/
aln_sink.cpp
2348 lines (2348 loc) · 52 KB
/
aln_sink.cpp
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#include <iomanip>
#include <limits>
#include "aln_sink.h"
#include "aligner_seed.h"
#include "util.h"
using namespace std;
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
{
state_ = UNPAIRED;
doneConcord_ = true;
doneDiscord_ = true;
doneUnpair1_ = false;
doneUnpair2_ = true;
exitConcord_ = ReportingState::EXIT_DID_NOT_ENTER;
exitDiscord_ = ReportingState::EXIT_DID_NOT_ENTER;
exitUnpair1_ = ReportingState::EXIT_DID_NOT_EXIT;
exitUnpair2_ = ReportingState::EXIT_DID_NOT_ENTER;
}
doneUnpair_ = doneUnpair1_ && doneUnpair2_;
done_ = false;
nconcord_ = ndiscord_ = nunpair1_ = nunpair2_ = 0;
}
bool ReportingState::foundConcordant()
{
assert(paired_);
assert_geq(state_, ReportingState::CONCORDANT_PAIRS);
assert(!doneConcord_);
nconcord_++;
areDone(nconcord_, doneConcord_, exitConcord_);
doneDiscord_ = true;
exitDiscord_ = ReportingState::EXIT_SHORT_CIRCUIT_TRUMPED;
if (doneConcord_)
{
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();
}
bool ReportingState::foundUnpaired(bool mate1)
{
assert_gt(state_, ReportingState::NO_READ);
if (mate1)
{
nunpair1_++;
if (!doneUnpair1_)
{
areDone(nunpair1_, doneUnpair1_, exitUnpair1_);
if (doneUnpair1_)
{
doneUnpair_ = doneUnpair1_ && doneUnpair2_;
updateDone();
}
}
if (nunpair1_ > 1)
{
doneDiscord_ = true;
exitDiscord_ = ReportingState::EXIT_NO_ALIGNMENTS;
}
}
else
{
nunpair2_++;
if (!doneUnpair2_)
{
areDone(nunpair2_, doneUnpair2_, exitUnpair2_);
if (doneUnpair2_)
{
doneUnpair_ = doneUnpair1_ && doneUnpair2_;
updateDone();
}
}
if (nunpair2_ > 1)
{
doneDiscord_ = true;
exitDiscord_ = ReportingState::EXIT_NO_ALIGNMENTS;
}
}
return done();
}
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_)
{
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());
}
void ReportingState::getReport(
uint64_t &nconcordAln,
uint64_t &ndiscordAln,
uint64_t &nunpair1Aln,
uint64_t &nunpair2Aln,
bool &pairMax,
bool &unpair1Max,
bool &unpair2Max)
const
{
nconcordAln = ndiscordAln = nunpair1Aln = nunpair2Aln = 0;
pairMax = unpair1Max = unpair2Max = false;
assert_gt(p_.khits, 0);
assert_gt(p_.mhits, 0);
if (paired_)
{
if (exitConcord_ == ReportingState::EXIT_SHORT_CIRCUIT_k)
{
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;
if (p_.mixed)
{
unpair1Max = nunpair1_ > (uint64_t)p_.mhits;
unpair2Max = nunpair2_ > (uint64_t)p_.mhits;
}
nconcordAln = 1;
return;
}
else if (exitConcord_ == ReportingState::EXIT_WITH_ALIGNMENTS)
{
assert_gt(nconcord_, 0);
nconcordAln = min<uint64_t>(nconcord_, p_.khits);
return;
}
assert(!p_.mhitsSet() || nconcord_ <= (uint64_t)p_.mhits + 1);
if (exitDiscord_ == ReportingState::EXIT_WITH_ALIGNMENTS)
{
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)
{
return;
}
if (exitUnpair1_ == ReportingState::EXIT_SHORT_CIRCUIT_k)
{
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;
nunpair1Aln = 1;
}
else if (exitUnpair1_ == ReportingState::EXIT_WITH_ALIGNMENTS)
{
assert_gt(nunpair1_, 0);
nunpair1Aln = min<uint64_t>(nunpair1_, (uint64_t)p_.khits);
}
assert(!p_.mhitsSet() || paired_ || nunpair1_ <= (uint64_t)p_.mhits + 1);
if (exitUnpair2_ == ReportingState::EXIT_SHORT_CIRCUIT_k)
{
nunpair2Aln = p_.khits;
}
else if (exitUnpair2_ == ReportingState::EXIT_SHORT_CIRCUIT_M)
{
assert(p_.msample);
assert_gt(nunpair2_, 0);
unpair2Max = true;
nunpair2Aln = 1;
}
else if (exitUnpair2_ == ReportingState::EXIT_WITH_ALIGNMENTS)
{
assert_gt(nunpair2_, 0);
nunpair2Aln = min<uint64_t>(nunpair2_, (uint64_t)p_.khits);
}
assert(!p_.mhitsSet() || paired_ || nunpair2_ <= (uint64_t)p_.mhits + 1);
}
inline void ReportingState::areDone(
uint64_t cnt,
