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/*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Bowtie 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef ALN_SINK_H_
#define ALN_SINK_H_
#include <limits>
#include <utility>
#include <map>
#include "read.h"
#include "ds.h"
#include "simple_func.h"
#include "outq.h"
#include "aligner_result.h"
#include "hyperloglogplus.h"
#include "timer.h"
#include "taxonomy.h"
// Forward decl
template <typename index_t>
class SeedResults;
enum {
OUTPUT_SAM = 1
};
struct ReadCounts {
uint32_t n_reads;
uint32_t sum_score;
double summed_hit_len;
double weighted_reads;
uint32_t n_unique_reads;
};
/**
* Metrics summarizing the species level information we have
*/
struct SpeciesMetrics {
//
struct IDs {
EList<uint64_t, 5> ids;
bool operator<(const IDs& o) const {
if(ids.size() != o.ids.size()) return ids.size() < o.ids.size();
for(size_t i = 0; i < ids.size(); i++) {
assert_lt(i, o.ids.size());
if(ids[i] != o.ids[i]) return ids[i] < o.ids[i];
}
return false;
}
IDs& operator=(const IDs& other) {
if(this == &other)
return *this;
ids = other.ids;
return *this;
}
};
SpeciesMetrics():mutex_m() {
reset();
}
void reset() {
species_counts.clear();
//for(map<uint32_t, HyperLogLogPlusMinus<uint64_t> >::iterator it = this->species_kmers.begin(); it != this->species_kmers.end(); ++it) {
// it->second.reset();
//} //TODO: is this required?
species_kmers.clear();
num_non_leaves = 0;
}
void init(
const map<uint64_t, ReadCounts>& species_counts_,
const map<uint64_t, HyperLogLogPlusMinus<uint64_t> >& species_kmers_,
const map<IDs, uint64_t>& observed_)
{
species_counts = species_counts_;
species_kmers = species_kmers_;
observed = observed_;
num_non_leaves = 0;
}
/**
* 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 SpeciesMetrics& met, bool getLock = false) {
ThreadSafe ts(&mutex_m, getLock);
// update species read count
for(map<uint64_t, ReadCounts>::const_iterator it = met.species_counts.begin(); it != met.species_counts.end(); ++it) {
if (species_counts.find(it->first) == species_counts.end()) {
species_counts[it->first] = it->second;
} else {
species_counts[it->first].n_reads += it->second.n_reads;
species_counts[it->first].sum_score += it->second.sum_score;
species_counts[it->first].summed_hit_len += it->second.summed_hit_len;
species_counts[it->first].weighted_reads += it->second.weighted_reads;
species_counts[it->first].n_unique_reads += it->second.n_unique_reads;
}
}
// update species k-mers
for(map<uint64_t, HyperLogLogPlusMinus<uint64_t> >::const_iterator it = met.species_kmers.begin(); it != met.species_kmers.end(); ++it) {
species_kmers[it->first].merge(&(it->second));
}
for(map<IDs, uint64_t>::const_iterator itr = met.observed.begin(); itr != met.observed.end(); itr++) {
const IDs& ids = itr->first;
uint64_t count = itr->second;
if(observed.find(ids) == observed.end()) {
observed[ids] = count;
} else {
observed[ids] += count;
}
}
}
void addSpeciesCounts(
uint64_t taxID,
int64_t score,
int64_t max_score,
double summed_hit_len,
double weighted_read,
uint32_t nresult)
{
species_counts[taxID].n_reads += 1;
species_counts[taxID].sum_score += 1;
species_counts[taxID].weighted_reads += weighted_read;
species_counts[taxID].summed_hit_len += summed_hit_len;
if(nresult == 1) {
species_counts[taxID].n_unique_reads += 1;
}
// Only consider good hits for abundance analysis
// DK - for debugging purposes
if(score >= max_score) {
cur_ids.ids.push_back(taxID);
if(cur_ids.ids.size() == nresult) {
cur_ids.ids.sort();
if(observed.find(cur_ids) == observed.end()) {
observed[cur_ids] = 1;
} else {
observed[cur_ids] += 1;
}
cur_ids.ids.clear();
}
}
}
void addAllKmers(
uint64_t taxID,
const BTDnaString &btdna,
size_t begin,
size_t len) {
#ifdef FLORIAN_DEBUG
cerr << "add all kmers for " << taxID << " from " << begin << " for " << len << ": " << string(btdna.toZBuf()).substr(begin,len) << endl;
#endif
uint64_t kmer = btdna.int_kmer<uint64_t>(begin,begin+len);
species_kmers[taxID].add(kmer);
size_t i = begin;
while (i+32 < len) {
kmer = btdna.next_kmer(kmer,i);
species_kmers[taxID].add(kmer);
++i;
}
}
size_t nDistinctKmers(uint64_t taxID) {
return(species_kmers[taxID].cardinality());
}
static void EM(
const map<IDs, uint64_t>& observed,
const map<uint64_t, EList<uint64_t> >& ancestors,
const map<uint64_t, uint64_t>& tid_to_num,
const EList<double>& p,
EList<double>& p_next,
const EList<size_t>& len)
{
assert_eq(p.size(), len.size());
// E step
p_next.fill(0.0);
// for each assigned read set
for(map<IDs, uint64_t>::const_iterator itr = observed.begin(); itr != observed.end(); itr++) {
const EList<uint64_t, 5>& ids = itr->first.ids; // all ids assigned to the read set
uint64_t count = itr->second; // number of reads in the read set
double psum = 0.0;
for(size_t i = 0; i < ids.size(); i++) {
uint64_t tid = ids[i];
// Leaves?
