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align.c
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/*******************************************************************************************
*
* Fast alignment discovery and trace generation along with utilites for displaying alignments
* Based on previously unpublished ideas from 2005, subsequently refined in 2013-14. Basic
* idea is to keep a dynamically selected interval of the f.r. waves from my 1986 O(nd) paper.
* A recent cool idea is to not record all the details of an alignment while discovering it
* but simply record trace points through which the optimal alignment passes every 100bp,
* allowing rapid recomputation of the alignment details between trace points.
*
* Author : Gene Myers
* First : June 2013
* Current: June 1, 2014
*
********************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#include <string.h>
#include <unistd.h>
#include <math.h>
#include <limits.h>
#include "DB.h"
#include "align.h"
#undef DEBUG_PASSES // Show forward / backward extension termini for Local_Alignment
#undef DEBUG_POINTS // Show trace points
#undef DEBUG_WAVE // Show waves of Local_Alignment
#undef SHOW_MATCH_WAVE // For waves of Local_Alignment also show # of matches
#undef SHOW_TRAIL // Show trace at the end of forward and reverse passes
#undef SHOW_TPS // Show trace points as they are encountered in a wave
#undef DEBUG_EXTEND // Show waves of Extend_Until_Overlap
#undef DEBUG_ALIGN // Show division points of Compute_Trace
#undef DEBUG_TRACE // Show trace additions for Compute_Trace
#undef DEBUG_SCRIPT // Show script additions for Compute_Trace
#undef DEBUG_AWAVE // Show F/R waves of Compute_Trace
#undef SHOW_TRACE // Show full trace for Print_Alignment
#undef WAVE_STATS
/****************************************************************************************\
* *
* Working Storage Abstraction *
* *
\****************************************************************************************/
typedef struct // Hidden from the user, working space for each thread
{ int vecmax;
void *vector;
int celmax;
void *cells;
int pntmax;
void *points;
int tramax;
void *trace;
} _Work_Data;
Work_Data *New_Work_Data()
{ _Work_Data *work;
work = (_Work_Data *) Malloc(sizeof(_Work_Data),"Allocating work data block");
if (work == NULL)
EXIT(NULL);
work->vecmax = 0;
work->vector = NULL;
work->pntmax = 0;
work->points = NULL;
work->tramax = 0;
work->trace = NULL;
work->celmax = 0;
work->cells = NULL;
return ((Work_Data *) work);
}
static int enlarge_vector(_Work_Data *work, int newmax)
{ void *vec;
int max;
max = ((int) (newmax*1.2)) + 10000;
vec = Realloc(work->vector,max,"Enlarging DP vector");
if (vec == NULL)
EXIT(1);
work->vecmax = max;
work->vector = vec;
return (0);
}
static int enlarge_points(_Work_Data *work, int newmax)
{ void *vec;
int max;
max = ((int) (newmax*1.2)) + 10000;
vec = Realloc(work->points,max,"Enlarging point vector");
if (vec == NULL)
