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papara.cpp
1737 lines (1206 loc) · 56.4 KB
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papara.cpp
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/*
* Copyright (C) 2009-2012 Simon A. Berger
*
* This file is part of papara.
*
* papara 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.
*
* papara 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 papara. If not, see <http://www.gnu.org/licenses/>.
*/
#include <stdint.h>
#include <iomanip>
#include <boost/bind.hpp>
#include <boost/dynamic_bitset.hpp>
#include <iterator>
#include "ivymike/fasta.h"
#include "ivymike/demangle.h"
#include "ivymike/time.h"
#include "papara.h"
#include "vec_unit.h"
#include "align_pvec_vec.h"
#include "stepwise_align.h"
#include "align_utils.h"
using namespace ivy_mike;
using namespace ivy_mike::tree_parser_ms;
using namespace papara;
bool papara::g_dump_aux = false;
class log_stream_buffer : public std::streambuf
{
public:
log_stream_buffer() : buffer_(120) {
}
void post( char overflow, char *start, char *end ) {
for( std::vector< std::ostream* >::iterator it = log_tees.begin(); it != log_tees.end(); ++it ) {
std::copy( start, end, std::ostream_iterator<char>( *(*it) ));
if( overflow != 0 ) {
(*it)->put(overflow);
}
}
for( std::vector< log_sink* >::iterator it = log_sinks.begin(); it != log_sinks.end(); ++it ) {
(*it)->post( overflow, start, end );
}
}
int_type overflow(int c) {
post( c, pbase(), epptr() );
setp(&buffer_.front(), (&buffer_.back()) + 1);
return 1;
}
int sync() {
// std::cout << "sync:";
// std::copy( pbase(), pptr(), std::ostream_iterator<char>(std::cout));
// std::cout << std::endl;
post( 0, pbase(), pptr() );
setp(&buffer_.front(), (&buffer_.back()) + 1);
return 0;
}
void add_tee( std::ostream *os ) {
log_tees.push_back(os);
}
void remove_tee( std::ostream *os ) {
std::vector<std::ostream *>::iterator it = std::find( log_tees.begin(), log_tees.end(), os );
if( it != log_tees.end() ) {
log_tees.erase(it);
}
}
void add_sink( log_sink *s ) {
log_sinks.push_back(s);
}
void remove_sink( log_sink *s ) {
std::vector<log_sink *>::iterator it = std::find( log_sinks.begin(), log_sinks.end(), s );
if( it != log_sinks.end() ) {
log_sinks.erase(it);
}
}
private:
// copy ctor and assignment not implemented;
// copying not allowed
log_stream_buffer(const log_stream_buffer &);
log_stream_buffer &operator= (const log_stream_buffer &);
std::vector<char> buffer_;
std::vector<std::ostream *> log_tees;
std::vector<log_sink *> log_sinks;
};
// // lifted from http://www.horstmann.com/cpp/iostreams.html
// class log_stream_buffer : public std::filebuf
// {
// std::vector<std::ostream *> log_tees;
//
// public:
// log_stream_buffer() {
// //filebuf::open("NUL", ios::out);
// }
//
// void open(const char *fname);
// // void close() {
// // // _win.close(); filebuf::close();
// //
// // }
// virtual int sync();
//
// void add_tee( std::ostream *os ) {
// log_tees.push_back(os);
// }
// void remove_tee( std::ostream *os ) {
// std::vector<std::ostream *>::iterator it = std::find( log_tees.begin(), log_tees.end(), os );
// if( it != log_tees.end() ) {
// log_tees.erase(it);
// }
// }
// private:
//
// };
// void log_stream_buffer::open(const char *fname)
// {
// std::filebuf::close();
// if( fname != 0 ) {
// std::cerr << "log file: " << fname << "\n";
// std::filebuf::open(fname, std::ios::out | std::ios::app | std::ios::trunc );