map<uint64_t, uint64_t>::const_iterator id_itr = tid_to_num.find(tid);
if(id_itr != tid_to_num.end()) {
uint64_t num = id_itr->second;
assert_lt(num, p.size());
psum += p[num];
} else { // Ancestors
map<uint64_t, EList<uint64_t> >::const_iterator a_itr = ancestors.find(tid);
if(a_itr == ancestors.end())
continue;
const EList<uint64_t>& children = a_itr->second;
for(size_t c = 0; c < children.size(); c++) {
uint64_t c_tid = children[c];
map<uint64_t, uint64_t>::const_iterator id_itr = tid_to_num.find(c_tid);
if(id_itr == tid_to_num.end())
continue;
uint64_t c_num = id_itr->second;
psum += p[c_num];
}
}
}
if(psum == 0.0) continue;
for(size_t i = 0; i < ids.size(); i++) {
uint64_t tid = ids[i];
// Leaves?
map<uint64_t, uint64_t>::const_iterator id_itr = tid_to_num.find(tid);
if(id_itr != tid_to_num.end()) {
uint64_t num = id_itr->second;
assert_leq(p[num], psum);
p_next[num] += (count * (p[num] / psum));
} else {
map<uint64_t, EList<uint64_t> >::const_iterator a_itr = ancestors.find(tid);
if(a_itr == ancestors.end())
continue;
const EList<uint64_t>& children = a_itr->second;
for(size_t c = 0; c < children.size(); c++) {
uint64_t c_tid = children[c];
map<uint64_t, uint64_t>::const_iterator id_itr = tid_to_num.find(c_tid);
if(id_itr == tid_to_num.end())
continue;
uint64_t c_num = id_itr->second;
p_next[c_num] += (count * (p[c_num] / psum));
}
}
}
}
// M step
double sum = 0.0;
for(size_t i = 0; i < p_next.size(); i++) {
sum += (p_next[i] / len[i]);
}
for(size_t i = 0; i < p_next.size(); i++) {
p_next[i] = p_next[i] / len[i] / sum;
}
}
void calculateAbundance(const Ebwt<uint64_t>& ebwt, uint8_t rank)
{
const map<uint64_t, TaxonomyNode>& tree = ebwt.tree();
// Find leaves
set<uint64_t> leaves;
for(map<IDs, uint64_t>::iterator itr = observed.begin(); itr != observed.end(); itr++) {
const IDs& ids = itr->first;
for(size_t i = 0; i < ids.ids.size(); i++) {
uint64_t tid = ids.ids[i];
map<uint64_t, TaxonomyNode>::const_iterator tree_itr = tree.find(tid);
if(tree_itr == tree.end())
continue;
const TaxonomyNode& node = tree_itr->second;
if(!node.leaf) {
//if(tax_rank_num[node.rank] > tax_rank_num[rank]) {
continue;
//}
}
leaves.insert(tree_itr->first);
}
}
#ifdef DAEHWAN_DEBUG
cerr << "\t\tnumber of leaves: " << leaves.size() << endl;
#endif
// Find all descendants coming from the same ancestor
map<uint64_t, EList<uint64_t> > ancestors;
for(map<IDs, uint64_t>::iterator itr = observed.begin(); itr != observed.end(); itr++) {
const IDs& ids = itr->first;
for(size_t i = 0; i < ids.ids.size(); i++) {
uint64_t tid = ids.ids[i];
if(leaves.find(tid) != leaves.end())
continue;
if(ancestors.find(tid) != ancestors.end())
continue;
ancestors[tid].clear();
for(set<uint64_t> ::const_iterator leaf_itr = leaves.begin(); leaf_itr != leaves.end(); leaf_itr++) {
uint64_t tid2 = *leaf_itr;
assert(tree.find(tid2) != tree.end());
assert(tree.find(tid2)->second.leaf);
uint64_t temp_tid2 = tid2;
while(true) {
map<uint64_t, TaxonomyNode>::const_iterator tree_itr = tree.find(temp_tid2);
if(tree_itr == tree.end())
break;
