shufflePortion(i-streak, streak, rnd);
}
streak = 0;
}
}
if(streak > 1) {
buf.shufflePortion(buf.size() - streak, streak, rnd);
}
select.clear();
for(size_t i = 0; i < buf.size(); i++) {
index_t add = buf[i].second;
if(i >= num && !(*rs1)[add].repeat()) {
assert(rs2 == NULL || !(*rs2)[add].repeat());
break;
}
select.push_back(add);
}
if(!secondary_) {
assert_geq(buf.size(), select.size());
for(size_t i = 0; i + 1 < select.size(); i++) {
if(buf[i].first != buf[i+1].first) {
select.resize(i+1);
break;
}
}
}
// Returns index of the representative alignment, but in 'select' also
// returns the indexes of the next best selected alignments in order by
// score.
return selectBuf_[0].second;
}
/**
* 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.
*
* Return the "representative" alignment. This is simply the first one
* selected. That will also be what SAM calls the "primary" alignment.
*/
template <typename index_t>
size_t AlnSinkWrap<index_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
{
assert(init_);
assert(repOk());
assert_gt(num, 0);
size_t sz = rs.size();
if(sz < num) {
num = sz;
}
if(sz < 1) {
return 0;
}
select.resize((size_t)num);
if(sz == 1) {
assert_eq(1, num);
select[0] = 0;
return 0;
}
// Select a random offset into the list of alignments
uint32_t off = rnd.nextU32() % (uint32_t)sz;
uint32_t offOrig = off;
// Now take elements starting at that offset, wrapping around to 0 if
// necessary. Leave the rest.
for(size_t i = 0; i < num; i++) {
select[i] = off;
off++;
if(off == sz) {
off = 0;
}
}
return offOrig;
}
#define NOT_SUPPRESSED !suppress_[field++]
#define BEGIN_FIELD { \
if(firstfield) firstfield = false; \
else o.append('\t'); \
}
#define WRITE_TAB { \
if(firstfield) firstfield = false; \
else o.append('\t'); \
}
#define WRITE_NUM(o, x) { \
itoa10(x, buf); \
o.append(buf); \
}
/**
* Print a seed summary to the first output stream in the outs_ list.
*/
template <typename index_t>
void AlnSink<index_t>::reportSeedSummary(
BTString& o,
const Read& rd,
TReadId rdid,
size_t threadId,
const SeedResults<index_t>& rs,
bool getLock)
{
appendSeedSummary(
o, // string to write to
rd, // read
rdid, // read id
rs.numOffs()*2, // # seeds tried
rs.nonzeroOffsets(), // # seeds with non-empty results
rs.numRanges(), // # ranges for all seed hits
rs.numElts(), // # elements for all seed hits
rs.numOffs(), // # seeds tried from fw read
rs.nonzeroOffsetsFw(), // # seeds with non-empty results from fw read
rs.numRangesFw(), // # ranges for seed hits from fw read
rs.numEltsFw(), // # elements for seed hits from fw read
rs.numOffs(), // # seeds tried from rc read
rs.nonzeroOffsetsRc(), // # seeds with non-empty results from fw read
rs.numRangesRc(), // # ranges for seed hits from fw read
rs.numEltsRc()); // # elements for seed hits from fw read
}
/**
* Print an empty seed summary to the first output stream in the outs_ list.
*/
template <typename index_t>
void AlnSink<index_t>::reportEmptySeedSummary(
BTString& o,
const Read& rd,
TReadId rdid,
size_t threadId,
bool getLock)
{
appendSeedSummary(
o, // string to append to
rd, // read
rdid, // read id
0, // # seeds tried
0, // # seeds with non-empty results
0, // # ranges for all seed hits
0, // # elements for all seed hits
0, // # seeds tried from fw read
0, // # seeds with non-empty results from fw read
0, // # ranges for seed hits from fw read
0, // # elements for seed hits from fw read
0, // # seeds tried from rc read
0, // # seeds with non-empty results from fw read
0, // # ranges for seed hits from fw read
0); // # elements for seed hits from fw read
}
/**
* Print the given string. If ws = true, print only up to and not
* including the first space or tab. Useful for printing reference
* names.
*/
template<typename T>
static inline void printUptoWs(
BTString& s,
const T& str,
bool chopws)
{
size_t len = str.length();
for(size_t i = 0; i < len; i++) {
if(!chopws || (str[i] != ' ' && str[i] != '\t')) {
s.append(str[i]);
} else {
break;
}
}
}
/**
* Append a batch of unresolved seed alignment summary 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-sumamry
* verbose-mode format.
