/usr/include/anfo/index.h is in libanfo0-dev 0.98-4.
This file is owned by root:root, with mode 0o644.
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// This file is part of ANFO
//
// ANFO 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.
//
// Anfo 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 Anfo. If not, see <http://www.gnu.org/licenses/>.
#ifndef INCLUDED_INDEX_H
#define INCLUDED_INDEX_H
#include "config.pb.h"
#include "sequence.h"
#include "util.h"
#include <algorithm>
#include <iostream>
#include <limits>
#include <list>
#include <map>
#include <string>
#include <utility>
#include <vector>
#include <glob.h>
#include <sys/mman.h>
//! \brief a genome as stored in a DNA file
//! This class mmaps a DNA file and wraps it with a sensible interface.
class CompactGenome
{
public:
// Why are we using indices here instead of pointers? Because
// pointers would be internal and make copying of this object a
// lot harder.
// key is offset into genome, value is (index of sequence, index
// of contig)
typedef std::map< uint32_t, std::pair< int, int > > ContigMap ;
// value is index of contig
typedef std::map< uint32_t, int > PosnMap1 ;
// first half of value is index of sequence
typedef std::map< std::string, std::pair< int, PosnMap1 > > PosnMap ;
static void cleanup( const CompactGenome* ) {}
private:
DnaP base_ ;
size_t file_size_ ;
uint32_t length_ ;
int fd_ ;
ContigMap contig_map_ ;
PosnMap posn_map_ ;
CompactGenome( const CompactGenome& ) ; // not implemented
void operator = ( const CompactGenome& ) ; // not implemented
~CompactGenome() ; // must control life cycle
friend class Metagenome ;
public:
config::Genome g_ ;
mutable int refcount_ ;
public:
//! \brief makes accessible a genome file
//! \param name file name of the genome
//! \param c program configuration, needed for the search path
CompactGenome( const std::string& name ) ;
void add_ref() const { ++refcount_ ; }
std::string name() const { return g_.name() ; }
std::string describe() const
{
std::string d = g_.name() ;
if( g_.has_description() ) d += " (" + g_.description() + ")" ;
return d ;
}
uint32_t total_size() const { return g_.total_size() ; }
uint32_t raw_size() const { return length_ ; }
DnaP get_base() const { return base_ ; }
//! \brief scan over finite words of the dna
//! Fixed size words in the genome are iterated. The words may
//! well contain ambiguity codes, but are guaranteed not to
//! contain gaps.
//!
//! Words are encoded as four bits per nucleotide, first nucleotide in
//! the MSB(!). See ::make_dense_word for why that makes sense. Unused
//! MSBs in words passed to mk_word contain junk, do not rely on
//! them.
//!
//! The functor objects in the following will be passed by
//! value. Make sure they are tiny and that their function call
//! operators can be inlined.
//!
//! \param w word size, 4*w must not be more than there are bits
//! in an unsigned long long.
//! \param mk_word functor object called to transform a
//! sequence of ambiguity codes into words of
//! nucleotides
//! \param mk_gap functor that's called at every gap
//! \param slice scan this slice of a big genome
//! \param slices total number of slices
//! \param msg if set, switches on progress reports and is
//! included in them
template< typename F, typename G > void scan_words( unsigned w, F mk_word, G mk_gap, int slice = 0, int slices = 1, const char* msg = 0 ) const ;
const ContigMap &get_contig_map() const { return contig_map_ ; }
//! \brief translates a DNA pointer back to sequence coordinates
//! If the DNA pointer points into this genome, it is translated
//! to the name of the sequence and the offset into it. The
//! strand is disregarded, the result is the same regardless of
//! the direction the pointer would be moving in.
//! \param pos position to be translated
//! \param offset is assigned the offset after translation
//! \return pointer to sequence that includes the hit, else null
const config::Sequence *translate_back( DnaP pos, uint32_t& offset ) const ;
//! \brief translates "human" cooordinates into a pointer
//! Return 0 if anything goes wrong.
DnaP find_pos( const std::string& seq, uint32_t pos ) const ;
enum { signature = 0x31414e44u } ; // DNA1
private:
//! \brief reports a position while scanning
//! \internal
static void report( uint32_t, uint32_t, const char* ) ;
} ;
//! \brief Representation of a list of seeds.
//! A seed is described by a size and two coordinates. One is the start
//! on the query sequence, the other we choose to be the "diagonal"
//! (difference between coordinates), since seeds on the same or close
//! diagonal will usually be combined. Offset is negative for rc'ed
//! matches, in this case its magnitude is the actual offset from the
//! end of the sequence.