const TaxonomyNode& node = tree_itr->second;
if(tid == node.parent_tid) {
ancestors[tid].push_back(tid2);
}
if(temp_tid2 == node.parent_tid)
break;
temp_tid2 = node.parent_tid;
}
}
ancestors[tid].sort();
}
}
#ifdef DAEHWAN_DEBUG
cerr << "\t\tnumber of ancestors: " << ancestors.size() << endl;
for(map<uint64_t, EList<uint64_t> >::const_iterator itr = ancestors.begin(); itr != ancestors.end(); itr++) {
uint64_t tid = itr->first;
const EList<uint64_t>& children = itr->second;
if(children.size() <= 0)
continue;
map<uint64_t, TaxonomyNode>::const_iterator tree_itr = tree.find(tid);
if(tree_itr == tree.end())
continue;
const TaxonomyNode& node = tree_itr->second;
cerr << "\t\t\t" << tid << ": " << children.size() << "\t" << get_tax_rank(node.rank) << endl;
cerr << "\t\t\t\t";
for(size_t i = 0; i < children.size(); i++) {
cerr << children[i];
if(i + 1 < children.size())
cerr << ",";
if(i > 10) {
cerr << " ...";
break;
}
}
cerr << endl;
}
uint64_t test_tid = 0, test_tid2 = 0;
#endif
// Lengths of genomes (or contigs)
const map<uint64_t, uint64_t>& size_table = ebwt.size();
// Initialize probabilities
map<uint64_t, uint64_t> tid_to_num; // taxonomic ID to corresponding element of a list
EList<double> p;
EList<size_t> len; // genome lengths
for(map<IDs, uint64_t>::iterator itr = observed.begin(); itr != observed.end(); itr++) {
const IDs& ids = itr->first;
uint64_t count = itr->second;
for(size_t i = 0; i < ids.ids.size(); i++) {
uint64_t tid = ids.ids[i];
if(leaves.find(tid) == leaves.end())
continue;
#ifdef DAEHWAN_DEBUG
if((tid == test_tid || tid == test_tid2) &&
count >= 100) {
cerr << tid << ": " << count << "\t";
for(size_t j = 0; j < ids.ids.size(); j++) {
cerr << ids.ids[j];
if(j + 1 < ids.ids.size())
cerr << ",";
}
cerr << endl;
}
#endif
if(tid_to_num.find(tid) == tid_to_num.end()) {
tid_to_num[tid] = p.size();
p.push_back(1.0 / ids.ids.size() * count);
map<uint64_t, uint64_t>::const_iterator size_itr = size_table.find(tid);
if(size_itr != size_table.end()) {
len.push_back(size_itr->second);
} else {
len.push_back(std::numeric_limits<size_t>::max());
}
} else {
uint64_t num = tid_to_num[tid];
assert_lt(num, p.size());
p[num] += (1.0 / ids.ids.size() * count);
}
}
}
assert_eq(p.size(), len.size());
{
double sum = 0.0;
for(size_t i = 0; i < p.size(); i++) {
sum += (p[i] / len[i]);
}
for(size_t i = 0; i < p.size(); i++) {
p[i] = (p[i] / len[i]) / sum;
}
}
EList<double> p_next; p_next.resizeExact(p.size());
EList<double> p_next2; p_next2.resizeExact(p.size());
EList<double> p_r; p_r.resizeExact(p.size());
EList<double> p_v; p_v.resizeExact(p.size());
size_t num_iteration = 0;
double diff = 0.0;
while(true) {
#ifdef DAEHWAN_DEBUG
if(num_iteration % 50 == 0) {
if(test_tid != 0 || test_tid2 != 0)
cerr << "iter " << num_iteration << endl;
if(test_tid != 0)
cerr << "\t" << test_tid << ": " << p[tid_to_num[test_tid]] << endl;
if(test_tid2 != 0)
cerr << "\t" << test_tid2 << ": " << p[tid_to_num[test_tid2]] << endl;
}
#endif
// Accelerated version of EM - SQUAREM iteration
// Varadhan, R. & Roland, C. Scand. J. Stat. 35, 335–353 (2008).
