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aln_sink.cpp
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aln_sink.cpp
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/*
* Copyright 2011, Ben Langmead <[email protected]>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Bowtie 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#include <iomanip>
#include <limits>
#include "aln_sink.h"
#include "aligner_seed.h"
#include "util.h"
using namespace std;
/**
* Initialize state machine with a new read. The state we start in depends
* on whether it's paired-end or unpaired.
*/
void ReportingState::nextRead(bool paired) {
paired_ = paired;
if(paired) {
state_ = CONCORDANT_PAIRS;
doneConcord_ = false;
doneDiscord_ = p_.discord ? false : true;
doneUnpair1_ = p_.mixed ? false : true;
doneUnpair2_ = p_.mixed ? false : true;
exitConcord_ = ReportingState::EXIT_DID_NOT_EXIT;
exitDiscord_ = p_.discord ?
ReportingState::EXIT_DID_NOT_EXIT :
ReportingState::EXIT_DID_NOT_ENTER;
exitUnpair1_ = p_.mixed ?
ReportingState::EXIT_DID_NOT_EXIT :
ReportingState::EXIT_DID_NOT_ENTER;
exitUnpair2_ = p_.mixed ?
ReportingState::EXIT_DID_NOT_EXIT :
ReportingState::EXIT_DID_NOT_ENTER;
} else {
// Unpaired
state_ = UNPAIRED;
doneConcord_ = true;
doneDiscord_ = true;
doneUnpair1_ = false;
doneUnpair2_ = true;
exitConcord_ = ReportingState::EXIT_DID_NOT_ENTER; // not relevant
exitDiscord_ = ReportingState::EXIT_DID_NOT_ENTER; // not relevant
exitUnpair1_ = ReportingState::EXIT_DID_NOT_EXIT;
exitUnpair2_ = ReportingState::EXIT_DID_NOT_ENTER; // not relevant
}
doneUnpair_ = doneUnpair1_ && doneUnpair2_;
done_ = false;
nconcord_ = ndiscord_ = nunpair1_ = nunpair2_ = 0;
}
/**
* Caller uses this member function to indicate that one additional
* concordant alignment has been found.
*/
bool ReportingState::foundConcordant() {
assert(paired_);
assert_geq(state_, ReportingState::CONCORDANT_PAIRS);
assert(!doneConcord_);
nconcord_++;
areDone(nconcord_, doneConcord_, exitConcord_);
// No need to search for discordant alignments if there are one or more
// concordant alignments.
doneDiscord_ = true;
exitDiscord_ = ReportingState::EXIT_SHORT_CIRCUIT_TRUMPED;
if(doneConcord_) {
// If we're finished looking for concordant alignments, do we have to
// continue on to search for unpaired alignments? Only if our exit
// from the concordant stage is EXIT_SHORT_CIRCUIT_M. If it's
// EXIT_SHORT_CIRCUIT_k or EXIT_WITH_ALIGNMENTS, we can skip unpaired.
assert_neq(ReportingState::EXIT_NO_ALIGNMENTS, exitConcord_);
if(exitConcord_ != ReportingState::EXIT_SHORT_CIRCUIT_M) {
if(!doneUnpair1_) {
doneUnpair1_ = true;
exitUnpair1_ = ReportingState::EXIT_SHORT_CIRCUIT_TRUMPED;
}
if(!doneUnpair2_) {
doneUnpair2_ = true;
exitUnpair2_ = ReportingState::EXIT_SHORT_CIRCUIT_TRUMPED;
}
}
}
updateDone();
return done();
}
/**
* Caller uses this member function to indicate that one additional unpaired
* mate alignment has been found for the specified mate.
*/
bool ReportingState::foundUnpaired(bool mate1) {
assert_gt(state_, ReportingState::NO_READ);
// Note: it's not right to assert !doneUnpair1_/!doneUnpair2_ here.