*
* The seed summary format is:
*
* - One line per read
* - A typical line consists of a set of tab-delimited fields:
*
* 1. Read name
* 2. Total number of seeds extracted from the read
* 3. Total number of seeds that aligned to the reference at
* least once (always <= field 2)
* 4. Total number of distinct BW ranges found in all seed hits
* (always >= field 3)
* 5. Total number of distinct BW elements found in all seed
* hits (always >= field 4)
* 6-9.: Like 2-5. but just for seeds extracted from the
* forward representation of the read
* 10-13.: Like 2-5. but just for seeds extracted from the
* reverse-complement representation of the read
*
* Note that fields 6 and 10 should add to field 2, 7 and 11
* should add to 3, etc.
*
* - Lines for reads that are filtered out for any reason (e.g. too
* many Ns) have columns 2 through 13 set to 0.
*/
template <typename index_t>
void AlnSink<index_t>::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)
{
char buf[1024];
bool firstfield = true;
//
// Read name
//
BEGIN_FIELD;
printUptoWs(o, rd.name, true);
//
// Total number of seeds tried
//
BEGIN_FIELD;
WRITE_NUM(o, seedsTried);
//
// Total number of seeds tried where at least one range was found.
//
BEGIN_FIELD;
WRITE_NUM(o, nonzero);
//
// Total number of ranges found
//
BEGIN_FIELD;
WRITE_NUM(o, ranges);
//
// Total number of elements found
//
BEGIN_FIELD;
WRITE_NUM(o, elts);
//
// The same four numbers, but only for seeds extracted from the
// forward read representation.
//
BEGIN_FIELD;
WRITE_NUM(o, seedsTriedFw);
BEGIN_FIELD;
WRITE_NUM(o, nonzeroFw);
BEGIN_FIELD;
WRITE_NUM(o, rangesFw);
BEGIN_FIELD;
WRITE_NUM(o, eltsFw);
//
// The same four numbers, but only for seeds extracted from the
// reverse complement read representation.
//
BEGIN_FIELD;
WRITE_NUM(o, seedsTriedRc);
BEGIN_FIELD;
WRITE_NUM(o, nonzeroRc);
BEGIN_FIELD;
WRITE_NUM(o, rangesRc);
BEGIN_FIELD;
WRITE_NUM(o, eltsRc);
o.append('\n');
}
/**
* Append a single hit to the given output stream in Bowtie's
* verbose-mode format.
*/
template <typename index_t>
void AlnSinkSam<index_t>::appendMate(
BTString& o, // append to this string
StackedAln& staln, // store stacked alignment struct here
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,
const Mapq& mapqCalc,
const Scoring& sc)
{
if(rs == NULL && samc_.omitUnalignedReads()) {
return;
}
char buf[1024];
char mapqInps[1024];
if(rs != NULL) {
staln.reset();
rs->initStacked(rd, staln);
staln.leftAlign(false /* not past MMs */);
}
int offAdj = 0;
// QNAME
samc_.printReadName(o, rd.name, flags.partOfPair());
o.append('\t');
// FLAG
int fl = 0;
if(flags.partOfPair()) {
fl |= SAM_FLAG_PAIRED;
if(flags.alignedConcordant()) {
fl |= SAM_FLAG_MAPPED_PAIRED;
}
if(!flags.mateAligned()) {
// Other fragment is unmapped
fl |= SAM_FLAG_MATE_UNMAPPED;
}
fl |= (flags.readMate1() ?
SAM_FLAG_FIRST_IN_PAIR : SAM_FLAG_SECOND_IN_PAIR);
if(flags.mateAligned() && rso != NULL) {
if(!rso->fw()) {
fl |= SAM_FLAG_MATE_STRAND;
}
}
}
if(!flags.isPrimary()) {
fl |= SAM_FLAG_NOT_PRIMARY;
}
if(rs != NULL && !rs->fw()) {
fl |= SAM_FLAG_QUERY_STRAND;
}
if(rs == NULL) {
// Failed to align
fl |= SAM_FLAG_UNMAPPED;
}
itoa10<int>(fl, buf);
o.append(buf);
o.append('\t');
// RNAME
if(rs != NULL) {
samc_.printRefNameFromIndex(o, (size_t)rs->refid(), rs->repeat());
o.append('\t');
} else {
if(summ.orefid() != -1) {
// Opposite mate aligned but this one didn't - print the opposite
// mate's RNAME and POS as is customary
assert(flags.partOfPair());
samc_.printRefNameFromIndex(o, (size_t)summ.orefid());
} else {
// No alignment
o.append('*');
}
o.append('\t');
}
// POS
// Note: POS is *after* soft clipping. I.e. POS points to the
// upstream-most character *involved in the clipped alignment*.