// Also, this algorithm is used in Sailfish - http://www.nature.com/nbt/journal/v32/n5/full/nbt.2862.html
#if 1
EM(observed, ancestors, tid_to_num, p, p_next, len);
EM(observed, ancestors, tid_to_num, p_next, p_next2, len);
double sum_squared_r = 0.0, sum_squared_v = 0.0;
for(size_t i = 0; i < p.size(); i++) {
p_r[i] = p_next[i] - p[i];
sum_squared_r += (p_r[i] * p_r[i]);
p_v[i] = p_next2[i] - p_next[i] - p_r[i];
sum_squared_v += (p_v[i] * p_v[i]);
}
if(sum_squared_v > 0.0) {
double gamma = -sqrt(sum_squared_r / sum_squared_v);
for(size_t i = 0; i < p.size(); i++) {
p_next2[i] = max(0.0, p[i] - 2 * gamma * p_r[i] + gamma * gamma * p_v[i]);
}
EM(observed, ancestors, tid_to_num, p_next2, p_next, len);
}
#else
EM(observed, ancestors, tid_to_num, p, p_next, len);
#endif
diff = 0.0;
for(size_t i = 0; i < p.size(); i++) {
diff += (p[i] > p_next[i] ? p[i] - p_next[i] : p_next[i] - p[i]);
}
if(diff < 0.0000000001) break;
if(++num_iteration >= 10000) break;
p = p_next;
}
cerr << "Number of iterations in EM algorithm: " << num_iteration << endl;
cerr << "Probability diff. (P - P_prev) in the last iteration: " << diff << endl;
{
// Calculate abundance normalized by genome size
abundance_len.clear();
double sum = 0.0;
for(map<uint64_t, uint64_t>::iterator itr = tid_to_num.begin(); itr != tid_to_num.end(); itr++) {
uint64_t tid = itr->first;
uint64_t num = itr->second;
assert_lt(num, p.size());
abundance_len[tid] = p[num];
sum += (p[num] * len[num]);
}
// Calculate abundance without genome size taken into account
abundance.clear();
for(map<uint64_t, uint64_t>::iterator itr = tid_to_num.begin(); itr != tid_to_num.end(); itr++) {
uint64_t tid = itr->first;
uint64_t num = itr->second;
assert_lt(num, p.size());
abundance[tid] = (p[num] * len[num]) / sum;
}
}
}
map<uint64_t, ReadCounts> species_counts; // read count per species
map<uint64_t, HyperLogLogPlusMinus<uint64_t> > species_kmers; // unique k-mer count per species
map<IDs, uint64_t> observed;
IDs cur_ids;
uint32_t num_non_leaves;
map<uint64_t, double> abundance; // abundance without genome size taken into consideration
map<uint64_t, double> abundance_len; // abundance normalized by genome size
MUTEX_T mutex_m;
};
/**
* 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);
}
void init(
uint64_t nread_,
uint64_t npaired_,
uint64_t nunpaired_,
uint64_t nconcord_uni_)
{
nread = nread_;
npaired = npaired_;
nunpaired = nunpaired_;
nconcord_uni = nconcord_uni_;
}
/**
* 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;
}
uint64_t nread; // # reads
uint64_t npaired; // # pairs
uint64_t nunpaired; // # unpaired reads
// Paired
// Concordant
uint64_t nconcord_uni; // # pairs with unique concordant alns
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_, bool compressed_)
{
init(khits_, compressed_);
}
void init(THitInt khits_, bool compressed_)
{
khits = khits_; // -k (or high if -a)
if(compressed_) {
ihits = max<THitInt>(khits, 5) * 4;
} else {
ihits = max<THitInt>(khits, 5) * 40;
}
}
#ifndef NDEBUG
/**
* Check that reporting parameters are internally consistent.
*/
bool repOk() const {
assert_geq(khits, 1);
return true;
}
#endif
inline THitInt mult() const {
return khits;
}
// Number of assignments to report
THitInt khits;
// Number of internal assignments
THitInt ihits;
};
/**
* 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
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_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;
doneConcord_ = false;
exitConcord_ = 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) const; // # concordant alignments to report
/**
* 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_; }
/**
* Return true iff all alignment stages have been exited.
*/
inline bool done() const { return done_; }
inline uint64_t numConcordant() const { return nconcord_; }
inline int exitConcordant() const { return exitConcord_; }
/**
* Return ReportingParams object governing this ReportingState.
*/
const ReportingParams& params() const {
return p_;
}
protected:
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
bool doneConcord_; // true iff we're no longner interested in concordants
int exitConcord_; // flag indicating how we exited concordant 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 EList<uint32_t>& tab_fmt_cols,
bool quiet) :
oq_(oq),
refnames_(refnames),
tab_fmt_cols_(tab_fmt_cols),
quiet_(quiet)
{
}
/**
* 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,
size_t threadId,
const Read *rd1,
const Read *rd2,
const TReadId rdid,
AlnRes *rs1,
AlnRes *rs2,
const AlnSetSumm& summ,
const PerReadMetrics& prm,
SpeciesMetrics& sm,
bool report2,
size_t n_results) = 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
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 PerReadMetrics& prm, // per-read metrics
SpeciesMetrics& sm, // species metrics
bool getLock = true) // true iff lock held by caller
{
assert(rd1 != NULL || rd2 != NULL);
assert(rs1 != NULL || rs2 != NULL);
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, threadId, rd1, rd2, rdid, r1, r2, summ, prm, sm, true, select1.size());
}
}
/**
* 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
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 PerReadMetrics& prm, // per-read metrics
bool report2, // report alns for both mates?
bool getLock = true) // true iff lock held by caller
{
// FIXME: reportUnaligned does nothing
//append(o, threadId, rd1, rd2, rdid, NULL, NULL, summ, prm, NULL,report2);
}
/**
* Print summary of how many reads aligned, failed to align and aligned
* repetitively. Write it to stderr. Optionally write Hadoop counter
* updates.