// assert(std::filebuf::is_open());
// }
//
// }
// int log_stream_buffer::sync()
// {
// // pbase();
// // pptr()
// //
// // int count = std::filebuf::out_waiting();
// // _win.append(pbase(), count);
// std::cerr << "sync: " << std::distance(pbase(), pptr()) << "\n";
// for( std::vector< std::ostream* >::iterator it = log_tees.begin(); it != log_tees.end(); ++it ) {
// std::copy( pbase(), pptr(), std::ostream_iterator<char>( *(*it) ));
// }
// return std::filebuf::sync();
// }
static log_stream_buffer ls_buf;
std::ostream papara::lout(&ls_buf);
static ivy_mike::mutex log_buffer_mutex;
// open_log_file::open_log_file( const char *filename ) {
//
// ivy_mike::lock_guard<ivy_mike::mutex> lock( log_buffer_mutex );
// if( log_is_open ) {
// std::cerr << "papara logfile is already open." << std::endl;
// abort();
// }
//
//
// ls_buf.open(filename);
// log_is_open = true;
// }
// open_log_file::~open_log_file() {
// ivy_mike::lock_guard<ivy_mike::mutex> lock( log_buffer_mutex );
// if( !log_is_open ) {
// std::cerr << "papara logfile is already closed. (This should be impossible) " << std::endl;
// abort();
// }
// ls_buf.close();
// log_is_open = false;
// }
add_log_tee::add_log_tee( std::ostream &os ) : os_(os) {
ivy_mike::lock_guard<ivy_mike::mutex> lock( log_buffer_mutex );
ls_buf.add_tee(&os);
}
add_log_tee::~add_log_tee() {
ivy_mike::lock_guard<ivy_mike::mutex> lock( log_buffer_mutex );
ls_buf.remove_tee(&os_);
}
add_log_sink::add_log_sink( log_sink *s ) : s_(s) {
ivy_mike::lock_guard<ivy_mike::mutex> lock( log_buffer_mutex );
ls_buf.add_sink(s);
}
add_log_sink::~add_log_sink() {
ivy_mike::lock_guard<ivy_mike::mutex> lock( log_buffer_mutex );
ls_buf.remove_sink(s_);
}
std::string papara::get_version_string() {
return std::string( "2.5" );
}
template<typename seq_tag>
queries<seq_tag>::queries( const std::string &opt_qs_name ) {
// if( !opt_qs_name.empty() ) {
//
// read query sequences
//
if( !opt_qs_name.empty() ) {
std::ifstream qsf( opt_qs_name.c_str() );
if( !qsf.good() ) {
throw std::runtime_error( "cannot open qs file");
}
// mix them with the qs from the ref alignment <-- WTF? must have been sniffing whiteboard cleaner... the qs are read before the ref seqs...
read_fasta( qsf, m_qs_names, m_qs_seqs);
}
// if( m_qs_names.empty() ) {
// throw std::runtime_error( "no qs" );
// }
std::for_each( m_qs_names.begin(), m_qs_names.end(), std::ptr_fun( normalize_name ));
//
// setup qs best-score/best-edge lists
//
m_qs_pvecs.resize( m_qs_names.size() );
// }
// m_qs_bestscore.resize(m_qs_names.size());
// std::fill( m_qs_bestscore.begin(), m_qs_bestscore.end(), 32000);
// m_qs_bestedge.resize(m_qs_names.size());
}
template<typename seq_tag>
void queries<seq_tag>::preprocess() {
//
// preprocess query sequences
//
if( m_qs_seqs.empty() ) {
throw std::runtime_error( "no query sequences" );
}
assert( m_qs_seqs.size() == m_qs_names.size() );
m_qs_pvecs.resize(m_qs_seqs.size());
m_qs_cseqs.resize(m_qs_seqs.size());
std::vector<bool> bad_characters( 256, false );
for( size_t i = 0; i < m_qs_seqs.size(); i++ ) {
// seq_to_nongappy_pvec( m_qs_seqs[i], m_qs_pvecs[i] );
// static void seq_to_nongappy_pvec( std::vector<uint8_t> &seq, std::vector<uint8_t> &pvec ) {
// the following line means: transform sequence to pvec using seq_model::s2p as mapping
// function and only append the mapped character into pvec, if it corresponds to a single (=non gap)
// character.
