const void test_large_string_size (void)
{
ELIM (sizeof large_string == MAX + 1);
/* The following expressions are not folded without optimization. */
ELIM ('a' == large_string[0]);
ELIM ('\0' == large_string[1233]);
ELIM ('b' == large_string[1234]);
ELIM ('\0' == large_string[1235]);
ELIM ('\0' == large_string[MAX - 1]);
}
void test_nulstring (void)
{
T (a2_implicit, 0);
T (a3_implicit, 0);
T (a3_nul, 0);
T (a5_nul1, 0);
T (a7_nul2, 0);
T (ax_2_nul, 2);
T (ax_3_nul, 3);
T (ax_3_des_nul, 3);
T (ax_100_3, 3);
T (ax_100_3 + 4, 0);
ELIM (101 == sizeof ax_100_3);
ELIM ('\0' == ax_100_3[100]);
/* Verify that all three character arrays have the same length
as the string literal they are initialized with. */
T (S, 255);
T (c256, 255);
T ((const char*)sc256, 255);
T ((const char*)uc256, 255);
/* Verify that all three character arrays have the same contents
as the string literal they are initialized with. */
ELIM (0 == memcmp (c256, S, sizeof c256));
ELIM (0 == memcmp (c256, (const char*)sc256, sizeof c256));
ELIM (0 == memcmp (c256, (const char*)uc256, sizeof c256));
ELIM (0 == strcmp (c256, (const char*)sc256));
ELIM (0 == strcmp (c256, (const char*)uc256));
/* Verify that the char16_t array has the expected contents. */
ELIM (c16_4[0] == 1 && c16_4[1] == 0x7fff
&& c16_4[2] == 0x8000 && c16_4[3] == 0xffff
&& c16_4[4] == 0);
}
static int buildModel(int nolink, int nolap, int elim, int max_comp, int max_expn)
{ int first, last;
FILE *input;
DAZZ_READ *reads;
LA *local;
Pile *pile;
void *tbuffer;
int *panels, *plists;
Overlap ovl;
int64 novl;
int a, pos;
int omax, n, m;
int64 smax, tlen;
int btip, etip;
int npan, nspl, nlas;
reads = MODEL.db1->reads;
input = MODEL.input;
first = MODEL.first;
last = MODEL.last;
rewind(input);
fread(&novl,sizeof(int64),1,input);
fread(&TRACE_SPACING,sizeof(int),1,input);
if (TRACE_SPACING <= TRACE_XOVR && TRACE_SPACING != 0)
TBYTES = sizeof(uint8);
else
TBYTES = sizeof(uint16);
if (TRACE_SPACING > 0)
PANEL_SIZE = ((PANEL_TARGET-1)/TRACE_SPACING+1)*TRACE_SPACING;
else
PANEL_SIZE = ((PANEL_TARGET-1)/100+1)*100;
Read_Overlap(input,&ovl);
if (ovl.aread >= first)
MODEL.first = first = ovl.aread;
else
while (ovl.aread < first)
{ fseek(input,TBYTES*ovl.path.tlen,SEEK_CUR);
Read_Overlap(input,&ovl);
novl -= 1;
}
local = (LA *) Malloc(novl*sizeof(LA),"Allocating alignments");
if (local == NULL)
return (-1);
pile = (Pile *) Malloc(((last-first)+1)*sizeof(Pile),"Allocating piles");
if (pile == NULL)
{ free(local);
return (-1);
}
pile -= first;
npan = nspl = nlas = 0;
pos = PILE_SPACING/2;
a = first-1;
omax = m = n = 0;
smax = 0;
while (ovl.aread < last)
{ while (a < ovl.aread)
{ int j, b, e, p;
if (a >= first)
{ if (reads[a].rlen < PANEL_FUDGE)
p = 0;
else
p = ((reads[a].rlen-PANEL_FUDGE) / PANEL_SIZE);
for (j = m; j < n; j++)
{ b = local[j].abpos / PANEL_SIZE;
e = (local[j].aepos-1) / PANEL_SIZE;
if (e > p)
e = p;
nlas += e-b;
}
nspl += 1;
npan += p+1;
}
a += 1;
pile[a].first = n;
pile[a].where = pos;
pile[a].offset = ftello(input) - OvlIOSize;
pile[a].panels = npan;
if (n-m > omax)
omax = n-m;
m = n;
pos += reads[a].rlen + PILE_SPACING;
}
local[n].bread = (ovl.bread << 1);
if (COMP(ovl.flags))
local[n].bread |= 0x1;
local[n].bbpos = ovl.path.bbpos;