*/
void printAlSumm(
const ReportingMetrics& met,
size_t repThresh, // threshold for uniqueness, or max if no thresh
bool discord, // looked for discordant alignments
bool mixed, // looked for unpaired alignments where paired failed?
bool hadoopOut); // output Hadoop counters?
/**
* Called when all alignments are complete. It is assumed that no
* synchronization is necessary.
*/
void finish(
size_t repThresh,
bool discord,
bool mixed,
bool hadoopOut)
{
// Close output streams
if(!quiet_) {
printAlSumm(
met_,
repThresh,
discord,
mixed,
hadoopOut);
}
}
#ifndef NDEBUG
/**
* Check that hit sink is internally consistent.
*/
bool repOk() const { return true; }
#endif
//
// Related to reporting seed hits
//
/**
* Given a Read and associated, filled-in SeedResults objects,
* print a record summarizing the seed hits.
*/
void reportSeedSummary(
BTString& o,
const Read& rd,
TReadId rdid,
size_t threadId,
const SeedResults<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 EList<uint32_t>& tab_fmt_cols_; // Columns that are printed in tabular format
bool quiet_; // true -> don't print alignment stats at the end
ReportingMetrics met_; // global repository of reporting metrics
};
/**
* Per-thread hit sink "wrapper" for the MultiSeed aligner. Encapsulates
* aspects of the MultiSeed aligner hit sink that are per-thread. This
* includes aspects relating to:
*
* (a) Enforcement of the reporting policy
* (b) Tallying of results
* (c) Storing of results for the previous read in case this allows us to
* short-circuit some work for the next read (i.e. if it's identical)
*
* PHASED ALIGNMENT ASSUMPTION
*
* We make some assumptions about how alignment proceeds when we try to
* short-circuit work for identical reads. Specifically, we assume that for
* each read the aligner proceeds in a series of stages (or perhaps just one
* stage). In each stage, the aligner either:
*
* (a) Finds no alignments, or
* (b) Finds some alignments and short circuits out of the stage with some
* random reporting involved (e.g. in -k and/or -M modes), or
* (c) Finds all of the alignments in the stage
*
* In the event of (a), the aligner proceeds to the next stage and keeps
* trying; we can skip the stage entirely for the next read if it's identical.
* In the event of (b), or (c), the aligner stops and does not proceed to
* further stages. In the event of (b1), if the next read is identical we
* would like to tell the aligner to start again at the beginning of the stage
* that was short-circuited.
*
* In any event, the rs1_/rs2_/rs1u_/rs2u_ fields contain the alignments found
* in the last alignment stage attempted.
*
* HANDLING REPORTING LIMITS
*
* The user can specify reporting limits, like -k (specifies number of
* alignments to report out of those found) and -M (specifies a ceiling s.t. if
* there are more alignments than the ceiling, read is called repetitive and
* best found is reported). Enforcing these limits is straightforward for
* unpaired alignments: if a new alignment causes us to exceed the -M ceiling,
* we can stop looking.
*
* The case where both paired-end and unpaired alignments are possible is
* trickier. Once we have a number of unpaired alignments that exceeds the
* ceiling, we can stop looking *for unpaired alignments* - but we can't
* necessarily stop looking for paired-end alignments, since there may yet be
* more to find. However, if the input read is not a pair, then we can stop at
* this point. If the input read is a pair and we have a number of paired
* aligments that exceeds the -M ceiling, we can stop looking.
*
* CONCORDANT & DISCORDANT, PAIRED & UNPAIRED
*
* A note on paired-end alignment: Clearly, if an input read is
* paired-end and we find either concordant or discordant paired-end
* alignments for the read, then we would like to tally and report
* those alignments as such (and not as groups of 2 unpaired
* alignments). And if we fail to find any paired-end alignments, but
* we do find some unpaired alignments for one mate or the other, then
* we should clearly tally and report those alignments as unpaired
* alignments (if the user so desires).
*
* The situation is murkier when there are no paired-end alignments,
* but there are unpaired alignments for *both* mates. In this case,
* we might want to pick out zero or more pairs of mates and classify
* those pairs as discordant paired-end alignments. And we might want
* to classify the remaining alignments as unpaired. But how do we
* pick which pairs if any to call discordant?