//!
//! Here we actually represent a list of seeds by two pointers into a
//! list of reference coordinates. The first entry is chached in the
//! data structure itself, so it selves to represent both lists and
//! single seeds.
//!
//! The list of seeds in index files is sorted backwards (more or less
//! an artefact of the way indexes are built), so we can merge these
//! lists instead of copying and sorting them.
struct Matches
{
const uint32_t *begin, *end ;
int32_t offs ;
uint16_t wordsize ;
uint16_t stride ;
int64_t diag ;
} ;
// Match lists are sorted backwards by reference coordinate (an artefact
// of the index construction process) and therefore backwards by
// diagonal (ref-coordinate minus offset, by definition); we also choose
// to sort backwards on the offset.
struct compare_match_lists {
bool operator()( const Matches &a, const Matches &b ) {
if( b.diag < a.diag ) return true ;
if( a.diag < b.diag ) return false ;
return b.offs < a.offs ;
}
} ;
struct compare_matches_for_heap {
// note the `wrong' order; this is intended for a heap!
bool operator()( const Matches &a, const Matches &b ) {
return compare_match_lists()( b, a ) ;
}
} ;
//! \brief Collection of short matches.
//! We actually collect the ranges of sorted(!) matches in the index
//! data structure, then merge-sort them on demand. The calling
//! sequence is to first post() ranges of index entries, then
//! start_traversal(), then look at the first seed using get(), and
//! remove them one by one using take() until the structure becomes
//! empty().
class PreSeeds
{
private:
struct equal_match_lists {
bool operator()( const Matches &a, const Matches &b ) {
return a.begin == b.begin && a.offs == b.offs ;
}
} ;
std::vector< Matches > heap_ ;
bool normalize()
{
while( heap_.back().begin != heap_.back().end &&
*heap_.back().begin % heap_.back().stride != 0 )
++heap_.back().begin ;
if( heap_.back().begin == heap_.back().end ) {
heap_.pop_back() ;
return false ;
}
else {
heap_.back().diag = (int64_t)(*heap_.back().begin) - (int64_t)(heap_.back().offs) ;
return true ;
}
}
public:
PreSeeds() {}
void post( const uint32_t *begin, const uint32_t *end, int32_t offs, int wordsize, int stride )
{
if( begin != end ) {
heap_.push_back( Matches() ) ;
heap_.back().begin = begin ;
heap_.back().end = end ;
heap_.back().offs = offs ;
heap_.back().wordsize = wordsize ;
heap_.back().stride = stride ;
normalize() ;
}
}
bool empty() const { return heap_.empty() ; }
const Matches& get() const { return heap_.front() ; }
void start_traversal() {
std::sort( heap_.begin(), heap_.end(), compare_match_lists() ) ;
heap_.erase( std::unique( heap_.begin(), heap_.end(), equal_match_lists() ), heap_.end() ) ;
std::make_heap( heap_.begin(), heap_.end(), compare_matches_for_heap() ) ;
}
void take()
{
std::pop_heap( heap_.begin(), heap_.end(), compare_matches_for_heap() ) ;
++heap_.back().begin ;
assert( heap_.back().begin == heap_.back().end ||
heap_.back().begin[-1] > heap_.back().begin[0] ) ;
if( normalize() ) std::push_heap( heap_.begin(), heap_.end(), compare_matches_for_heap() ) ;
}
} ;
inline std::ostream& operator << ( std::ostream& o, const Matches& s )
{
return o << '@' << s.offs << '+' << s.diag << ':' << s.wordsize ;
}
class FixedIndex
{
public:
struct LookupParams {
uint32_t cutoff ; // more common seeds will be ignored
uint32_t allow_mismatches ; // number of changed positions per seed word
uint32_t wordsize ; // nucleotides per seed word
uint32_t stride ; // tiling stepsize
} ;
enum { signature = 0x33584449u } ; // "IDX3"
FixedIndex() : p_(0), base(0), secondary(0), first_level_len(0), length(0), fd_(0), refcount_(0) {}
//! \brief loads an index from a file
//! \param name filename
FixedIndex( const std::string &name ) ;
~FixedIndex() { if( p_ ) munmap( (void*)p_, length ) ; if( fd_ != -1 ) close( fd_ ) ; }