local[n].bepos = ovl.path.bepos;
local[n].btip = btip = tiplen(ovl.path.abpos,ovl.path.bbpos);
local[n].etip = etip = tiplen(reads[ovl.aread].rlen-ovl.path.aepos,
MODEL.db2->reads[ovl.bread].rlen-ovl.path.bepos);
local[n].abpos = ovl.path.abpos - btip;
local[n].aepos = ovl.path.aepos + etip;
local[n].toff = ftell(input);
if (CHAIN_START(ovl.flags))
local[n].etip |= STRT_FLAG;
if (CHAIN_NEXT(ovl.flags))
local[n].etip |= SUCC_FLAG;
if (ELIM(ovl.flags))
local[n].etip |= ELIM_BIT;
n += 1;
tlen = TBYTES*ovl.path.tlen;
if (smax < tlen)
smax = tlen;
fseeko(input,tlen,SEEK_CUR);
if (feof(input))
break;
if (Read_Overlap(input,&ovl))
break;
}
{ int j, b, e, p;
if (a < last-1)
{ MODEL.last = last = a+1;
pile = (Pile *) Realloc(pile+first,((last-first)+1)*sizeof(Pile),"Reallocating piles");
pile -= first;
}
if (a >= first)
{ if (reads[a].rlen < PANEL_FUDGE)
p = 0;
else
p = ((reads[a].rlen-PANEL_FUDGE) / PANEL_SIZE);
for (j = m; j < n; j++)
{ b = local[j].abpos / PANEL_SIZE;
e = (local[j].aepos-1) / PANEL_SIZE;
if (e > p)
e = p;
nlas += e-b;
}
nspl += 1;
npan += p+1;
}
pile[last].first = n;
pile[last].where = pos;
pile[last].offset = ftello(input) - OvlIOSize;
pile[last].panels = npan;
if (n-m > omax)
omax = n-m;
pile[last].where -= PILE_SPACING/2;
pile[last].offset += OvlIOSize;
if (n < novl)
local = (LA *) Realloc(local,n*sizeof(LA),"Allocating alignments");
}
{ LA *temp;
nlas = n + nlas;
panels = (int *) Malloc((npan+1)*sizeof(int),"Panels");
if (panels == NULL)
goto error;
plists = (int *) Malloc(nlas*sizeof(int),"Panel Lists");
if (plists == NULL)
goto error;
temp = (LA *) Realloc(local,(n+1)*sizeof(LA),"Finalizing alignments");
if (temp == NULL)
goto error;
local = temp;
tbuffer = Malloc(smax,"Allocating trace buffer");
if (tbuffer == NULL)
goto error;
}
{ int a, k;
int *manels;
int *count;
for (k = 0; k <= npan; k++)
panels[k] = 0;
manels = panels+1;
for (a = first; a < last; a++)
{ int j, b, e, p;
count = manels + pile[a].panels;
if (reads[a].rlen < PANEL_FUDGE)
p = 0;
else
p = ((reads[a].rlen-PANEL_FUDGE) / PANEL_SIZE);
for (j = pile[a].first; j < pile[a+1].first; j++)
{ b = local[j].abpos / PANEL_SIZE;
e = (local[j].aepos-1) / PANEL_SIZE;
if (e > p)
e = p;
for (k = b; k <= e; k++)
count[k] += 1;
}
}
for (k = 2; k <= npan; k++)
panels[k] += panels[k-1];
for (a = first; a < last; a++)
{ int j, b, e, p;
count = panels + pile[a].panels;
if (reads[a].rlen < PANEL_FUDGE)
p = 0;
else
p = ((reads[a].rlen-PANEL_FUDGE) / PANEL_SIZE);
p = ((reads[a].rlen-PANEL_FUDGE) / PANEL_SIZE);
for (j = pile[a].first; j < pile[a+1].first; j++)
{ b = local[j].abpos / PANEL_SIZE;
e = (local[j].aepos-1) / PANEL_SIZE;
if (e > p)
e = p;
for (k = b; k <= e; k++)
plists[count[k]++] = j;
local[j].abpos += local[j].btip;
local[j].aepos -= (local[j].etip & DATA_ETIP);
}
}
for (k = npan; k >= 1; k--)
panels[k] = panels[k-1];
panels[0] = 0;
}
MODEL.local = local;
MODEL.pile = pile;
MODEL.omax = omax;
MODEL.tbuf = tbuffer;
MODEL.tspace = TRACE_SPACING;
MODEL.tbytes = TBYTES;
MODEL.panels = panels;
MODEL.plists = plists;
UNDEFINED = 0;
if (reLayoutModel(nolink,nolap,elim,max_comp,max_expn))
{ UNDEFINED = 1;
goto error;
}
return (0);
error:
free(local);
free(pile+first);
return (1);
}