// Even if we're done with finding
if(mate1) {
nunpair1_++;
// Did we just finish with this mate?
if(!doneUnpair1_) {
areDone(nunpair1_, doneUnpair1_, exitUnpair1_);
if(doneUnpair1_) {
doneUnpair_ = doneUnpair1_ && doneUnpair2_;
updateDone();
}
}
if(nunpair1_ > 1) {
doneDiscord_ = true;
exitDiscord_ = ReportingState::EXIT_NO_ALIGNMENTS;
}
} else {
nunpair2_++;
// Did we just finish with this mate?
if(!doneUnpair2_) {
areDone(nunpair2_, doneUnpair2_, exitUnpair2_);
if(doneUnpair2_) {
doneUnpair_ = doneUnpair1_ && doneUnpair2_;
updateDone();
}
}
if(nunpair2_ > 1) {
doneDiscord_ = true;
exitDiscord_ = ReportingState::EXIT_NO_ALIGNMENTS;
}
}
return done();
}
/**
* 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 ReportingState::finish() {
if(!doneConcord_) {
doneConcord_ = true;
exitConcord_ =
((nconcord_ > 0) ?
ReportingState::EXIT_WITH_ALIGNMENTS :
ReportingState::EXIT_NO_ALIGNMENTS);
}
assert_gt(exitConcord_, EXIT_DID_NOT_EXIT);
if(!doneUnpair1_) {
doneUnpair1_ = true;
exitUnpair1_ =
((nunpair1_ > 0) ?
ReportingState::EXIT_WITH_ALIGNMENTS :
ReportingState::EXIT_NO_ALIGNMENTS);
}
assert_gt(exitUnpair1_, EXIT_DID_NOT_EXIT);
if(!doneUnpair2_) {
doneUnpair2_ = true;
exitUnpair2_ =
((nunpair2_ > 0) ?
ReportingState::EXIT_WITH_ALIGNMENTS :
ReportingState::EXIT_NO_ALIGNMENTS);
}
assert_gt(exitUnpair2_, EXIT_DID_NOT_EXIT);
if(!doneDiscord_) {
// Check if the unpaired alignments should be converted to a single
// discordant paired-end alignment.
assert_eq(0, ndiscord_);
if(nconcord_ == 0 && nunpair1_ == 1 && nunpair2_ == 1) {
convertUnpairedToDiscordant();
}
doneDiscord_ = true;
exitDiscord_ =
((ndiscord_ > 0) ?
ReportingState::EXIT_WITH_ALIGNMENTS :
ReportingState::EXIT_NO_ALIGNMENTS);
}
assert(!paired_ || exitDiscord_ > ReportingState::EXIT_DID_NOT_EXIT);
doneUnpair_ = done_ = true;
assert(done());
}
/**
* 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 ReportingState::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
{
nconcordAln = ndiscordAln = nunpair1Aln = nunpair2Aln = 0;
pairMax = unpair1Max = unpair2Max = false;
assert_gt(p_.khits, 0);
assert_gt(p_.mhits, 0);
if(paired_) {
// Do we have 1 or more concordant alignments to report?
if(exitConcord_ == ReportingState::EXIT_SHORT_CIRCUIT_k) {
// k at random
assert_geq(nconcord_, (uint64_t)p_.khits);
nconcordAln = p_.khits;
return;
} else if(exitConcord_ == ReportingState::EXIT_SHORT_CIRCUIT_M) {
assert(p_.msample);
assert_gt(nconcord_, 0);
pairMax = true; // repetitive concordant alignments
if(p_.mixed) {
unpair1Max = nunpair1_ > (uint64_t)p_.mhits;
unpair2Max = nunpair2_ > (uint64_t)p_.mhits;
}
// Not sure if this is OK
nconcordAln = 1; // 1 at random
return;
} else if(exitConcord_ == ReportingState::EXIT_WITH_ALIGNMENTS) {
assert_gt(nconcord_, 0);
// <= k at random
nconcordAln = min<uint64_t>(nconcord_, p_.khits);
return;
}
assert(!p_.mhitsSet() || nconcord_ <= (uint64_t)p_.mhits+1);
// Do we have a discordant alignment to report?
if(exitDiscord_ == ReportingState::EXIT_WITH_ALIGNMENTS) {
// Report discordant
assert(p_.discord);
ndiscordAln = 1;
return;
}
}
assert_neq(ReportingState::EXIT_SHORT_CIRCUIT_TRUMPED, exitUnpair1_);
assert_neq(ReportingState::EXIT_SHORT_CIRCUIT_TRUMPED, exitUnpair2_);
if((paired_ && !p_.mixed) || nunpair1_ + nunpair2_ == 0) {
// Unpaired alignments either not reportable or non-existant
return;
}
// Do we have 1 or more alignments for mate #1 to report?