EXIT(1);
work->pntmax = max;
work->points = vec;
return (0);
}
static int enlarge_trace(_Work_Data *work, int newmax)
{ void *vec;
int max;
max = ((int) (newmax*1.2)) + 10000;
vec = Realloc(work->trace,max,"Enlarging trace vector");
if (vec == NULL)
EXIT(1);
work->tramax = max;
work->trace = vec;
return (0);
}
void Free_Work_Data(Work_Data *ework)
{ _Work_Data *work = (_Work_Data *) ework;
if (work->vector != NULL)
free(work->vector);
if (work->cells != NULL)
free(work->cells);
if (work->trace != NULL)
free(work->trace);
if (work->points != NULL)
free(work->points);
free(work);
}
/****************************************************************************************\
* *
* ADAPTIVE PATH FINDING *
* *
\****************************************************************************************/
// Absolute/Fixed Parameters
#define BVEC uint64 // Can be uint32 if PATH_LEN <= 32
#define TRIM_LEN 15 // Report as the tip, the last wave maximum for which the last
// 2*TRIM_LEN edits are prefix-positive at rate ave_corr*f(bias)
// (max value is 20)
#define PATH_LEN 60 // Follow the last PATH_LEN columns/edges (max value is 63)
// Derivative fixed parameters
#define PATH_TOP 0x1000000000000000ll // Must be 1 << PATH_LEN
#define PATH_INT 0x0fffffffffffffffll // Must be PATH_TOP-1
#define TRIM_MASK 0x7fff // Must be (1 << TRIM_LEN) - 1
#define TRIM_MLAG 200 // How far can last trim point be behind best point
#define WAVE_LAG 30 // How far can worst point be behind the best point
static double Bias_Factor[10] = { .690, .690, .690, .690, .780,
.850, .900, .933, .966, 1.000 };
// Adjustable paramters
typedef struct
{ double ave_corr;
int trace_space;
int reach;
float freq[4];
int ave_path;
int16 *score;
int16 *table;
} _Align_Spec;
/* Fill in bit table: TABLE[x] = 1 iff the alignment modeled by x (1 = match, 0 = mismatch)
has a non-negative score for every suffix of the alignment under the scoring scheme
where match = MATCH and mismatch = -1. MATCH is set so that an alignment with TRIM_PCT
matches has zero score ( (1-TRIM_PCT) / TRIM_PCT ). */
#define FRACTION 1000 // Implicit fractional part of scores, i.e. score = x/FRACTION
typedef struct
{ int mscore;
int dscore;
int16 *table;
int16 *score;
} Table_Bits;
static void set_table(int bit, int prefix, int score, int max, Table_Bits *parms)
{ if (bit >= TRIM_LEN)
{ parms->table[prefix] = (int16) (score-max);
parms->score[prefix] = (int16) score;
}
else
{ if (score > max)
max = score;
set_table(bit+1,(prefix<<1),score - parms->dscore,max,parms);
set_table(bit+1,(prefix<<1) | 1,score + parms->mscore,max,parms);
}
}
/* Create an alignment specification record including path tip tables & values */
Align_Spec *New_Align_Spec(double ave_corr, int trace_space, float *freq, int reach)
{ _Align_Spec *spec;
Table_Bits parms;
double match;
int bias;
spec = (_Align_Spec *) Malloc(sizeof(_Align_Spec),"Allocating alignment specification");
if (spec == NULL)
EXIT(NULL);