*
* Because the most obvious use for discordant pairs is for identifying
* large-scale variation, like rearrangements or large indels, we would
* usually like to be conservative about what we call a discordant
* alignment. If there's a good chance that one or the other of the
* two mates has a good alignment to another place on the genome, this
* compromises the evidence for the large-scale variant. For this
* reason, Bowtie 2's policy is: if there are no paired-end alignments
* and there is *exactly one alignment each* for both mates, then the
* two alignments are paired and treated as a discordant paired-end
* alignment. Otherwise, all alignments are treated as unpaired
* alignments.
*
* When both paired and unpaired alignments are discovered by the
* aligner, only the paired alignments are reported by default. This
* is sensible considering relative likelihoods: if a good paired-end
* alignment is found, it is much more likely that the placement of
* the two mates implied by that paired alignment is correct than any
* placement implied by an unpaired alignment.
*
*
*/
template <typename index_t>
class AlnSinkWrap {
public:
AlnSinkWrap(
AlnSink<index_t>& g, // AlnSink being wrapped
const ReportingParams& rp, // Parameters governing reporting
size_t threadId, // Thread ID
bool secondary = false) : // Secondary alignments
g_(g),
rp_(rp),
threadid_(threadId),
secondary_(secondary),
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
rs_(), // mate 1 alignments for paired-end alignments
select_(), // for selecting random subsets for mate 1
st_(rp) // reporting state - what's left to do?
{
assert(rp_.repOk());
}
AlnSink<index_t>& getSink() {
return(g_);
}
/**
* 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
SpeciesMetrics& smet, // species metrics
const PerReadMetrics& prm, // per-read metrics
bool suppressSeedSummary = true,
bool suppressAlignments = false);
/**
* Called by the aligner when a new unpaired or paired alignment is
* discovered in the given stage. This function checks whether the
* addition of this alignment causes the reporting policy to be
* violated (by meeting or exceeding the limits set by -k, -m, -M),
* in which case true is returned immediately and the aligner is
* short circuited. Otherwise, the alignment is tallied and false
* is returned.
*/
bool report(
int stage,
const AlnRes* rs);
#ifndef NDEBUG
/**
* Check that hit sink wrapper is internally consistent.
*/
bool repOk() const {
if(init_) {
assert(rd1_ != NULL);
assert_neq(std::numeric_limits<TReadId>::max(), rdid_);
}
return true;
}
#endif
/**
* Return true iff no alignments have been reported to this wrapper
* since the last call to nextRead().
*/
bool empty() const {
return rs_.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_;}
SpeciesMetrics& speciesMetrics() { return g_.speciesMetrics(); }
/**
* 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_;
}
/**
*
*/
void getPair(const EList<AlnRes>*& rs) const { rs = &rs_; }
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);
/**
* 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>* rs, // alignments to select from (mate 1)
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
bool secondary_; // allow for secondary alignments
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> rs_; // paired alignments for mate #1
EList<size_t> select_; // 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_;
};
/**
* 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(
Ebwt<index_t>* ebwt,
OutputQueue& oq, // output queue
const StrList& refnames, // reference names
const EList<uint32_t>& tab_fmt_cols, // columns to output in the tabular format
bool quiet) :
AlnSink<index_t>(oq,
refnames,
tab_fmt_cols,
quiet),
ebwt_(ebwt)
{ }
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
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 PerReadMetrics& prm, // per-read metrics
SpeciesMetrics& sm, // species metrics
bool report2, // report alns for both mates
size_t n_results) // number of results for read
{
assert(rd1 != NULL || rd2 != NULL);
appendMate(*ebwt_, o, *rd1, rd2, rdid, rs1, rs2, summ, prm, sm, n_results);
}
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(
Ebwt<index_t>& ebwt,
BTString& o,
const Read& rd,
const Read* rdo,
const TReadId rdid,
AlnRes* rs,
AlnRes* rso,
const AlnSetSumm& summ,
const PerReadMetrics& prm, // per-read metrics
SpeciesMetrics& sm, // species metrics
size_t n_results);
Ebwt<index_t>* ebwt_;
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(
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
#if 0
bool canRep = repThresh != MAX_SIZE_T;
if(hadoopOut) {
cerr << "reporter:counter:Centrifuge,Reads processed," << met.nread << endl;
}
uint64_t totread = met.nread;
if(totread > 0) {
cerr << "" << met.nread << " reads (or pairs); of these:" << endl;
} else {
assert_eq(0, met.npaired);
assert_eq(0, met.nunpaired);
cerr << "" << totread << " reads (or pairs)" << endl;
}
if(totread > 0) {
// Concordants