if(exitUnpair1_ == ReportingState::EXIT_SHORT_CIRCUIT_k) {
// k at random
assert_geq(nunpair1_, (uint64_t)p_.khits);
nunpair1Aln = p_.khits;
} else if(exitUnpair1_ == ReportingState::EXIT_SHORT_CIRCUIT_M) {
assert(p_.msample);
assert_gt(nunpair1_, 0);
unpair1Max = true; // repetitive alignments for mate #1
nunpair1Aln = 1; // 1 at random
} else if(exitUnpair1_ == ReportingState::EXIT_WITH_ALIGNMENTS) {
assert_gt(nunpair1_, 0);
// <= k at random
nunpair1Aln = min<uint64_t>(nunpair1_, (uint64_t)p_.khits);
}
assert(!p_.mhitsSet() || paired_ || nunpair1_ <= (uint64_t)p_.mhits+1);
// Do we have 2 or more alignments for mate #2 to report?
if(exitUnpair2_ == ReportingState::EXIT_SHORT_CIRCUIT_k) {
// k at random
nunpair2Aln = p_.khits;
} else if(exitUnpair2_ == ReportingState::EXIT_SHORT_CIRCUIT_M) {
assert(p_.msample);
assert_gt(nunpair2_, 0);
unpair2Max = true; // repetitive alignments for mate #1
nunpair2Aln = 1; // 1 at random
} else if(exitUnpair2_ == ReportingState::EXIT_WITH_ALIGNMENTS) {
assert_gt(nunpair2_, 0);
// <= k at random
nunpair2Aln = min<uint64_t>(nunpair2_, (uint64_t)p_.khits);
}
assert(!p_.mhitsSet() || paired_ || nunpair2_ <= (uint64_t)p_.mhits+1);
}
/**
* 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 ReportingState::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)
{
assert(!done);
// Have we exceeded the -k limit?
assert_gt(p_.khits, 0);
assert_gt(p_.mhits, 0);
if(cnt >= (uint64_t)p_.khits && !p_.mhitsSet()) {
done = true;
exit = ReportingState::EXIT_SHORT_CIRCUIT_k;
}
// Have we exceeded the -m or -M limit?
else if(p_.mhitsSet() && cnt > (uint64_t)p_.mhits) {
done = true;
assert(p_.msample);
exit = ReportingState::EXIT_SHORT_CIRCUIT_M;
}
}
static 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.
*/
void AlnSink::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?
{
// 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) {
cerr << "reporter:counter:Bowtie,Reads processed," << met.nread << endl;
}
uint64_t totread = met.nread;
if(totread > 0) {
cerr << "" << met.nread << " reads; of these:" << endl;
} else {
assert_eq(0, met.npaired);
assert_eq(0, met.nunpaired);
cerr << "" << totread << " reads" << endl;
}
uint64_t totpair = met.npaired;
if(totpair > 0) {
// Paired output
cerr << " " << totpair << " (";
printPct(cerr, totpair, totread);
cerr << ") were paired; of these:" << endl;
// Concordants
cerr << " " << met.nconcord_0 << " (";
printPct(cerr, met.nconcord_0, met.npaired);
cerr << ") 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);
cerr << " " << met.nconcord_uni1 << " (";
printPct(cerr, met.nconcord_uni1, met.npaired);
cerr << ") aligned concordantly exactly 1 time" << endl;
// Print the number that aligned concordantly more than once but
// fewer times than the limit
cerr << " " << met.nconcord_uni2+met.nconcord_rep << " (";
printPct(cerr, met.nconcord_uni2+met.nconcord_rep, met.npaired);
cerr << ") 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);
cerr << " " << met.nconcord_uni1 << " (";
printPct(cerr, met.nconcord_uni1, met.npaired);
cerr << ") aligned concordantly exactly 1 time" << endl;
// Print the number that aligned concordantly more than once
cerr << " " << met.nconcord_uni2 << " (";
printPct(cerr, met.nconcord_uni2, met.npaired);
cerr << ") 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
cerr << " ----" << endl;
cerr << " " << met.nconcord_0
<< " pairs aligned concordantly 0 times; of these:" << endl;
// Discordants
cerr << " " << met.ndiscord << " (";