unsigned lookupS( const std::string& seq, PreSeeds&, const LookupParams &p, int *num_useless ) const ;
unsigned lookup1( Oligo, PreSeeds&, const LookupParams &p, int32_t offs, int *num_useless ) const ;
unsigned lookup1m( Oligo, PreSeeds&, const LookupParams &p, int32_t offs, int *num_useless ) const ;
unsigned lookup2m( Oligo, PreSeeds&, const LookupParams &p, int32_t offs, int *num_useless ) const ;
operator const void * () const { return base ; }
const config::CompactIndex& metadata() const { return meta_ ; }
void swap( FixedIndex& i ) {
std::swap( p_, i.p_ ) ;
std::swap( base, i.base ) ;
std::swap( secondary, i.secondary ) ;
std::swap( first_level_len, i.first_level_len ) ;
std::swap( length, i.length ) ;
std::swap( fd_, i.fd_ ) ;
}
private:
const void* p_ ;
const uint32_t *base, *secondary ;
uint32_t first_level_len ;
uint64_t length ;
int fd_ ;
config::CompactIndex meta_ ;
unsigned lookup1m( Oligo, PreSeeds&, const LookupParams &p, int32_t offs, int *num_useless, size_t ) const ;
public:
int refcount_ ;
} ;
class MetaIndex
{
private:
static std::map< std::string, FixedIndex* > map_ ;
public:
static const FixedIndex& add_ref( const std::string& name )
{
FixedIndex*& ix = map_[ name ] ;
if( !ix ) ix = new FixedIndex( name ) ;
++ix->refcount_ ;
return *ix ;
}
static void free_ref( const FixedIndex& ix )
{
for( std::map< std::string, FixedIndex* >::iterator i = map_.begin() ; i != map_.end() ; ++i )
if( i->second == &ix && !--i->second->refcount_ )
{
delete i->second ;
map_.erase( i ) ;
return ;
}
}
} ;
template< typename F, typename G > void CompactGenome::scan_words(
unsigned w, F mk_word, G mk_gap, int slice, int slices, const char* msg ) const
{
if( (unsigned)std::numeric_limits< Oligo >::digits < 4 * w )
throw "cannot build index: oligo doesn't fit" ;
// start here, in case we want slices
uint32_t offs = 2 * slice * (int64_t)length_ / slices ;
uint32_t eoffs = 2 * (slice+1) * (int64_t)length_ / slices ;
Oligo dna = 0 ;
// do not start before first contig (that's the header region)
assert( g_.sequence_size() && g_.sequence(0).contig_size() ) ;
offs = std::max( offs, g_.sequence(0).contig(0).offset()-1 ) ;
while( base_[ offs ] != 0 ) ++offs ; // find first gap
for( unsigned i = 0 ; i != w ; ++i ) // fill first word
{
dna <<= 4 ;
dna |= base_[ offs ] ;
++offs ;
}
report(offs,length_,msg) ;
// run to end of slice, but stop at gaps only
while( offs < eoffs || base_[ offs-1 ] )
{
if( (offs & 0xffffff) == 0 ) report(offs,length_,msg) ;
dna <<= 4 ;
dna |= base_[ offs ] ;
++offs ;
if( !base_[offs] ) mk_gap( offs ) ;
// throw away words containing gap symbols
// (This is necessary since we may want to construct
// discontiguous words, but not if a "don't care" position is a
// gap.)
bool clean = true ;
for( unsigned i = 0 ; i != w ; ++i )
clean &= ((dna >> (4*i)) & 0xf) != 0 ;
if( clean ) mk_word( w, offs-w, dna ) ;
}
if( msg ) std::clog << "\r\e[K" << std::flush ;
}
inline int put_seed( output::Seeds *ss, const Matches& s, int out )
{
int i = ss->ref_positions().size() - 1 ;
uint32_t oldref = ss->ref_positions().Get( i ) ;
int32_t oldqry = ss->query_positions().Get( i ) ;
uint32_t oldsiz = ss->seed_sizes().Get( i ) ;
// check for overlap (diag within 8, which is arbitrary...)
if( (s.offs < 0) == (oldqry < 0) &&
abs( s.diag - (int64_t)oldref + (int64_t)oldqry ) <= 8 )
{
if( s.wordsize > oldsiz ) // new one is bigger, overwrite
{
ss->mutable_ref_positions()->Set( i, s.diag + s.offs ) ;
ss->mutable_query_positions()->Set( i, s.offs ) ;
ss->mutable_seed_sizes()->Set( i, s.wordsize ) ;
}
return out ;
}
else
{
ss->mutable_ref_positions()->Add( s.diag + s.offs ) ;
ss->mutable_query_positions()->Add( s.offs ) ;
ss->mutable_seed_sizes()->Add( s.wordsize ) ;
return out+1 ;
}
}
//! \brief Combines short, adjacent seeds into longer ones.