std::vector<uint8_t> qs_tmp;
qs_tmp.reserve( m_qs_seqs[i].size() );
bool bad_char = false;
for( std::vector<uint8_t>::iterator it = m_qs_seqs[i].begin(), e = m_qs_seqs[i].end(); it != e; ++it ) {
if( !seq_model::is_known_sstate( *it ) ) {
bad_characters.at( *it ) = true;
bad_char = true;
} else {
qs_tmp.push_back( *it );
}
}
if( bad_char ) {
m_qs_seqs[i].swap( qs_tmp );
}
std::transform( m_qs_seqs[i].begin(), m_qs_seqs[i].end(),
back_insert_ifer(m_qs_cseqs[i], seq_model::cstate_is_single),
seq_model::s2c );
std::transform( m_qs_seqs[i].begin(), m_qs_seqs[i].end(),
back_insert_ifer(m_qs_pvecs[i], seq_model::pstate_is_single),
seq_model::s2p );
// std::cout << "preprocess: " << i << " " << m_qs_cseqs[i].size() << " " << m_qs_pvecs[i].size() << "\n";
if( m_qs_cseqs[i].size() != m_qs_pvecs[i].size() ) {
// check for quirks related to the p-state vs c-state representation
throw std::runtime_error( "mismatch between lengths of c-state and p-state representations of query sequence." );
}
// for( unsigned int i = 0; i < seq.size(); i++ ) {
// seq_model::pars_state_t ps = seq_model::s2p(seq[i]);
//
// if( seq_model::is_single(ps)) {
// pvec.push_back(ps);
// }
//
// }
}
// print warnings about deleted characters
bool warn_header = false;
for( std::vector<bool>::iterator it = bad_characters.begin(), e = bad_characters.end(); it != e; ++it ) {
if( *it ) {
if( !warn_header ) {
std::cout << "WARNING: there were unsupported characters in the query sequences. They will be deleted:\n";
warn_header = true;
}
std::cout << "deleted character: '" << uint8_t(std::distance( bad_characters.begin(), it )) << "'\n";
}
}
// if( write_testbench ) {
//
// write_qs_pvecs( "qs.bin" );
// write_ref_pvecs( "ref.bin" );
// }
}
// template<typename pvec_t, typename seq_tag>
// void queries<seq_tag>::init_partition_assignments( partassign::part_assignment &part_assign, references<pvec_t,seq_tag> &refs ) {
//
// }
template<typename seq_tag>
void queries<seq_tag>::add( const std::string& name, std::vector< uint8_t >& qs ) {
m_qs_names.push_back(name);
ivy_mike::push_back_swap(m_qs_seqs, qs );
}
template<typename seq_tag>
void queries<seq_tag>::write_pvecs(const char* name) {
std::ofstream os( name );
os << m_qs_pvecs.size();
for( typename std::vector< std::vector< pars_state_t > >::iterator it = m_qs_pvecs.begin(); it != m_qs_pvecs.end(); ++it ) {
os << " " << it->size() << " ";
os.write( (char *)it->data(), it->size() );
}
}
template<typename seq_tag>
size_t queries<seq_tag>::max_name_length() const {
size_t len = 0;
for( std::vector <std::string >::const_iterator it = m_qs_names.begin(); it != m_qs_names.end(); ++it ) {
len = std::max( len, it->size() );
}
return len;
}
template<typename seq_tag>
size_t queries<seq_tag>::calc_cups_per_ref(size_t ref_len) const {
size_t ct = 0;
typename std::vector<std::vector <pars_state_t> >::const_iterator first = m_qs_pvecs.begin();
const typename std::vector<std::vector <pars_state_t> >::const_iterator last = m_qs_pvecs.end();
for(; first != last; ++first ) {
//ct += (ref_len - first->size()) * first->size();
ct += ref_len * first->size(); // papara now uses the 'unbanded' aligner