printPct(cerr, met.ndiscord, met.nconcord_0);
cerr << ") 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
cerr << " ----" << endl;
cerr << " " << ncondiscord_0
<< " pairs aligned 0 times concordantly or discordantly; of these:" << endl;
cerr << " " << (ncondiscord_0 * 2) << " mates make up the pairs; of these:" << endl;
cerr << " " << met.nunp_0_0 << " " << "(";
printPct(cerr, met.nunp_0_0, ncondiscord_0 * 2);
cerr << ") 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);
cerr << " " << met.nunp_0_uni1 << " (";
printPct(cerr, met.nunp_0_uni1, ncondiscord_0 * 2);
cerr << ") aligned exactly 1 time" << endl;
// Print the number that aligned more than once but fewer times
// than the limit
cerr << " " << met.nunp_0_uni2+met.nunp_0_rep << " (";
printPct(cerr, met.nunp_0_uni2+met.nunp_0_rep, ncondiscord_0 * 2);
cerr << ") 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);
cerr << " " << met.nunp_0_uni1 << " (";
printPct(cerr, met.nunp_0_uni1, ncondiscord_0 * 2);
cerr << ") aligned exactly 1 time" << endl;
// Print the number that aligned more than once but fewer times
// than the limit
cerr << " " << met.nunp_0_uni2 << " (";
printPct(cerr, met.nunp_0_uni2, ncondiscord_0 * 2);
cerr << ") aligned >1 times" << endl;
}
//if(canRep) {
// // Bring out the repetitively aligned pair total so we can subtract discordants
// cerr << " ----" << endl;
// cerr << " " << met.nconcord_rep
// << " pairs aligned concordantly >" << repThresh
// << " times; of these:" << endl;
// cerr << " " << (met.nconcord_rep * 2) << " mates make up the pairs; of these:" << endl;
//
// cerr << " " << met.nunp_rep_0 << " (";
// printPct(cerr, met.nunp_rep_0, met.nconcord_rep * 2);
// cerr << ") aligned 0 times" << endl;
//
// cerr << " " << met.nunp_rep_uni << " (";
// printPct(cerr, met.nunp_rep_uni, met.nconcord_rep * 2);
// cerr << ") aligned >0 and <=" << repThresh << " times" << endl;
//
// cerr << " " << met.nunp_rep_rep << " (";
// printPct(cerr, met.nunp_rep_rep, met.nconcord_rep * 2);
// cerr << ") aligned >" << repThresh << " times" << endl;
//}
}
}
uint64_t totunpair = met.nunpaired;
if(totunpair > 0) {
// Unpaired output
cerr << " " << totunpair << " (";
printPct(cerr, totunpair, totread);
cerr << ") were unpaired; of these:" << endl;
cerr << " " << met.nunp_0 << " (";
printPct(cerr, met.nunp_0, met.nunpaired);
cerr << ") aligned 0 times" << endl;
if(hadoopOut) {
cerr << "reporter:counter:Bowtie 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);
cerr << " " << met.nunp_uni1 << " (";
printPct(cerr, met.nunp_uni1, met.nunpaired);
cerr << ") aligned exactly 1 time" << endl;
// Print the number that aligned more than once but fewer times
// than the limit
cerr << " " << met.nunp_uni2+met.nunp_rep << " (";
printPct(cerr, met.nunp_uni2+met.nunp_rep, met.nunpaired);
cerr << ") aligned >1 times" << endl;
} else {
// Print the number that aligned exactly once
assert_eq(met.nunp_uni, met.nunp_uni1+met.nunp_uni2);
cerr << " " << met.nunp_uni1 << " (";
printPct(cerr, met.nunp_uni1, met.nunpaired);
cerr << ") aligned exactly 1 time" << endl;
// Print the number that aligned more than once
cerr << " " << met.nunp_uni2 << " (";
printPct(cerr, met.nunp_uni2, met.nunpaired);
cerr << ") aligned >1 times" << endl;
}
}
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);
printPct(cerr, tot_al, tot_al_cand);
cerr << " overall alignment rate" << endl;
}
/**
* Return true iff the read in rd1/rd2 matches the last read handled, which
* should still be in rd1_/rd2_.
