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tandem.c
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tandem.c
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/*******************************************************************************************
*
* Adaption of the fast local alignment filter of "daligner" for finding alignments between
* a read and itself above the diagonal. Satellites create a "ladder" of these self alignments
* that can be detected in order to recognize said repetitive sequences within the read.
*
* Author : Gene Myers
* First : March 2016
* Current: March 27, 2016
*
********************************************************************************************/
// A complete threaded code for the filter
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#include <string.h>
#include <unistd.h>
#include <math.h>
#include <pthread.h>
#include "DB.h"
#include "align.h"
#include "tandem.h"
#define THREAD pthread_t
#define PANEL_SIZE 50000 // Size to break up very long A-reads
#define PANEL_OVERLAP 10000 // Overlap of A-panels
#define MATCH_CHUNK 100 // Max initial number of hits between two reads
#define TRACE_CHUNK 20000 // Max initial trace points in hits between two reads
#undef TEST_LSORT
#undef TEST_KSORT
#undef TEST_PAIRS
#undef TEST_CSORT
#define HOW_MANY 3000 // Print first HOW_MANY items for each of the TEST options above
#undef TEST_GATHER
#undef TEST_CONTAIN
#undef SHOW_OVERLAP // Show the cartoon
#undef SHOW_ALIGNMENT // Show the alignment
#define ALIGN_WIDTH 80 // Parameters for alignment
#define ALIGN_INDENT 20
#define ALIGN_BORDER 10
#ifdef SHOW_OVERLAP
#define NOTHREAD
#endif
#ifdef TEST_GATHER
#define NOTHREAD
#endif
#ifdef TEST_CONTAIN
#define NOTHREAD
#endif
typedef struct
{ uint64 p1; // The lower half
uint64 p2;
} Double;
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
typedef struct
{ uint64 code;
int rpos;
int read;
} KmerPos;
#else
typedef struct
{ uint64 code;
int read;
int rpos;
} KmerPos;
#endif
/*******************************************************************************************
*
* PARAMETER SETUP
*
********************************************************************************************/
static int Kmer;
static int Hitmin;
static int Binshift;
static int Kshift; // 2*Kmer
static uint64 Kmask; // 4^Kmer-1
static int NTHREADS; // Must be a power of 2
static int NSHIFT; // log_2 NTHREADS
int Set_Filter_Params(int kmer, int binshift, int hitmin, int nthreads)
{ if (kmer <= 1)
return (1);
Kmer = kmer;
Binshift = binshift;
Hitmin = hitmin;
Kshift = 2*Kmer;
if (Kmer == 32)
Kmask = 0xffffffffffffffffllu;
else
Kmask = (0x1llu << Kshift) - 1;
NTHREADS = 1;
NSHIFT = 0;
while (2*NTHREADS <= nthreads)
{ NTHREADS *= 2;
NSHIFT += 1;
}
return (0);
}
/*******************************************************************************************
*
* LEXICOGRAPHIC SORT
*
********************************************************************************************/
#define BMER 4
#define BSHIFT 8 // = 2*BMER
#define BPOWR 256 // = 2^BSHIFT
#define BMASK 0xffllu // = BPOWR-1
static uint64 QMASK; // = BMASK << NSHIFT
static int LEX_shift;
static int64 LEX_zsize;
static int LEX_last;