spec->ave_corr = ave_corr;
spec->trace_space = trace_space;
spec->reach = reach;
spec->freq[0] = freq[0];
spec->freq[1] = freq[1];
spec->freq[2] = freq[2];
spec->freq[3] = freq[3];
match = freq[0] + freq[3];
if (match > .5)
match = 1.-match;
bias = (int) ((match+.025)*20.-1.);
if (match < .2)
{ fprintf(stderr,"Warning: Base bias worse than 80/20%% ! (New_Align_Spec)\n");
fprintf(stderr," Capping bias at this ratio.\n");
bias = 3;
}
spec->ave_path = (int) (PATH_LEN * (1. - Bias_Factor[bias] * (1. - ave_corr)));
parms.mscore = (int) (FRACTION * Bias_Factor[bias] * (1. - ave_corr));
parms.dscore = FRACTION - parms.mscore;
parms.score = (int16 *) Malloc(sizeof(int16)*(TRIM_MASK+1)*2,"Allocating trim table");
if (parms.score == NULL)
{ free(spec);
EXIT(NULL);
}
parms.table = parms.score + (TRIM_MASK+1);
set_table(0,0,0,0,&parms);
spec->table = parms.table;
spec->score = parms.score;
return ((Align_Spec *) spec);
}
void Free_Align_Spec(Align_Spec *espec)
{ _Align_Spec *spec = (_Align_Spec *) espec;
free(spec->score);
free(spec);
}
double Average_Correlation(Align_Spec *espec)
{ return (((_Align_Spec *) espec)->ave_corr); }
int Trace_Spacing(Align_Spec *espec)
{ return (((_Align_Spec *) espec)->trace_space); }
float *Base_Frequencies(Align_Spec *espec)
{ return (((_Align_Spec *) espec)->freq); }
int Overlap_If_Possible(Align_Spec *espec)
{ return (((_Align_Spec *) espec)->reach); }
/****************************************************************************************\
* *
* LOCAL ALIGNMENT FINDER: forward_/reverse_wave and Local_Alignment *
* *
\****************************************************************************************/
#ifdef WAVE_STATS
static int64 MAX, TOT, NWV;
static int64 RESTARTS;
void Init_Stats()
{ MAX = TOT = NWV = 0;
RESTARTS = 0;
}
void Print_Stats()
{ printf("\nMax = %lld Ave = %.1f # = %lld\n",MAX,(1.*TOT)/NWV,NWV);
printf("\nRestarts = %lld\n",RESTARTS);
}
#endif
#ifdef DEBUG_WAVE
static void print_wave(int *V, int *M, int low, int hgh, int besta)
{ int k, bestk;
(void) M;
printf(" [%6d,%6d]: ",low,hgh);
for (k = low; k <= hgh; k++)
{ if (besta == V[k])
bestk = k;
// printf(" %3d",(V[k]+k)/2);
printf(" %3d",besta-V[k]);
}
printf(" : %d (%d,%d)\n",besta,(besta+bestk)/2,(besta-bestk)/2);
#ifdef SHOW_MATCH_WAVE
printf(" ");
for (k = low; k <= hgh; k++)
printf(" %3d",M[k]);
printf("\n");
#endif
fflush(stdout);
}
#endif
/* At each furthest reaching point, keep a-coordinate of point (V), bitvector
recording the last TRIM_LEN columns of the implied alignment (T), and the
# of matches (1-bits) in the bitvector (M). */
typedef struct
{ int ptr;
int diag;
int diff;
int mark;
} Pebble;
static int VectorEl = 6*sizeof(int) + sizeof(BVEC);
static int forward_wave(_Work_Data *work, _Align_Spec *spec, Alignment *align, Path *bpath,
int *mind, int maxd, int mida, int minp, int maxp, int aoff, int boff)
{ char *aseq = align->aseq;
char *bseq = align->bseq;
Path *apath = align->path;
int hgh, low, dif;