*/
bool AlnSinkWrap::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.
*/
int AlnSinkWrap::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();
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
*/
void AlnSinkWrap::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
{
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);
// Sort by score then pick from low to high
AlnScore bestUScore, bestP1Score, bestP2Score, bestCScore;
AlnScore bestUDist, bestP1Dist, bestP2Dist, bestCDist;
AlnScore bestUnchosenUScore, bestUnchosenP1Score, bestUnchosenP2Score, bestUnchosenCScore;
AlnScore bestUnchosenUDist, bestUnchosenP1Dist, bestUnchosenP2Dist, bestUnchosenCDist;
// TODO: should probably package these variables up so it's not
// such a pain to pass them around
size_t off = selectByScore(
&rs1_, &rs2_,
nconcord, select1_,
&rs1u_, &rs2u_,
bestUScore,
bestUDist,
bestP1Score,
bestP1Dist,
bestP2Score,
bestP2Dist,
bestCScore,
bestCDist,
bestUnchosenUScore,
bestUnchosenUDist,
bestUnchosenP1Score,
bestUnchosenP1Dist,
bestUnchosenP2Score,
bestUnchosenP2Dist,
bestUnchosenCScore,
bestUnchosenCDist,
rnd);
concordSumm.setBest(
bestUScore,
bestUDist,
bestP1Score,
bestP1Dist,
bestP2Score,
bestP2Dist,
bestCScore,
bestCDist,
bestUnchosenUScore,
bestUnchosenUDist,
bestUnchosenP1Score,
bestUnchosenP1Dist,
bestUnchosenP2Score,
bestUnchosenP2Dist,
bestUnchosenCScore,
bestUnchosenCDist);
assert(concordSumm.bestScore(true).valid());
assert(concordSumm.bestScore(false).valid());
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
scUnMapped,
xeq);
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
scUnMapped,
xeq);
// 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 the a given mate aligns to the forward strand.
SeedAlSumm ssm1, ssm2;
sr1->toSeedAlSumm(ssm1);
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_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,
false);
if(pairMax) {
met.nconcord_rep++;
} else {
met.nconcord_uni++;
assert(!rs1_.empty());
if(!concordSumm.bestUnchosenCScore().valid()) {
met.nconcord_uni1++;
} else {
met.nconcord_uni2++;
}
}
init_ = false;
//g_.outq().finishRead(obuf_, rdid_, threadid_);
return;
}
// Report disconcordant 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
scUnMapped,
xeq);
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
scUnMapped,
xeq);
SeedAlSumm ssm1, ssm2;
sr1->toSeedAlSumm(ssm1);
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()));
}
AlnScore bestUScore, bestP1Score, bestP2Score, bestCScore;
AlnScore bestUDist, bestP1Dist, bestP2Dist, bestCDist;
AlnScore bestUnchosenUScore, bestUnchosenP1Score, bestUnchosenP2Score, bestUnchosenCScore;
AlnScore bestUnchosenUDist, bestUnchosenP1Dist, bestUnchosenP2Dist, bestUnchosenCDist;
ASSERT_ONLY(size_t off =) selectByScore(
&rs1_, &rs2_,
ndiscord, select1_,
&rs1u_, &rs2u_,
bestUScore,
bestUDist,
bestP1Score,
bestP1Dist,
bestP2Score,
bestP2Dist,
bestCScore,
bestCDist,
bestUnchosenUScore,
bestUnchosenUDist,
bestUnchosenP1Score,
bestUnchosenP1Dist,
bestUnchosenP2Score,
bestUnchosenP2Dist,
bestUnchosenCScore,
bestUnchosenCDist,
rnd);
discordSumm.setBest(
bestUScore,
bestUDist,
bestP1Score,
bestP1Dist,
bestP2Score,
bestP2Dist,
bestCScore,
bestCDist,
bestUnchosenUScore,
bestUnchosenUDist,
bestUnchosenP1Score,
bestUnchosenP1Dist,
bestUnchosenP2Score,
bestUnchosenP2Dist,
bestUnchosenCScore,
bestUnchosenCDist);
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,
false);
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);
// 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(rs1u_.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(rs1u_.size() == 1) {
met.nunp_uni1++;