bool &done,
int &exit) const
{
assert(!done);
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;
}
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;
}
void AlnSink::printAlSumm(
const ReportingMetrics &met,
size_t repThresh,
bool discord,
bool mixed,
bool hadoopOut)
{
bool canRep = repThresh != MAX_SIZE_T;
if (hadoopOut)
{
cerr << "reporter:counter,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)
{
cerr << " " << totpair << " (";
printPct(cerr, totpair, totread);
cerr << ") were paired; of these:" << endl;
cerr << " " << met.nconcord_0 << " (";
printPct(cerr, met.nconcord_0, met.npaired);
cerr << ") aligned concordantly 0 times" << endl;
if (canRep)
{
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;
cerr << " " << met.nconcord_uni2 + met.nconcord_rep << " (";
printPct(cerr, met.nconcord_uni2 + met.nconcord_rep, met.npaired);
cerr << ") aligned concordantly >1 times" << endl;
}
else
{
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;
cerr << " " << met.nconcord_uni2 << " (";
printPct(cerr, met.nconcord_uni2, met.npaired);
cerr << ") aligned concordantly >1 times" << endl;
}
if (discord)
{
cerr << " ----" << endl;
cerr << " " << met.nconcord_0
<< " pairs aligned concordantly 0 times; of these:" << endl;
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)
{
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)
{
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;
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
{
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;
cerr << " " << met.nunp_0_uni2 << " (";
printPct(cerr, met.nunp_0_uni2, ncondiscord_0 * 2);
cerr << ") aligned >1 times" << endl;
}
}
}
uint64_t totunpair = met.nunpaired;
if (totunpair > 0)
{
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,Unpaired reads with 0 alignments,"
<< met.nunpaired << endl;
}
if (canRep)
{
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;
cerr << " " << met.nunp_uni2 + met.nunp_rep << " (";
printPct(cerr, met.nunp_uni2 + met.nunp_rep, met.nunpaired);
cerr << ") aligned >1 times" << endl;
}
else
{
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;
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;
}
bool AlnSinkWrap::sameRead(
const Read *rd1,
const Read *rd2,
bool qualitiesMatter)
{
bool same = false;
if (rd1_ != NULL || rd2_ != NULL)
{
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,
rd1->qual,
rd1_->patFw,
rd1_->qual,
qualitiesMatter);
}
if (m1same)
{
bool m2same = (rd2 == NULL && rd2_ == NULL);
if (!m2same)
{
m2same = Read::same(
rd2->patFw,
rd2->qual,
rd2_->patFw,
rd2_->qual,
qualitiesMatter);
}
same = m2same;
}
}
}
return same;
}
int AlnSinkWrap::nextRead(
const Read *rd1,
const Read *rd2,
TReadId rdid,
bool qualitiesMatter)
{
assert(!init_);
assert(rd1 != NULL || rd2 != NULL);
init_ = true;
if (rd1 != NULL)
{
rd1_ = rd1;
}
else
rd1_ = NULL;
if (rd2 != NULL)
{
rd2_ = rd2;
}
else
rd2_ = NULL;
rdid_ = rdid;
maxed1_ = false;
maxed2_ = false;
maxedOverall_ = false;
bestPair_ = best2Pair_ =
bestUnp1_ = best2Unp1_ =
bestUnp2_ = best2Unp2_ = std::numeric_limits<THitInt>::min();
rs1_.clear();
rs2_.clear();
rs1u_.clear();
rs2u_.clear();
st_.nextRead(readIsPair());
assert(empty());
assert(!maxed());
return 0;
}
void AlnSinkWrap::finishRead(
const SeedResults *sr1,
const SeedResults *sr2,
bool exhaust1,
bool exhaust2,
bool nfilt1,
bool nfilt2,
bool scfilt1,
bool scfilt2,
bool lenfilt1,
bool lenfilt2,
bool qcfilt1,
bool qcfilt2,
RandomSource &rnd,
ReportingMetrics &met,
const PerReadMetrics &prm,
const Scoring &sc,
bool suppressSeedSummary,
bool suppressAlignments,
bool scUnMapped,
bool xeq)
{
obuf_.clear();
OutputQueueMark qqm(g_.outq(), obuf_, rdid_, threadid_);