}
return ct;
}
template<typename seq_tag>
void queries<seq_tag>::normalize_name(std::string& str) {
std::string ns;
// replace runs of one or more whitespaces with an underscores
bool in_ws_run = false;
for( std::string::iterator it = str.begin(); it != str.end(); ++it ) {
if( std::isspace(*it) ) {
if( !in_ws_run ) {
if( (*it) != '\r' ) { // just ignore stupid windows line ends
ns.push_back( '_' );
}
in_ws_run = true;
}
} else {
ns.push_back(*it);
in_ws_run = false;
}
}
str.swap(ns);
}
//////////////////////////////////////////////////////////////
// references stuff
//////////////////////////////////////////////////////////////
template<typename pvec_t, typename seq_tag>
references<pvec_t,seq_tag>::references(const char* opt_tree_name, const char* opt_alignment_name, queries<seq_tag>* qs) : m_ln_pool(new ln_pool( std::unique_ptr<node_data_factory>(new my_fact<my_adata>) )), spg_(pvec_pgap::pgap_model, &pm_)
{
//std::cerr << "papara_nt instantiated as: " << typeid(*this).name() << "\n";
lout << "references container instantiated as: " << ivy_mike::demangle(typeid(*this).name()) << "\n";
// std::cerr << ivy_mike::isa<papara_nt<pvec_cgap> >(*this) << " " << ivy_mike::isa<papara_nt<pvec_pgap> >(*this) << "\n";
// load input data: ref-tree, ref-alignment and query sequences
//
// parse the reference tree
//
ln_pool &pool = *m_ln_pool;
tree_parser_ms::parser tp( opt_tree_name, pool );
tree_parser_ms::lnode * n = tp.parse();
n = towards_tree( n );
tree_ = std::shared_ptr<im_tree_parser::lnode>(n->get_smart_ptr());
//
// create map from tip names to tip nodes
//
typedef tip_collector<lnode> tc_t;
tc_t tc;
visit_lnode( n, tc );
//boost::dynamic_bitset<> found_tree_taxa( tc.m_nodes.size(), true );
std::map<std::string, std::shared_ptr<lnode> > name_to_lnode;
for( std::vector< std::shared_ptr<lnode> >::iterator it = tc.m_nodes.begin(); it != tc.m_nodes.end(); ++it ) {
// std::cout << (*it)->m_data->tipName << "\n";
name_to_lnode[(*it)->m_data->tipName] = *it;
}
{
//
// read reference alignment: store the ref-seqs in the tips of the ref-tree
//
multiple_alignment ref_ma;
ref_ma.load_phylip( opt_alignment_name );
std::vector<my_adata *> tmp_adata;
boost::dynamic_bitset<> unmasked;
for( unsigned int i = 0; i < ref_ma.names.size(); i++ ) {
std::map< std::string, std::shared_ptr<lnode> >::iterator it = name_to_lnode.find(ref_ma.names[i]);
// process sequences from the ref_ma depending on, if they are contained in the tree.
// if they are, they are 'swapped' into m_ref_seqs
// if they are not, into m_qs_seqs. (gaps in the QS are removed later)
//
// additionally, all columns that contain only gaps are removed from the reference sequences.
if( it != name_to_lnode.end() ) {
std::shared_ptr< lnode > ln = it->second;
// adata *ad = ln->m_data.get();
assert( ivy_mike::isa<my_adata>(ln->m_data.get()) ); //typeid(*ln->m_data.get()) == typeid(my_adata ) );
my_adata *adata = static_cast<my_adata *> (ln->m_data.get());
// store the adata ptr corresponding to the current ref sequence for later use.
// (their indices in m_ref_seqs and tmp_adata correspond.)