//! This is a cheap method to combine seeds: only overlapping and
//! adjacent seeds are combined, neighboring diagonals are not
//! considered. The code is short and direct, and works well even for
//! imperfect seeds.
//!
//! How to do this? We get seeds ordered first by diagonal (backwards,
//! actually), then backwards by offset. Seeds are adjacent iff they
//! have the same diagonal index and their offsets differ by no more
//! than the seed size. They can be combined on the fly easily.
//!
//! \note Formerly we tried to somehow deal with neighboring diagonals.
//! This has been declared as not worth the hassle, so it was
//! dropped. If we get seeds for the same region on neighboring
//! diagonals, they are useless repeats anyway and probably
//! excluded from the index to begin with. If gaps complicated
//! everything, well, tough luck, this only an approximation
//! anyway.
//!
//! \todo Seeds on neighboring diagonals can give rise to effectively
//! the same alignment. If that happens, the map quality goes
//! down the drain... Need a solution for that.
//!
//! \param v container of seeds, will be consumed
//! \param m minimum length of a good seed
//! \param ss output container for seed positions
//! \return number of good seeds produced
inline int combine_seeds( PreSeeds& v, uint32_t m, output::Seeds *ss )
{
int out = 0 ;
if( !v.empty() )
{
v.start_traversal() ;
// combine overlapping and adjacent seeds into larger ones
// PreSeeds::const_iterator a = v.begin(), e = v.end() ;
Matches s = v.get() ;
v.take() ;
for( ; !v.empty() ; v.take() )
{
const Matches& a = v.get() ;
assert( a.diag <= s.diag ) ;
if( a.diag == s.diag ) assert( a.offs <= s.offs ) ;
if( a.diag == s.diag &&
a.offs + (int32_t)a.wordsize >= s.offs )
{
s.wordsize += s.offs - a.offs ;
s.offs = a.offs ;
}
else
{
if( s.wordsize >= m ) out = put_seed( ss, s, out ) ;
s = a ;
}
}
if( s.wordsize >= m ) out = put_seed( ss, s, out ) ;
}
return out ;
}
typedef std::map< std::string, CompactGenome > Genomes ;
typedef std::map< std::string, FixedIndex > Indices ;
typedef Holder< const CompactGenome > GenomeHolder ;
class Metagenome
{
public:
static int nommap ;
static void make_room() ;
private:
// maps file name to genome object
typedef std::map< std::string, CompactGenome* > Genomes ;
// maps sequence id to genome object
typedef std::map< std::string, CompactGenome* > SeqMap1 ;
// maps genome id to sequence map
typedef std::map< std::string, SeqMap1 > SeqMap ;
Genomes genomes ;
SeqMap seq_map ;
std::list< std::string > path ;
static Metagenome the_metagenome ;
public:
Metagenome( const char* p ) ;
~Metagenome() { for( Genomes::iterator i = genomes.begin() ; i != genomes.end() ; ++i ) delete i->second ; }
static void add_path( const std::string& s ) { the_metagenome.path.push_front( s ) ; }
//! \brief finds a named sequence
//! If a genome is given, only genome files whose name starts with
//! the genome name are considered. If genome is empty, all files
//! are searched.
static GenomeHolder find_sequence( const std::string& genome, const std::string& seq ) ;
static GenomeHolder find_genome( const std::string& genome ) ;
static glob_t glob_path( const std::string& genome ) ;
static bool translate_to_genome_coords( DnaP pos, uint32_t &xpos, const config::Sequence** s_out = 0, const config::Genome** g_out = 0 ) ;
//! \brief replacement for mmap() that knows how to free memory
//! This is a wrapper wround mmap(). If the system mmap()
//! fails, it will try to free up some memory by forgetting
//! about an ephemeral genome and then call mmap again.
//! Parameters are passed to mmap() unchanged. If
//! Metagenome::nommap is set, doesn't mmap() the file
//! descriptor, but mmap()s /dev/zero instead and read()s the
//! requested region from the file descriptor (intended for file
//! systems where mmap() is agonizingly slow, e.g. GCFS).
static void *mmap( void *start, size_t length, int *fd, off_t offset ) ;
} ;
#endif
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