cerr << " " << met.nconcord << " (";
printPct(cerr, met.nconcord, met.npaired);
cerr << ") classified 0 times" << endl;
// Print the number that aligned concordantly exactly once
cerr << " " << met.nconcord_uni << " (";
printPct(cerr, met.nconcord_uni, met.npaired);
cerr << ") classified exactly 1 time" << endl;
#if 0
// Print the number that aligned concordantly more than once
cerr << " " << met.nconcord_uni2 << " (";
printPct(cerr, met.nconcord_uni2, met.npaired);
cerr << ") classified >1 times" << endl;
#endif
}
#if 0
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);
printPct(cerr, tot_al, tot_al_cand);
#endif
cerr << " overall classification rate" << endl;
#endif
}
/**
* 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;
rs_.clear(); // clear out paired-end alignments
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
SpeciesMetrics& smet, // species metrics
const PerReadMetrics& prm, // per-read metrics
bool suppressSeedSummary, // = true
bool suppressAlignments) // = 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);
}
}
// TODO FB: Cconsider counting species here, and allow to disable counting
if(!suppressAlignments) {
// Ask the ReportingState what to report
st_.finish();
uint64_t nconcord = 0;
bool pairMax = false;
st_.getReport(nconcord);
assert_leq(nconcord, rs_.size());
assert_gt(rp_.khits, 0);
met.nread++;
if(readIsPair()) {
met.npaired++;
} else {
met.nunpaired++;
}
// Report concordant paired-end alignments if possible
if(nconcord > 0) {
AlnSetSumm concordSumm(rd1_, rd2_, &rs_);
// Possibly select a random subset
size_t off;
if(sortByScore) {
// Sort by score then pick from low to high
off = selectByScore(&rs_, nconcord, select_, rnd);
} else {
// Select subset randomly
off = selectAlnsToReport(rs_, nconcord, select_, rnd);
}
assert_lt(off, rs_.size());
_unused(off); // make production build happy
assert(!select_.empty());
g_.reportHits(
obuf_,
threadid_,
rd1_,
rd2_,
rdid_,
select_,
NULL,
&rs_,
NULL,
pairMax,
concordSumm,
prm,
smet);
if(pairMax) {
// met.nconcord_rep++;
} else {
met.nconcord_uni++;
assert(!rs_.empty());
if(rs_.size() == 1) {
// met.nconcord_uni1++;
} else {
// met.nconcord_uni2++;
}
}
init_ = false;
// write read to file
//g_.outq().finishRead(obuf_, rdid_, threadid_);
return;
}
#if 0
// 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++;
} 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(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) {
// 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++;
}
}
#endif
} // 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* rs)
{
assert(init_);
assert(rs != NULL);
st_.foundConcordant();
rs_.push_back(*rs);
// Tally overall alignment score
TAlScore score = rs->score();
// Update best score so far
if(score > bestPair_) {
best2Pair_ = bestPair_;
bestPair_ = score;
} else if(score > best2Pair_) {
best2Pair_ = score;
}
return st_.done();
}
/**
* 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>* rs, // alignments to select from (mate 1)
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(rs != NULL);
size_t sz = rs->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 = (*rs)[i].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);
}
for(size_t i = 0; i < num; i++) { select[i] = buf[i].second; }
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); \
}
#define WRITE_STRING(o, x) { \
o.append(x.c_str()); \
}
template <typename T> inline
void appendNumber(BTString& o, const T x, char* buf) {
itoa10<T>(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)
{
#if 0
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
#endif
}
/**
* 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');
}
inline
void appendReadID(BTString& o, const BTString & rd_name) {
size_t namelen = rd_name.length();
if(namelen >= 2 &&
rd_name[namelen-2] == '/' &&
(rd_name[namelen-1] == '1' || rd_name[namelen-1] == '2' || rd_name[namelen-1] == '3'))
{
namelen -= 2;
}
for(size_t i = 0; i < namelen; i++) {
if(isspace(rd_name[i])) {
break;
}
o.append(rd_name[i]);
}
}
inline
void appendSeqID(BTString& o, const AlnRes* rs, const std::map<uint64_t, TaxonomyNode>& tree) {
bool leaf = true;
std::map<uint64_t, TaxonomyNode>::const_iterator itr = tree.find(rs->taxID());
if(itr != tree.end()) {
const TaxonomyNode& node = itr->second;
leaf = node.leaf;
}
// unique ID
if(leaf) {
o.append(rs->uid().c_str());
} else {
o.append(get_tax_rank_string(rs->taxRank()));
}
}
inline
void appendTaxID(BTString& o, uint64_t tid) {
char buf[1024];
uint64_t tid1 = tid & 0xffffffff;
uint64_t tid2 = tid >> 32;
itoa10<int64_t>(tid1, buf);
o.append(buf);
if(tid2 > 0) {
o.append(".");
itoa10<int64_t>(tid2, buf);
o.append(buf);
}
}
enum FIELD_DEF {
PLACEHOLDER=0,
PLACEHOLDER_STAR,
PLACEHOLDER_ZERO,
READ_ID,
SEQ_ID,
TAX_ID,
TAX_RANK,
TAX_NAME,
SCORE,
SCORE2,
HIT_LENGTH,
QUERY_LENGTH,
NUM_MATCHES,
SEQ,
SEQ1,
SEQ2,
QUAL,
QUAL1,
QUAL2
};
/**
* Append a single hit to the given output stream in Bowtie's
* verbose-mode format.