int vlen, vmin, vmax;
int *V, *M;
int *_V, *_M;
BVEC *T;
BVEC *_T;
int *HA, *HB;
int *_HA, *_HB;
int *NA, *NB;
int *_NA, *_NB;
Pebble *cells;
int avail, cmax;
int TRACE_SPACE = spec->trace_space;
int PATH_AVE = spec->ave_path;
int REACH = spec->reach;
int16 *SCORE = spec->score;
int16 *TABLE = spec->table;
int besta, besty;
int trima, trimy, trimd;
int trimha, trimhb;
int morea, morey, mored;
int moreha, morehb;
int more, morem, lasta;
int aclip, bclip;
hgh = maxd;
low = *mind;
dif = 0;
{ int span, wing;
span = (hgh-low)+1;
vlen = work->vecmax/VectorEl;
wing = (vlen - span)/2;
vmin = low - wing;
vmax = hgh + wing;
_V = ((int *) work->vector);
_M = _V + vlen;
_HA = _M + vlen;
_HB = _HA + vlen;
_NA = _HB + vlen;
_NB = _NA + vlen;
_T = ((BVEC *) (_NB + vlen));
V = _V-vmin;
M = _M-vmin;
HA = _HA-vmin;
HB = _HB-vmin;
NA = _NA-vmin;
NB = _NB-vmin;
T = _T-vmin;
cells = (Pebble *) (work->cells);
cmax = work->celmax;
avail = 0;
}
/* Compute 0-wave starting from mid-line */
more = 1;
aclip = INT32_MAX;
bclip = -INT32_MAX;
besta = trima = morea = lasta = mida;
besty = trimy = morey = (mida-hgh) >> 1;
trimd = mored = 0;
trimha = moreha = 0;
trimhb = morehb = 1;
morem = -1;
{ int k;
char *a;
a = aseq + hgh;
for (k = hgh; k >= low; k--)
{ int y, c, d;
int ha, hb;
int na, nb;
Pebble *pb;
y = (mida-k) >> 1;
if (avail >= cmax-1)
{ cmax = ((int) (avail*1.2)) + 10000;
cells = (Pebble *) Realloc(cells,cmax*sizeof(Pebble),"Reallocating trace cells");
if (cells == NULL)
EXIT(1);
work->celmax = cmax;
work->cells = (void *) cells;
}
na = (((y+k)+(TRACE_SPACE-aoff))/TRACE_SPACE-1)*TRACE_SPACE+aoff;
#ifdef SHOW_TPS
printf(" A %d: %d,%d,0,%d\n",avail,-1,k,na); fflush(stdout);
#endif
pb = cells+avail;
pb->ptr = -1;
pb->diag = k;
pb->diff = 0;
pb->mark = na;
ha = avail++;
na += TRACE_SPACE;
nb = ((y+(TRACE_SPACE-boff))/TRACE_SPACE-1)*TRACE_SPACE+boff;
#ifdef SHOW_TPS
printf(" B %d: %d,%d,0,%d\n",avail,-1,k,nb); fflush(stdout);
#endif
pb = cells+avail;
pb->ptr = -1;
pb->diag = k;
pb->diff = 0;
pb->mark = nb;
hb = avail++;
nb += TRACE_SPACE;
while (1)
{ c = bseq[y];
if (c == 4)
{ more = 0;
if (bclip < k)
bclip = k;
break;
}
d = a[y];
if (c != d)
{ if (d == 4)
{ more = 0;
aclip = k;
}
break;
}
y += 1;
}
c = (y << 1) + k;
while (y+k >= na)
{ if (avail >= cmax)
{ cmax = ((int) (avail*1.2)) + 10000;
cells = (Pebble *) Realloc(cells,cmax*sizeof(Pebble),"Reallocating trace cells");
if (cells == NULL)
EXIT(1);
work->celmax = cmax;
work->cells = (void *) cells;
}
#ifdef SHOW_TPS
printf(" A %d: %d,%d,0,%d\n",avail,ha,k,na); fflush(stdout);
#endif
pb = cells+avail;
pb->ptr = ha;
pb->diag = k;
pb->diff = 0;
pb->mark = na;
ha = avail++;
na += TRACE_SPACE;
}
while (y >= nb)
{ if (avail >= cmax)
{ cmax = ((int) (avail*1.2)) + 10000;
cells = (Pebble *) Realloc(cells,cmax*sizeof(Pebble),"Reallocating trace cells");
if (cells == NULL)
EXIT(1);
work->celmax = cmax;
work->cells = (void *) cells;
}
#ifdef SHOW_TPS
printf(" B %d: %d,%d,0,%d\n",avail,hb,k,nb); fflush(stdout);
