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#include "pilercr.h"
const int MAXIGAP = 5;
static Trapezoid *free_traps = NULL;
static Trapezoid eotrap;
static Trapezoid *eoterm = &eotrap;
static int HSORT(const void *l, const void *r)
{
FilterHit *x = (FilterHit *) l;
FilterHit *y = (FilterHit *) r;
return x->QFrom - y->QFrom;
}
Trapezoid *MergeFilterHits(const char *SeqT, int SeqLengthT, const char *SeqQ,
int SeqLengthQ, bool Self, const FilterHit *FilterHits, int FilterHitCount,
const FilterParams &FP, int *ptrTrapCount)
{
if (0 == FilterHitCount)
{
*ptrTrapCount = 0;
return 0;
}
qsort((void *) FilterHits, FilterHitCount, sizeof(FilterHit), HSORT);
#if DEBUG
{
// Verify sort order
for (int i = 0; i < FilterHitCount-1; ++i)
if (FilterHits[i+1].QFrom < FilterHits[i].QFrom)
Quit("Build_Trapezoids: not sorted");
}
#endif
const int TubeWidth = FP.TubeOffset + FP.SeedDiffs;
const int DPADDING = 2;
const int BINWIDE = TubeWidth - 1;
const int BPADDING = k + 2;
const int LPADDING = DPADDING + BINWIDE;
free_traps = NULL;
eoterm = &eotrap;
Trapezoid *traporder, *traplist, *tailend;
Trapezoid *b, *f, *t;
int i, nd, tp;
int trapcount;
#ifdef REPORT_SIZES
int traparea;
#endif
#ifdef REPORT_SIZES
traparea = 0;
#endif
eoterm->lft = SeqLengthQ+1+LPADDING;
eoterm->rgt = SeqLengthQ+1;
eoterm->bot = -1;
eoterm->top = SeqLengthQ+1;
eoterm->next = NULL;
trapcount = 0;
traporder = eoterm;
traplist = NULL;
for (i = 0; i < FilterHitCount; i++)
{ nd = - FilterHits[i].DiagIndex;
if (Self && nd <= FP.SeedDiffs)
continue;
tp = FilterHits[i].QFrom - BPADDING;
#ifdef TEST_TRAP
printf(" Diag %d [%d,%d]\n",
nd,FilterHits[i].QFrom,FilterHits[i].QTo);
#endif
f = NULL;
// for b in traporder
for (b = traporder; 1; b = t)
{ t = b->next;
if (b->top < tp)
{ trapcount += 1;
#ifdef REPORT_SIZES
traparea += (b->top - b->bot + 1) * (b->rgt - b->lft + 1);
#endif
if (f == NULL)
traporder = t;
else
f->next = t;
b->next = traplist;
traplist = b;
}
else if (nd > b->rgt + DPADDING)
f = b;
else if (nd >= b->lft - LPADDING)
{ if (nd+BINWIDE > b->rgt)
b->rgt = nd+BINWIDE;
if (nd < b->lft)
b->lft = nd;
if (FilterHits[i].QTo > b->top)
b->top = FilterHits[i].QTo;
if (f != NULL && f->rgt + DPADDING >= b->lft)
{ f->rgt = b->rgt;
if (f->bot > b->bot) f->bot = b->bot;
if (f->top < b->top) f->top = b->top;
f->next = t;
b->next = free_traps;
free_traps = b;
}
else if (t != NULL && t->lft - DPADDING <= b->rgt)
{ b->rgt = t->rgt;
if (b->bot > t->bot) b->bot = t->bot;
if (b->top < t->top) b->top = t->top;
b->next = t->next;
t->next = free_traps;
free_traps = t;
t = b->next;
f = b;
}
else
f = b;
break;
}
else
{
// Add to free_trap list
if (free_traps == NULL)
{ free_traps = (Trapezoid *) malloc(sizeof(Trapezoid));
if (free_traps == NULL)
Quit("out of memory Trapezoid scan FilterHits");
free_traps->next = NULL;
}
if (f == NULL)
f = traporder = free_traps;
else
f = f->next = free_traps;
free_traps = f->next;
f->next = b;
if (f->next == 0)
Log("f->next [3] %x\n", f);
f->top = FilterHits[i].QTo;
f->bot = FilterHits[i].QFrom;
f->lft = nd;
f->rgt = f->lft + BINWIDE;
f = b;
break;
}
}
#ifdef TEST_TRAP
printf(" Blist:");
for (b = traporder; b != NULL; b = b->next)
printf(" [%d,%d]x[%d,%d]",
b->bot,b->top,b->lft,b->rgt);
printf("\n");
#endif
}
for (b = traporder; b != eoterm; b = t)
{ t = b->next;
trapcount += 1;
#ifdef REPORT_SIZES
traparea += (b->top - b->bot + 1) * (b->rgt - b->lft + 1);
#endif
b->next = traplist;
traplist = b;
}
#ifdef REPORT_SIZES
