/usr/include/anfo/align_fwd.h is in libanfo0-dev 0.98-4+b1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 | #ifndef INCLUDED_ALIGN_FWD_H
#define INCLUDED_ALIGN_FWD_H
#include "logdom.h"
#include "sequence.h"
//! \page adna_alignment Operations on Ancient DNA Alignments
//! This type of alignment models aDNA as two additional states, one
//! with higher deamination rate, with an asymmetric substitution
//! matrix, and with affine gap costs. Additional parameters are all
//! static.
//!
//! \todo We actually don't need the parameter set to be static, and it
//! may even pay to have it configurable so differently
//! parameterized alignments an be mixed in a single run.
//!
//! @{
//! \brief substitution matrix
//! We prepare a full matrix of 16 ambiguity codes vs. 16 ambiguity
//! codes, this avoid the need for expensive additions in the log-domain
//! should the need to align ambiguity codes arise. First index is
//! "from" (reference code), second index is "to" (query code).
typedef Logdom subst_mat[16][16] ;
namespace config { class Aligner ; } ;
//! \brief parameters for simple_adna
//! One such parblock is a static variable for the aligner proper,
//! various support tools shunt additional structures around.
struct adna_parblock
{
enum {
mask_ss = 1,
mask_gap_ref = 2,
mask_gap_qry = 4,
mask_gaps = mask_gap_ref | mask_gap_ref,
num_states = 6
} ;
adna_parblock() {}
adna_parblock( const config::Aligner& conf ) ;
//! \brief DS substitution matrix, forward direction
subst_mat ds_mat ;
//! \brief SS substitution matrix, forward direction
//! Deamination shows up as C->T as it is best understood this way.
//! To process reverse-complemented deamination, we have to do
//! rev-complemented lookups while actually moving in the forward
//! (5'->3') direction. \see simple_adna::subst_penalty()
subst_mat ss_mat ;
//! \brief Penalty for extending an overhang.
//! Having a constant penalty for the overhang length models its
//! length distribution as geometric.
Logdom overhang_ext_penalty ;
//! \brief penalty for entering SS state
//! This is essentially the probability of having an overhang at
//! all.
Logdom overhang_enter_penalty ;
//! \brief gap open penalty
Logdom gap_open_penalty ;
//! \brief gap extension penalty
Logdom gap_ext_penalty ;
Logdom subst_penalty( int s, Ambicode r, const QSequence::Base &qry ) const
{
Logdom prob = Logdom::null() ;
for( uint8_t p = 0 ; p != 4 ; ++p )
prob += ( s & mask_ss ? ss_mat[r][1<<p] : ds_mat[r][1<<p] )
* Logdom::from_phred( qry.qscores[p] ) ;
return prob ;
}
} ;
std::ostream& operator << ( std::ostream&, const adna_parblock& ) ;
#endif
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