#endif
pb = cells+avail;
pb->ptr = hb;
pb->diag = k;
pb->diff = 0;
pb->mark = nb;
hb = avail++;
nb += TRACE_SPACE;
}
if (c > besta)
{ besta = trima = lasta = c;
besty = trimy = y;
trimha = ha;
trimhb = hb;
}
V[k] = c;
T[k] = PATH_INT;
M[k] = PATH_LEN;
HA[k] = ha;
HB[k] = hb;
NA[k] = na;
NB[k] = nb;
a -= 1;
}
}
if (more == 0)
{ if (bseq[besty] != 4 && aseq[besta - besty] != 4)
more = 1;
if (hgh >= aclip)
{ hgh = aclip-1;
if (morem <= M[aclip])
{ morem = M[aclip];
morea = V[aclip];
morey = (morea - aclip)/2;
moreha = HA[aclip];
morehb = HB[aclip];
}
}
if (low <= bclip)
{ low = bclip+1;
if (morem <= M[bclip])
{ morem = M[bclip];
morea = V[bclip];
morey = (morea - bclip)/2;
moreha = HA[bclip];
morehb = HB[bclip];
}
}
aclip = INT32_MAX;
bclip = -INT32_MAX;
}
#ifdef DEBUG_WAVE
printf("\nFORWARD WAVE:\n");
print_wave(V,M,low,hgh,besta);
#endif
/* Compute successive waves until no furthest reaching points remain */
while (more && lasta >= besta - TRIM_MLAG)
{ int k, n;
int ua, ub;
BVEC t;
int am, ac, ap;
char *a;
low -= 1;
hgh += 1;
if (low <= vmin || hgh >= vmax)
{ int span, wing;
int64 move;
int64 vd, md, had, hbd, nad, nbd, td;
span = (hgh-low)+1;
if (.8*vlen < span)
{ if (enlarge_vector(work,vlen*VectorEl))
EXIT(1);
move = ((void *) _V) - work->vector;
vlen = work->vecmax/VectorEl;
_V = (int *) work->vector;
_M = _V + vlen;
_HA = _M + vlen;
_HB = _HA + vlen;
_NA = _HB + vlen;
_NB = _NA + vlen;
_T = ((BVEC *) (_NB + vlen));
}
else
move = 0;
wing = (vlen - span)/2;
vd = ((void *) ( _V+wing)) - (((void *) ( V+low)) - move);
md = ((void *) ( _M+wing)) - (((void *) ( M+low)) - move);
had = ((void *) (_HA+wing)) - (((void *) (HA+low)) - move);
hbd = ((void *) (_HB+wing)) - (((void *) (HB+low)) - move);
nad = ((void *) (_NA+wing)) - (((void *) (NA+low)) - move);
nbd = ((void *) (_NB+wing)) - (((void *) (NB+low)) - move);
td = ((void *) ( _T+wing)) - (((void *) ( T+low)) - move);
if (vd < 0)
memmove( _V+wing, ((void *) ( V+low)) - move, span*sizeof(int));
if (md < 0)
memmove( _M+wing, ((void *) ( M+low)) - move, span*sizeof(int));
if (had < 0)
memmove(_HA+wing, ((void *) (HA+low)) - move, span*sizeof(int));
if (hbd < 0)
memmove(_HB+wing, ((void *) (HB+low)) - move, span*sizeof(int));
if (nad < 0)
memmove(_NA+wing, ((void *) (NA+low)) - move, span*sizeof(int));
if (nbd < 0)
memmove(_NB+wing, ((void *) (NB+low)) - move, span*sizeof(int));
if (td < 0)
memmove( _T+wing, ((void *) ( T+low)) - move, span*sizeof(BVEC));
if (td > 0)
memmove( _T+wing, ((void *) ( T+low)) - move, span*sizeof(BVEC));
if (nbd > 0)
memmove(_NB+wing, ((void *) (NB+low)) - move, span*sizeof(int));
if (nad > 0)
memmove(_NA+wing, ((void *) (NA+low)) - move, span*sizeof(int));
if (hbd > 0)
memmove(_HB+wing, ((void *) (HB+low)) - move, span*sizeof(int));
if (had > 0)
memmove(_HA+wing, ((void *) (HA+low)) - move, span*sizeof(int));
if (md > 0)
memmove( _M+wing, ((void *) ( M+low)) - move, span*sizeof(int));
if (vd > 0)