*/
template <typename index_t>
void AlnSinkSam<index_t>::appendMate(
Ebwt<index_t>& ebwt,
BTString& o, // append to this string
const Read& rd,
const Read* rdo,
const TReadId rdid,
AlnRes* rs,
AlnRes* rso,
const AlnSetSumm& summ,
const PerReadMetrics& prm,
SpeciesMetrics& sm,
size_t n_results)
{
if(rs == NULL) {
return;
}
char buf[1024];
bool firstfield = true;
uint64_t taxid = rs->taxID();
const basic_string<char> empty_string = "";
for (int i=0; i < this->tab_fmt_cols_.size(); ++i) {
BEGIN_FIELD;
switch (this->tab_fmt_cols_[i]) {
case READ_ID: appendReadID(o, rd.name); break;
case SEQ_ID: appendSeqID(o, rs, ebwt.tree()); break;
case SEQ: o.append((string(rd.patFw.toZBuf()) +
(rdo == NULL? "" : "_" + string(rdo->patFw.toZBuf()))).c_str()); break;
case QUAL: o.append((string(rd.qual.toZBuf()) +
(rdo == NULL? "" : "_" + string(rdo->qual.toZBuf()))).c_str()); break;
case SEQ1: o.append(rd.patFw.toZBuf()); break;
case QUAL1: o.append(rd.qual.toZBuf()); break;
case SEQ2: o.append(rdo == NULL? empty_string.c_str() : rdo->patFw.toZBuf()); break;
case QUAL2: o.append(rdo == NULL? empty_string.c_str() : rdo->qual.toZBuf()); break;
case TAX_ID: appendTaxID(o, taxid); break;
case TAX_RANK: o.append(get_tax_rank_string(rs->taxRank())); break;
case TAX_NAME: o.append(find_or_use_default(ebwt.name(), taxid, empty_string).c_str()); break;
case SCORE: appendNumber<uint64_t>(o, rs->score(), buf); break;
case SCORE2: appendNumber<uint64_t>(o,
(summ.secbest().valid()? summ.secbest().score() : 0),
buf); break;
case HIT_LENGTH: appendNumber<uint64_t>(o, rs->summedHitLen(), buf); break;
case QUERY_LENGTH: appendNumber<uint64_t>(o,
(rd.patFw.length() + (rdo != NULL ? rdo->patFw.length() : 0)),
buf); break;
case NUM_MATCHES: appendNumber<uint64_t>(o, n_results, buf); break;
case PLACEHOLDER: o.append("");
case PLACEHOLDER_STAR: o.append("*");
case PLACEHOLDER_ZERO: o.append("0");
default: ;
}
}
o.append("\n");
// species counting
sm.addSpeciesCounts(
rs->taxID(),
rs->score(),
rs->max_score(),
rs->summedHitLen(),
1.0 / n_results,
(uint32_t)n_results);
// only count k-mers if the read is unique
if (n_results == 1) {
for (size_t i = 0; i< rs->nReadPositions(); ++i) {
sm.addAllKmers(rs->taxID(),
rs->isFw()? rd.patFw : rd.patRc,
rs->readPositions(i).first,
rs->readPositions(i).second);
}
}
// (sc[rs->speciesID_])++;
}
// #include <iomanip>
/**
* 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;
state_ = CONCORDANT_PAIRS;
doneConcord_ = false;
exitConcord_ = ReportingState::EXIT_DID_NOT_EXIT;
done_ = false;
nconcord_ = 0;
}
/**
* Caller uses this member function to indicate that one additional
* concordant alignment has been found.
*/
bool ReportingState::foundConcordant() {
assert_geq(state_, ReportingState::CONCORDANT_PAIRS);
assert(!doneConcord_);
nconcord_++;
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_);
}
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) {
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);
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) const // # concordant alignments to report
{
nconcordAln = 0;
assert_gt(p_.khits, 0);
// 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_WITH_ALIGNMENTS) {
assert_gt(nconcord_, 0);
// <= k at random
nconcordAln = min<uint64_t>(nconcord_, p_.khits);
return;
}
}
#if 0
/**
* 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;
}
}
#endif
#endif /*ndef ALN_SINK_H_*/
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