assert( tmp_adata.size() == m_ref_seqs.size() );
tmp_adata.push_back(adata);
m_ref_names.push_back(std::string() );
m_ref_seqs.push_back(std::vector<uint8_t>() );
m_ref_names.back().swap( ref_ma.names[i] );
m_ref_seqs.back().swap( ref_ma.data[i] );
// mark all non-gap positions of the current reference in bit-vector 'unmasked'
const std::vector<uint8_t> &seq = m_ref_seqs.back();
if( unmasked.empty() ) {
unmasked.resize( seq.size() );
}
assert( unmasked.size() == seq.size() );
for( size_t j = 0, e = seq.size(); j != e; ++j ) {
try {
unmasked[j] |= !seq_model::pstate_is_gap( seq_model::s2p(seq[j]));
} catch( sequence_model::illegal_character x ) {
std::cerr << "illegal character in file '" << opt_alignment_name << "'" << std::endl;
std::cerr << "row: " << i + 1 << " (name: " << m_ref_names.back() << ")" << std::endl;
std::cerr << "col: " << j + 1 << " (char: '" << seq[j] << "')" << std::endl;
abort();
}
}
// erase it from the name to lnode* map, so that it can be used to ideantify tree-taxa without corresponding entries in the alignment
name_to_lnode.erase(it);
} else {
qs->add(ref_ma.names[i], ref_ma.data[i]); // REMARK: the second parameter is 'moved-from' (should be an rvalue-ref)
}
}
if( !name_to_lnode.empty() ) {
std::cerr << "error: there are " << name_to_lnode.size() << " taxa in the tree with no corresponding sequence in the reference alignment. names:\n";
for( std::map< std::string, std::shared_ptr< lnode > >::iterator it = name_to_lnode.begin(); it != name_to_lnode.end(); ++it ) {
std::cout << it->first << "\n";
}
throw std::runtime_error( "bailing out due to inconsitent input data\n" );
}
{
// remove all 'pure-gap' columns from the ref sequences
assert( tmp_adata.size() == m_ref_seqs.size() );
// retrieve a list of non-gap indices from the bit-vector
std::vector<size_t> unmasked_idx;
{
size_t i = unmasked.find_first();
while( i != unmasked.npos ) {
// std::cout << "um: " << i << "\n";
unmasked_idx.push_back(i);
i = unmasked.find_next(i);
}
}
for( size_t i = 0, e = m_ref_seqs.size(); i != e; ++i ) {
std::vector<uint8_t> seq_tmp;
seq_tmp.reserve(unmasked_idx.size());
const std::vector<uint8_t> &seq_orig = m_ref_seqs[i];
// copy all unmasked ref characters to seq_tmp
for( std::vector<size_t>::iterator it = unmasked_idx.begin(); it != unmasked_idx.end(); ++it ) {
assert( *it < seq_orig.size() );
seq_tmp.push_back( seq_orig[*it] );
}
m_ref_seqs[i].swap( seq_tmp );
//initialize the corresponding adata object with the cleaned ref seq.
tmp_adata.at(i)->init_pvec( m_ref_seqs[i] );
}
}
}
pm_.reset( m_ref_seqs );
std::cout << "p: " << pm_.setup_pmatrix(0.1) << "\n";
// initialize empty non-gap map. It is lazily filled as needed when necessary
ref_ng_map_.resize( m_ref_seqs.size() );
//
// collect list of edges
//
visit_edges( n, m_ec );
lout << "edges: " << m_ec.m_edges.size() << "\n";
}
template<typename pvec_t, typename seq_tag>
void references<pvec_t,seq_tag>::build_ref_vecs() {
// pre-create the ancestral state vectors. This step is necessary for the threaded version, because otherwise, each
// thread would need an independent copy of the tree to do concurrent newviews. Anyway, having a copy of the tree
// in each thread will most likely use more memory than storing the pre-calculated vectors.
// TODO: maybe try lazy create/cache of the asv's in the threads
ivy_mike::timer t1;
assert( m_ref_aux.empty() && m_ref_pvecs.empty() );
m_ref_pvecs.reserve( m_ec.m_edges.size() );
m_ref_aux.reserve( m_ec.m_edges.size() );
for( size_t i = 0; i < m_ec.m_edges.size(); i++ ) {
pvec_t root_pvec;
// std::cout << "newview for branch " << i << ": " << *(m_ec.m_edges[i].first->m_data) << " " << *(m_ec.m_edges[i].second->m_data) << "\n";
if( i == 340 ) {
g_dump_aux = true;
}
driver<pvec_t,seq_tag>::do_newview( root_pvec, m_ec.m_edges[i].first, m_ec.m_edges[i].second, true );
g_dump_aux = false;
// TODO: try something fancy with rvalue refs...