memmove( _V+wing, ((void *) ( V+low)) - move, span*sizeof(int));
vmin = low-wing;
vmax = hgh+wing;
V = _V-vmin;
M = _M-vmin;
HA = _HA-vmin;
HB = _HB-vmin;
NA = _NA-vmin;
NB = _NB-vmin;
T = _T-vmin;
}
if (low >= minp)
{ NA[low] = NA[low+1];
NB[low] = NB[low+1];
V[low] = -1;
}
else
low += 1;
if (hgh <= maxp)
{ NA[hgh] = NA[hgh-1];
NB[hgh] = NB[hgh-1];
V[hgh] = am = -1;
}
else
am = V[--hgh];
dif += 1;
ac = V[hgh+1] = V[low-1] = -1;
a = aseq + hgh;
t = PATH_INT;
n = PATH_LEN;
ua = ub = -1;
for (k = hgh; k >= low; k--)
{ int y, m;
int ha, hb;
int c, d;
BVEC b;
Pebble *pb;
ap = ac;
ac = am;
am = V[d = k-1];
if (ac < am)
if (am < ap)
{ c = ap+1;
m = n;
b = t;
ha = ua;
hb = ub;
}
else
{ c = am+1;
m = M[d];
b = T[d];
ha = HA[d];
hb = HB[d];
}
else
if (ac < ap)
{ c = ap+1;
m = n;
b = t;
ha = ua;
hb = ub;
}
else
{ c = ac+2;
m = M[k];
b = T[k];
ha = HA[k];
hb = HB[k];
}
if ((b & PATH_TOP) != 0)
m -= 1;
b <<= 1;
y = (c-k) >> 1;
while (1)
{ c = bseq[y];
if (c == 4)
{ more = 0;
if (bclip < k)
bclip = k;
break;
}
d = a[y];
if (c != d)
{ if (d == 4)
{ more = 0;
aclip = k;
}
break;
}
y += 1;
if ((b & PATH_TOP) == 0)
m += 1;
b = (b << 1) | 1;
}
c = (y << 1) + k;
while (y+k >= NA[k])
{ if (cells[ha].mark < NA[k])
{ if (avail >= cmax)
{ cmax = ((int) (avail*1.2)) + 10000;
cells = (Pebble *) Realloc(cells,cmax*sizeof(Pebble),
"Reallocating trace cells");
if (cells == NULL)
EXIT(1);
work->celmax = cmax;
work->cells = (void *) cells;
}
#ifdef SHOW_TPS
printf(" A %d: %d,%d,%d,%d\n",avail,ha,k,dif,NA[k]); fflush(stdout);
#endif
pb = cells+avail;
pb->ptr = ha;
pb->diag = k;
pb->diff = dif;
pb->mark = NA[k];
ha = avail++;
}
NA[k] += TRACE_SPACE;
}
while (y >= NB[k])
{ if (cells[hb].mark < NB[k])
{ if (avail >= cmax)
{ cmax = ((int) (avail*1.2)) + 10000;
cells = (Pebble *) Realloc(cells,cmax*sizeof(Pebble),
"Reallocating trace cells");
if (cells == NULL)
EXIT(1);
work->celmax = cmax;
work->cells = (void *) cells;
}
#ifdef SHOW_TPS
printf(" B %d: %d,%d,%d,%d\n",avail,hb,k,dif,NB[k]); fflush(stdout);
#endif
pb = cells+avail;
pb->ptr = hb;
pb->diag = k;
pb->diff = dif;
pb->mark = NB[k];
hb = avail++;
}
NB[k] += TRACE_SPACE;
}
if (c > besta)
{ besta = c;
besty = y;
if (m >= PATH_AVE)
{ lasta = c;
if (TABLE[b & TRIM_MASK] >= 0)
if (TABLE[(b >> TRIM_LEN) & TRIM_MASK] + SCORE[b & TRIM_MASK] >= 0)
{ trima = c;
trimy = y;
trimd = dif;
trimha = ha;
trimhb = hb;
}
}
}
t = T[k];
n = M[k];
ua = HA[k];
ub = HB[k];
V[k] = c;
T[k] = b;
M[k] = m;
HA[k] = ha;
HB[k] = hb;
a -= 1;
}
if (more == 0)
{ if (bseq[besty] != 4 && aseq[besta-besty] != 4)
more = 1;
if (hgh >= aclip)
{ hgh = aclip-1;
if (morem <= M[aclip])
{ morem = M[aclip];
morea = V[aclip];
morey = (morea - aclip)/2;
mored = dif;
moreha = HA[aclip];
morehb = HB[aclip];
}
}
if (low <= bclip)
{ low = bclip+1;
if (morem <= M[bclip])
{ morem = M[bclip];
morea = V[bclip];
morey = (morea - bclip)/2;
mored = dif;
moreha = HA[bclip];
morehb = HB[bclip];
}
}
aclip = INT32_MAX;
bclip = -INT32_MAX;
}