printf("\n %9d trapezoids of area %d (%f%% of matrix)\n",
trapcount,traparea,(100.*trapcount/SeqLengthT)/SeqLengthQ);
fflush(stdout);
#endif
{ int lag, lst, lclip;
int abot, atop;
#ifdef TEST_TRAPTRIM
printf("SeqQ trimming:\n");
#endif
for (b = traplist; b != NULL; b = b->next)
{ lag = (b->bot-MAXIGAP)+1;
if (lag < 0) lag = 0;
lst = b->top+MAXIGAP;
if (lst > SeqLengthQ) lst = SeqLengthQ;
#ifdef TEST_TRAPTRIM
printf(" [%d,%d]x[%d,%d] = %d\n",
b->bot,b->top,b->lft,b->rgt,b->top - b->bot + 1);
#endif
for (i = lag; i < lst; i++)
{ if (CharToLetter[(unsigned char) (SeqQ[i])] >= 0)
{ if (i-lag >= MAXIGAP)
{ if (lag - b->bot > 0)
{ if (free_traps == NULL)
{ free_traps = (Trapezoid *) malloc(sizeof(Trapezoid));
if (free_traps == NULL)
Quit("out of memory Trapezoid cutter");
free_traps->next = NULL;
}
t = free_traps->next;
*free_traps = *b;
b->next = free_traps;
free_traps = t;
b->top = lag;
b = b->next;
b->bot = i;
trapcount += 1;
}
else
b->bot = i;
#ifdef TEST_TRAPTRIM
printf(" Cut trap SeqQ[%d,%d]\n",lag,i);
#endif
}
lag = i+1;
}
}
if (i-lag >= MAXIGAP)
b->top = lag;
}
#ifdef TEST_TRAPTRIM
printf("SeqT trimming:\n");
#endif
tailend = NULL;
for (b = traplist; b != NULL; b = b->next)
{ if (b->top - b->bot < k) continue;
abot = b->bot - b->rgt;
atop = b->top - b->lft;
#ifdef TEST_TRAPTRIM
printf(" [%d,%d]x[%d,%d] = %d\n",
b->bot,b->top,b->lft,b->rgt,b->top - b->bot + 1);
#endif
lag = (abot - MAXIGAP) + 1;
if (lag < 0) lag = 0;
lst = atop + MAXIGAP;
if (lst > SeqLengthT) lst = SeqLengthT;
lclip = abot;
for (i = lag; i < lst; i++)
{ if (CharToLetter[(unsigned char) (SeqT[i])] >= 0)
{ if (i-lag >= MAXIGAP)
{ if (lag > lclip)
{ if (free_traps == NULL)
{ free_traps = (Trapezoid *) malloc(sizeof(Trapezoid));
if (free_traps == NULL)
Quit("out of memory Trapezoid cutter");
free_traps->next = NULL;
}
t = free_traps->next;
*free_traps = *b;
b->next = free_traps;
free_traps = t;
#ifdef TEST_TRAPTRIM
printf(" Clip to %d,%d\n",lclip,lag);
#endif
{ int x, m;
x = lclip + b->lft;
if (b->bot < x)
b->bot = x;
x = lag + b->rgt;
if (b->top > x)
b->top = x;
m = (b->bot + b->top) / 2;
x = m - lag;
if (b->lft < x)
b->lft = x;
x = m - lclip;
if (b->rgt > x)
b->rgt = x;
#ifdef TEST_TRAPTRIM
printf(" [%d,%d]x[%d,%d] = %d\n",
b->bot,b->top,b->lft,b->rgt,b->top-b->bot+1);
#endif
}
b = b->next;
trapcount += 1;
}
lclip = i;
}
lag = i+1;
}
}
if (i-lag < MAXIGAP)
lag = atop;
#ifdef TEST_TRAPTRIM
printf(" Clip to %d,%d\n",lclip,lag);
#endif
{ int x, m;
x = lclip + b->lft;
if (b->bot < x)
b->bot = x;
x = lag + b->rgt;
if (b->top > x)
b->top = x;
m = (b->bot + b->top) / 2;
x = m - lag;
if (b->lft < x)
b->lft = x;
x = m - lclip;
if (b->rgt > x)
b->rgt = x;
#ifdef TEST_TRAPTRIM
printf(" [%d,%d]x[%d,%d] = %d\n",
b->bot,b->top,b->lft,b->rgt,b->top-b->bot+1);
#endif
}
tailend = b;
}
}
if (tailend != NULL)
{
if (free_traps == NULL)
{
free_traps = (Trapezoid *) malloc(sizeof(Trapezoid));
if (free_traps == NULL)
Quit("out of memory Trapezoid cutter");
free_traps->next = NULL;
}
tailend->next = free_traps;
free_traps = traplist;
}
#ifdef REPORT_SIZES
printf(" %9d trimmed trap.s of area %d (%f%% of matrix)\n",
trapcount,traparea,(100.*trapcount/SeqLengthT)/SeqLengthQ);
fflush(stdout);
#endif
*ptrTrapCount = trapcount;
return traplist;
}
int SumTrapLengths(const Trapezoid *Traps)
{
int Sum = 0;
for (const Trapezoid *T = Traps; T; T = T->next)
{
const int Length = T->top - T->bot;
Sum += Length;
}
return Sum;
}
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