m_ref_pvecs.push_back( std::vector<int>() );
m_ref_aux.push_back( std::vector<unsigned int>() );
root_pvec.to_int_vec(m_ref_pvecs.back());
root_pvec.to_aux_vec(m_ref_aux.back());
m_ref_gapp.push_back( std::vector<double>() );
if( ivy_mike::same_type<pvec_t,pvec_pgap>::result ) {
// WTF: this is why mixing static and dynamic polymorphism is a BAD idea!
pvec_pgap *rvp = reinterpret_cast<pvec_pgap *>(&root_pvec);
rvp->to_gap_post_vec(m_ref_gapp.back());
// std::transform( m_ref_gapp.back().begin(), m_ref_gapp.back().end(), std::ostream_iterator<int>(std::cout), ivy_mike::scaler_clamp<double>(10,0,9) );
//
// std::cout << "\n";
}
}
// std::cout << "pvecs created: " << t1.elapsed() << "\n";
}
template<typename pvec_t, typename seq_tag>
const std::vector<int> &references<pvec_t,seq_tag>::ng_map_at( size_t i ) {
std::vector<int> &ng_map = ref_ng_map_.at(i);
if( !ng_map.empty() ) {
return ng_map;
}
//std::vector<int> map;
std::vector< uint8_t > &seq = m_ref_seqs.at(i);
assert( seq.size() < size_t(std::numeric_limits<int>::max()) );
for( size_t i = 0; i < seq.size(); ++i ) {
bool is_gap = seq_model::pstate_is_gap( seq_model::s2p(seq[i]));
if( !is_gap ) {
ng_map.push_back(int(i));
}
}
//ng_map.shrink_to_fit();
std::vector<int>(ng_map).swap(ng_map); // old fashioned shrink_to_fit
return ng_map;
}
template<typename pvec_t, typename seq_tag>
void references<pvec_t,seq_tag>::write_pvecs(const char* name) {
std::ofstream os( name );
os << m_ref_pvecs.size();
for( size_t i = 0; i < m_ref_pvecs.size(); ++i ) {
os << " " << m_ref_pvecs[i].size() << " ";
os.write( (char *)m_ref_pvecs[i].data(), m_ref_pvecs[i].size() * sizeof(int));
os.write( (char *)m_ref_aux[i].data(), m_ref_aux[i].size() * sizeof(unsigned int));
}
}
template<typename pvec_t, typename seq_tag>
size_t references<pvec_t,seq_tag>::max_name_length() const {
size_t len = 0;
for( std::vector <std::string >::const_iterator it = m_ref_names.begin(); it != m_ref_names.end(); ++it ) {
len = std::max( len, it->size() );
}
return len;
}
bool scoring_results::offer(size_t qs, size_t ref, int score) {
ivy_mike::lock_guard<ivy_mike::mutex> lock(mtx_);
candss_.at( qs ).offer( score, ref );
if( best_score_.at(qs) < score || (best_score_.at(qs) == score && ref < best_ref_.at(qs))) {
best_score_[qs] = score;
best_ref_.at(qs) = ref;
return true;
}
return false;
}
namespace papara {
void scoring_results::candidates::offer(int score, size_t ref) {
candidate c( score,ref);
insert(std::lower_bound( begin(), end(), c), c );
if( size() > max_num_) {
pop_back();
}
}
bool scoring_results::candidate::operator<(const scoring_results::candidate& other) const {
if( score_ > other.score_ ) {
return true;
} else {
if( score_ == other.score_ ) {
return ref_ < other.ref_;
} else {
return false;
}
}
}
////////////////////////////////////////////////////////
// driver stuff
////////////////////////////////////////////////////////
template<typename seq_tag>
class worker {
const static size_t VW = vu_config<seq_tag>::width;
typedef typename vu_config<seq_tag>::scalar vu_scalar_t;
typedef typename block_queue<seq_tag>::block_t block_t;
typedef model<seq_tag> seq_model;