n = besta - WAVE_LAG;
while (hgh >= low)
if (V[hgh] < n)
hgh -= 1;
else
{ while (V[low] < n)
low += 1;
break;
}
#ifdef WAVE_STATS
k = (hgh-low)+1;
if (k > MAX)
MAX = k;
TOT += k;
NWV += 1;
#endif
#ifdef DEBUG_WAVE
print_wave(V,M,low,hgh,besta);
#endif
}
{ uint16 *atrace = (uint16 *) apath->trace;
uint16 *btrace = (uint16 *) bpath->trace;
int atlen, btlen;
int trimx;
int a, b, k, h;
int d, e;
if (morem >= 0 && REACH)
{ trimx = morea-morey;
trimy = morey;
trimd = mored;
trimha = moreha;
trimhb = morehb;
}
else
trimx = trima-trimy;
atlen = btlen = 0;
a = -1;
for (h = trimha; h >= 0; h = b)
{ b = cells[h].ptr;
cells[h].ptr = a;
a = h;
}
h = a;
k = cells[h].diag;
b = (mida-k)/2;
e = 0;
#ifdef SHOW_TRAIL
printf(" A path = (%5d,%5d)\n",(mida+k)/2,b); fflush(stdout);
#endif
for (h = cells[h].ptr; h >= 0; h = cells[h].ptr)
{ k = cells[h].diag;
a = cells[h].mark - k;
d = cells[h].diff;
atrace[atlen++] = (uint16) (d-e);
atrace[atlen++] = (uint16) (a-b);
#ifdef SHOW_TRAIL
printf(" %4d: (%5d,%5d): %3d / %3d\n",h,a+k,a,d-e,a-b); fflush(stdout);
#endif
b = a;
e = d;
}
if (b+k != trimx)
{ atrace[atlen++] = (uint16) (trimd-e);
atrace[atlen++] = (uint16) (trimy-b);
#ifdef SHOW_TRAIL
printf(" (%5d,%5d): %3d / %3d\n",trimx,trimy,trimd-e,trimy-b); fflush(stdout);
#endif
}
else if (b != trimy)
{ atrace[atlen-1] = (uint16) (atrace[atlen-1] + (trimy-b));
atrace[atlen-2] = (uint16) (atrace[atlen-2] + (trimd-e));
#ifdef SHOW_TRAIL
printf(" @ (%5d,%5d): %3d / %3d\n",trimx,trimy,trimd-e,trimy-b); fflush(stdout);
#endif
}
a = -1;
for (h = trimhb; h >= 0; h = b)
{ b = cells[h].ptr;
cells[h].ptr = a;
a = h;
}
h = a;
k = cells[h].diag;
b = (mida+k)/2;
e = 0;
low = k;
#ifdef SHOW_TRAIL
printf(" B path = (%5d,%5d)\n",b,(mida-k)/2); fflush(stdout);
#endif
for (h = cells[h].ptr; h >= 0; h = cells[h].ptr)
{ k = cells[h].diag;
a = cells[h].mark + k;
d = cells[h].diff;
btrace[btlen++] = (uint16) (d-e);
btrace[btlen++] = (uint16) (a-b);
#ifdef SHOW_TRAIL
printf(" %4d: (%5d,%5d): %3d / %3d\n",h,a,a-k,d-e,a-b); fflush(stdout);
#endif
b = a;
e = d;
}
if (b-k != trimy)
{ btrace[btlen++] = (uint16) (trimd-e);
btrace[btlen++] = (uint16) (trimx-b);
#ifdef SHOW_TRAIL
printf(" (%5d,%5d): %3d / %3d\n",trimx,trimy,trimd-e,trimx-b); fflush(stdout);
#endif
}
else if (b != trimx)
{ btrace[btlen-1] = (uint16) (btrace[btlen-1] + (trimx-b));
btrace[btlen-2] = (uint16) (btrace[btlen-2] + (trimd-e));
#ifdef SHOW_TRAIL
printf(" @ (%5d,%5d): %3d / %3d\n",trimx,trimy,trimd-e,trimx-b); fflush(stdout);
#endif
}
apath->aepos = trimx;
apath->bepos = trimy;
apath->diffs = trimd;
apath->tlen = atlen;
bpath->tlen = btlen;
}
*mind = low;
return (0);
}
/*** Reverse Wave ***/
static int reverse_wave(_Work_Data *work, _Align_Spec *spec, Alignment *align, Path *bpath,
int mind, int maxd, int mida, int minp, int maxp, int aoff, int boff)
{ char *aseq = align->aseq - 1;
char *bseq = align->bseq - 1;
Path *apath = align->path;
int hgh, low, dif;
int vlen, vmin, vmax;
int *V, *M;