assert(init_);
if (!suppressSeedSummary)
{
if (sr1 != NULL)
{
assert(rd1_ != NULL);
g_.reportSeedSummary(obuf_, *rd1_, rdid_, threadid_, *sr1, true);
}
else if (rd1_ != NULL)
{
g_.reportEmptySeedSummary(obuf_, *rd1_, rdid_, true);
}
if (sr2 != NULL)
{
assert(rd2_ != NULL);
g_.reportSeedSummary(obuf_, *rd2_, rdid_, threadid_, *sr2, true);
}
else if (rd2_ != NULL)
{
g_.reportEmptySeedSummary(obuf_, *rd2_, rdid_, true);
}
}
if (!suppressAlignments)
{
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++;
}
if (nconcord > 0)
{
AlnSetSumm concordSumm(
rd1_, rd2_, &rs1_, &rs2_, &rs1u_, &rs2u_,
exhaust1, exhaust2, -1, -1);
AlnScore bestUScore, bestP1Score, bestP2Score, bestCScore;
AlnScore bestUDist, bestP1Dist, bestP2Dist, bestCDist;
AlnScore bestUnchosenUScore, bestUnchosenP1Score, bestUnchosenP2Score, bestUnchosenCScore;
AlnScore bestUnchosenUDist, bestUnchosenP1Dist, bestUnchosenP2Dist, bestUnchosenCDist;
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,
true,
rs2->fw(),
scUnMapped,
xeq);
AlnFlags flags2(
ALN_FLAG_PAIR_CONCORD_MATE2,
st_.params().mhitsSet(),
unpair2Max,
pairMax,
nfilt2,
scfilt2,
lenfilt2,
qcfilt2,
st_.params().mixed,
false,
true,
rs1->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_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 (rs1_.size() == 1)
{
met.nconcord_uni1++;
}
else
{
met.nconcord_uni2++;
}
}
init_ = false;
return;
}
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,
true,
rs2->fw(),
scUnMapped,
xeq);
AlnFlags flags2(
ALN_FLAG_PAIR_DISCORD_MATE2,
st_.params().mhitsSet(),
false,
pairMax,
nfilt2,
scfilt2,
lenfilt2,
qcfilt2,
st_.params().mixed,
false,
true,
rs1->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;
return;
}
assert(!pairMax);
if (readIsPair())
{
met.nconcord_0++;
}
if (rd1_ != NULL)
{
if (nunpair1 > 0)
{
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++;
}
else
{
met.nunp_uni2++;
}
}
}
}
else if (unpair1Max)
{
if (readIsPair())
met.nunp_0_rep++;
else
met.nunp_rep++;
}
else
{
if (readIsPair())
met.nunp_0_0++;
else
met.nunp_0++;
}
}
if (rd2_ != NULL)
{
if (nunpair2 > 0)
{
if (readIsPair())
{
if (unpair2Max)
met.nunp_0_rep++;
else
{
assert(!rs2u_.empty());
met.nunp_0_uni++;
if (rs2u_.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 (rs2u_.size() == 1)
{
met.nunp_uni1++;
}
else
{
met.nunp_uni2++;
}
}
}
}
else if (unpair2Max)
{
if (readIsPair())
met.nunp_0_rep++;
else
met.nunp_rep++;
}
else
{
if (readIsPair())
met.nunp_0_0++;
else
met.nunp_0++;
}
}
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;
if (rep1)
{
summ1.init(
rd1_, NULL, NULL, NULL, &rs1u_, NULL,
exhaust1, exhaust2, -1, -1);
AlnScore bestUScore, bestP1Score, bestP2Score, bestCScore;
AlnScore bestUDist, bestP1Dist, bestP2Dist, bestCDist;
AlnScore bestUnchosenUScore, bestUnchosenP1Score, bestUnchosenP2Score, bestUnchosenCScore;
AlnScore bestUnchosenUDist, bestUnchosenP1Dist, bestUnchosenP2Dist, bestUnchosenCDist;
size_t off = selectByScore(
&rs1u_, NULL, nunpair1, select1_, NULL, NULL,
bestUScore,
bestUDist,
bestP1Score,
bestP1Dist,
bestP2Score,
bestP2Dist,
bestCScore,
bestCDist,
bestUnchosenUScore,
bestUnchosenUDist,
bestUnchosenP1Score,
bestUnchosenP1Dist,
bestUnchosenP2Score,
bestUnchosenP2Dist,
bestUnchosenCScore,
bestUnchosenCDist,
rnd);
summ1.setBest(
bestUScore,
bestUDist,
bestP1Score,
bestP1Dist,
bestP2Score,
bestP2Dist,
bestCScore,
bestCDist,
bestUnchosenUScore,
bestUnchosenUDist,
bestUnchosenP1Score,
bestUnchosenP1Dist,
bestUnchosenP2Score,
bestUnchosenP2Dist,
bestUnchosenCScore,
bestUnchosenCDist);
repRs1 = &rs1u_[off];
}
else if (rd1_ != NULL)
{
assert(!unpair1Max);
}
if (rep2)
{
summ2.init(
NULL, rd2_, NULL, NULL, NULL, &rs2u_,