block_queue<seq_tag> &block_queue_;
scoring_results &results_;
const queries<seq_tag> &qs_;
const size_t rank_;
const papara_score_parameters sp_;
static void copy_to_profile( const block_t &block, aligned_buffer<vu_scalar_t> *prof, aligned_buffer<vu_scalar_t> *aux_prof ) {
size_t reflen = block.ref_len;
assert( reflen * VW == prof->size() );
assert( reflen * VW == aux_prof->size() );
typename aligned_buffer<vu_scalar_t>::iterator it = prof->begin();
typename aligned_buffer<vu_scalar_t>::iterator ait = aux_prof->begin();
// std::cout << "reflen: " << reflen << " " << size_t(&(*it)) << "\n";
for( size_t i = 0; i < reflen; ++i ) {
for( size_t j = 0; j < VW; ++j ) {
// std::cout << "ij: " << i << " " << j << " " << pvecs[j].size() << "\n";
*it = vu_scalar_t(block.seqptrs[j][i]);
*ait = (block.auxptrs[j][i] == AUX_CGAP) ? vu_scalar_t(-1) : 0;
++it;
++ait;
}
}
assert( it == prof->end());
assert( ait == aux_prof->end());
}
public:
worker( block_queue<seq_tag> *bq, scoring_results *res, const queries<seq_tag> &qs, size_t rank, const papara_score_parameters &sp )
: block_queue_(*bq), results_(*res), qs_(qs), rank_(rank), sp_(sp) {}
void operator()() {
ivy_mike::timer tstatus;
ivy_mike::timer tprint;
uint64_t cups_per_ref = -1;
uint64_t ncup = 0;
uint64_t inner_iters = 0;
uint64_t ticks_all = 0;
uint64_t ncup_short = 0;
uint64_t inner_iters_short = 0;
uint64_t ticks_all_short = 0;
aligned_buffer<vu_scalar_t> pvec_prof;
aligned_buffer<vu_scalar_t> aux_prof;
align_vec_arrays<vu_scalar_t> arrays;
aligned_buffer<vu_scalar_t> out_scores(VW);
aligned_buffer<vu_scalar_t> out_scores2(VW);
size_t queue_size;
size_t init_queue_size = -1;
while( true ) {
block_t block;
if( !block_queue_.get_block(&block, &queue_size)) {
break;
}
if( init_queue_size == size_t(-1) ) {
init_queue_size = queue_size;
}
if( cups_per_ref == uint64_t(-1) ) {
cups_per_ref = qs_.calc_cups_per_ref(block.ref_len );
}
#if 1
// assert( VW == 8 );
pvec_prof.resize( VW * block.ref_len );
aux_prof.resize( VW * block.ref_len );
copy_to_profile(block, &pvec_prof, &aux_prof );
pvec_aligner_vec<vu_scalar_t,VW> pav( block.seqptrs, block.auxptrs, block.ref_len, sp_.match, sp_.match_cgap, sp_.gap_open, sp_.gap_extend, seq_model::c2p, seq_model::num_cstates() );
// const align_pvec_score<vu_scalar_t,VW> aligner( block.seqptrs, block.auxptrs, block.ref_len, score_mismatch, score_match_cgap, score_gap_open, score_gap_extend );
for( unsigned int i = 0; i < qs_.size(); i++ ) {
//align_pvec_score_vec<vu_scalar_t, VW, false, typename seq_model::pars_state_t>( pvec_prof, aux_prof, qs_.pvec_at(i), score_match, score_match_cgap, score_gap_open, score_gap_extend, out_scores, arrays );
std::pair<size_t,size_t> bounds = qs_.get_per_qs_bounds( i );
// std::cout << "bounds: " << bounds.first << " " << bounds.second << "\n";
// if no bounds are available, get_per_qs_bounds will return [size_t(-1),size_t(-1)], which align is supposed to interpret as 'full range'
pav.align( qs_.cseq_at(i).begin(), qs_.cseq_at(i).end(), sp_.match, sp_.match_cgap, sp_.gap_open, sp_.gap_extend, out_scores.begin(), bounds.first, bounds.second );
//aligner.align(qs_.pvec_at(i).begin(), qs_.pvec_at(i).end());