if(rs != NULL) {
itoa10<int64_t>(rs->refoff()+1+offAdj, buf);
o.append(buf);
o.append('\t');
} else {
if(summ.orefid() != -1) {
// Opposite mate aligned but this one didn't - print the opposite
// mate's RNAME and POS as is customary
assert(flags.partOfPair());
itoa10<int64_t>(summ.orefoff()+1+offAdj, buf);
o.append(buf);
} else {
// No alignment
o.append('0');
}
o.append('\t');
}
// MAPQ
mapqInps[0] = '\0';
if(rs != NULL) {
itoa10<TMapq>(mapqCalc.mapq(
summ, flags, rd.mate < 2, rd.length(),
rdo == NULL ? 0 : rdo->length(), mapqInps), buf);
o.append(buf);
o.append('\t');
} else {
// No alignment
o.append("0\t");
}
// CIGAR
if(rs != NULL) {
staln.buildCigar(false);
staln.writeCigar(&o, NULL);
o.append('\t');
} else {
// No alignment
o.append("*\t");
}
// RNEXT
if(rs != NULL && flags.partOfPair()) {
if(rso != NULL && (rs->refid() != rso->refid() || rs->repeat() != rso->repeat())) {
samc_.printRefNameFromIndex(o, (size_t)rso->refid(), rso->repeat());
o.append('\t');
} else {
o.append("=\t");
}
} else if(summ.orefid() != -1) {
// The convention if this mate fails to align but the other doesn't is
// to copy the mate's details into here
o.append("=\t");
} else {
o.append("*\t");
}
// PNEXT
if(rs != NULL && flags.partOfPair()) {
if(rso != NULL) {
itoa10<int64_t>(rso->refoff()+1, buf);
o.append(buf);
o.append('\t');
} else {
// The convenstion is that if this mate aligns but the opposite
// doesn't, we print this mate's offset here
itoa10<int64_t>(rs->refoff()+1, buf);
o.append(buf);
o.append('\t');
}
} else if(summ.orefid() != -1) {
// The convention if this mate fails to align but the other doesn't is
// to copy the mate's details into here
itoa10<int64_t>(summ.orefoff()+1, buf);
o.append(buf);
o.append('\t');
} else {
o.append("0\t");
}
// ISIZE
if(rs != NULL && rs->isFraglenSet()) {
itoa10<int64_t>(rs->fragmentLength(), buf);
o.append(buf);
o.append('\t');
} else {
// No fragment
o.append("0\t");
}
// SEQ
if(!flags.isPrimary() && samc_.omitSecondarySeqQual()) {
o.append('*');
} else {
// Print the read
if(rd.patFw.length() == 0) {
o.append('*');
} else {
if(rs == NULL || rs->fw()) {
o.append(rd.patFw.toZBuf());
} else {
o.append(rd.patRc.toZBuf());
}
}
}
o.append('\t');
// QUAL
if(!flags.isPrimary() && samc_.omitSecondarySeqQual()) {
o.append('*');
} else {
// Print the quals
if(rd.qual.length() == 0) {
o.append('*');
} else {
if(rs == NULL || rs->fw()) {
o.append(rd.qual.toZBuf());
} else {
o.append(rd.qualRev.toZBuf());
}
}
}
o.append('\t');
//
// Optional fields
//
if(rs != NULL) {
samc_.printAlignedOptFlags(
o, // output buffer
true, // first opt flag printed is first overall?
rd, // read
*rs, // individual alignment result
staln, // stacked alignment
flags, // alignment flags
summ, // summary of alignments for this read
ssm, // seed alignment summary
prm, // per-read metrics
sc, // scoring scheme
mapqInps, // inputs to MAPQ calculation
this->altdb_);
} else {
samc_.printEmptyOptFlags(
o, // output buffer
true, // first opt flag printed is first overall?
rd, // read
flags, // alignment flags
summ, // summary of alignments for this read
ssm, // seed alignment summary
prm, // per-read metrics
sc); // scoring scheme
}
o.append('\n');
}
#endif /*ndef ALN_SINK_H_*/