//const vu_scalar_t *score_vec = aligner.get_scores();
//ncup += block.num_valid * block.ref_len * qs_.pvec_at(i).size();
#if 0 // test against old version
align_pvec_score_vec<vu_scalar_t, VW>( pvec_prof.begin(), pvec_prof.end(), aux_prof.begin(), qs_.pvec_at(i).begin(), qs_.pvec_at(i).end(), score_match, score_match_cgap, score_gap_open, score_gap_extend, out_scores2.begin(), arrays );
bool eq = std::equal( out_scores.begin(), out_scores.end(), out_scores2.begin() );
if( !eq ) {
std::cout << "meeeeeeep!\n";
}
//std::cout << "eq: " << eq << "\n";
#endif
// std::cout << "scores: ";
// std::copy( out_scores.begin(), out_scores.end(), std::ostream_iterator<int>(std::cout, "\n" ) );
// std::cout << "\n";
results_.offer( i, block.edges, block.edges + block.num_valid, out_scores.begin() );
}
ncup += block.num_valid * cups_per_ref;
ncup_short += block.num_valid * cups_per_ref;
ticks_all += pav.ticks_all();
ticks_all_short += pav.ticks_all();
inner_iters += pav.inner_iters_all();
inner_iters_short += pav.inner_iters_all();
if( rank_ == 0 && tprint.elapsed() > 10 ) {
//std::cout << "thread " << rank_ << " " << ncup << " in " << tstatus.elapsed() << " : "
float fdone = (init_queue_size - queue_size) / float(init_queue_size);
lout << fdone * 100 << "% done. ";
lout << ncup / (tstatus.elapsed() * 1e9) << " gncup/s, " << ticks_all / double(inner_iters) << " tpili (short: " << ncup_short / (tprint.elapsed() * 1e9) << ", " << ticks_all_short / double(inner_iters_short) << ")" << std::endl;
ncup_short = 0;
ticks_all_short = 0;
inner_iters_short = 0;
tprint = ivy_mike::timer();
}
}
#else
// assert( block.gapp_ptrs[0] != 0 );
// assert( VW == 4 );
// const align_pvec_gapp_score<4> aligner( block.seqptrs, block.gapp_ptrs, block.ref_len, score_mismatch, score_match_cgap, score_gap_open, score_gap_extend );
// for( unsigned int i = 0; i < m_pnt.m_qs_names.size(); i++ ) {
//
// size_t stride = 1;
// size_t aux_stride = 1;
//
// aligner.align(m_pnt.m_qs_pvecs[i]);
// const float *score_vec = aligner.get_scores();
//
// ncup += block.num_valid * block.ref_len * m_pnt.m_qs_pvecs[i].size();
// {
// ivy_mike::lock_guard<ivy_mike::mutex> lock( m_pnt.m_qmtx );
//
// for( int k = 0; k < block.num_valid; k++ ) {
//
//
//
// if( score_vec[k] < m_pnt.m_qs_bestscore[i] || (score_vec[k] == m_pnt.m_qs_bestscore[i] && block.edges[k] < m_pnt.m_qs_bestedge[i] )) {
// const bool validate = false;
// if( validate ) {
// const int *seqptr = block.seqptrs[k];
// const double *gapp_ptr = block.gapp_ptrs[k];
//
//// std::vector<double> gapp_tmp(gapp_ptr, gapp_ptr + block.ref_len);
//
//
// pars_align_gapp_seq pas( seqptr, m_pnt.m_qs_pvecs[i].data(), block.ref_len, m_pnt.m_qs_pvecs[i].size(), stride, gapp_ptr, aux_stride, seq_arrays_gapp, 0, score_gap_open, score_gap_extend, score_mismatch, score_match_cgap );
// int res = pas.alignFreeshift(INT_MAX);
//
// if( res != score_vec[k] ) {
//
//
// std::cout << "meeeeeeep! score: " << score_vec[k] << " " << res << "\n";
// }
// }
//
// m_pnt.m_qs_bestscore[i] = score_vec[k];
// m_pnt.m_qs_bestedge[i] = block.edges[k];
// }
// }
// }
// }
// }
#endif
{