static int LEX_next;
static Double *LEX_src;
static Double *LEX_trg;
typedef struct
{ int64 beg;
int64 end;
int64 tptr[BPOWR];
int64 *sptr;
} Lex_Arg;
static void *lex_thread(void *arg)
{ Lex_Arg *data = (Lex_Arg *) arg;
int64 *sptr = data->sptr;
int64 *tptr = data->tptr;
int shift = LEX_shift; // Must be a multiple of 8 in [0,120]
int qshift = (LEX_next - LEX_shift) - NSHIFT;
int64 zsize = LEX_zsize;
Double *src = LEX_src;
Double *trg = LEX_trg;
int64 i, n, x;
uint64 c, b;
n = data->end;
if (shift >= 64)
{ shift -= 64;
if (LEX_last)
for (i = data->beg; i < n; i++)
{ c = src[i].p2;
b = (c >> shift);
x = tptr[b&BMASK]++;
trg[x] = src[i];
}
else
for (i = data->beg; i < n; i++)
{ c = src[i].p2;
b = (c >> shift);
x = tptr[b&BMASK]++;
trg[x] = src[i];
sptr[((b >> qshift) & QMASK) + x/zsize] += 1;
}
}
else if ( ! LEX_last && LEX_next >= 64) // && LEX_shift < 64
{ qshift = (LEX_next - 64) - NSHIFT;
if (qshift < 0)
for (i = data->beg; i < n; i++)
{ c = src[i].p1;
b = (c >> shift);
x = tptr[b&BMASK]++;
trg[x] = src[i];
sptr[((src[i].p2 << NSHIFT) & QMASK) + x/zsize] += 1;
}
else
for (i = data->beg; i < n; i++)
{ c = src[i].p1;
b = (c >> shift);
x = tptr[b&BMASK]++;
trg[x] = src[i];
sptr[((src[i].p2 >> qshift) & QMASK) + x/zsize] += 1;
}
}
else // LEX_last || LEX_next < 64
if (LEX_last)
if (shift == 0)
for (i = data->beg; i < n; i++)
{ c = src[i].p1;
x = tptr[c&BMASK]++;
trg[x] = src[i];
}
else
for (i = data->beg; i < n; i++)
{ c = src[i].p1;
b = (c >> shift);
x = tptr[b&BMASK]++;
trg[x] = src[i];
}
else
if (shift == 0)
for (i = data->beg; i < n; i++)
{ c = src[i].p1;
x = tptr[c&BMASK]++;
trg[x] = src[i];
sptr[((c >> qshift) & QMASK) + x/zsize] += 1;
}
else
for (i = data->beg; i < n; i++)
{ c = src[i].p1;
b = (c >> shift);
x = tptr[b&BMASK]++;
trg[x] = src[i];
sptr[((b >> qshift) & QMASK) + x/zsize] += 1;
}
return (NULL);
}
static Double *lex_sort(int bytes[16], Double *src, Double *trg, Lex_Arg *parmx)
{ THREAD threads[NTHREADS];
int64 len, x, y;
Double *xch;
int i, j, k, z;
int b, c, fb;
len = parmx[NTHREADS-1].end;
LEX_zsize = (len-1)/NTHREADS + 1;
LEX_src = src;
LEX_trg = trg;
QMASK = (BMASK << NSHIFT);
for (c = 0; c < 16; c++)
if (bytes[c])
break;
fb = c;
for (b = c; b < 16; b = c)
{ for (c = b+1; c < 16; c++)
if (bytes[c])
break;
LEX_last = (c >= 16);
LEX_shift = (b << 3);
LEX_next = (c << 3);
if (b == fb)
{ for (i = 0; i < NTHREADS; i++)
for (z = 0; z < NTHREADS*BPOWR; z++)
parmx[i].sptr[z] = 0;
}
else
{ x = 0;
for (i = 0; i < NTHREADS; i++)
{ parmx[i].beg = x;
x = LEX_zsize*(i+1);
if (x > len)
x = len;
parmx[i].end = x;
for (j = 0; j < BPOWR; j++)
parmx[i].tptr[j] = 0;
}
parmx[NTHREADS-1].end = len;
for (j = 0; j < BPOWR; j++)
{ k = (j << NSHIFT);
for (z = 0; z < NTHREADS; z++)
for (i = 0; i < NTHREADS; i++)
{ parmx[i].tptr[j] += parmx[z].sptr[k+i];
parmx[z].sptr[k+i] = 0;
}
}
}
x = 0;
for (j = 0; j < BPOWR; j++)
for (i = 0; i < NTHREADS; i++)
{ y = parmx[i].tptr[j];
parmx[i].tptr[j] = x;
x += y;
}
for (i = 0; i < NTHREADS; i++)
pthread_create(threads+i,NULL,lex_thread,parmx+i);
for (i = 0; i < NTHREADS; i++)
pthread_join(threads[i],NULL);
xch = LEX_src;
LEX_src = LEX_trg;
LEX_trg = xch;
#ifdef TEST_LSORT
printf("\nLSORT %d\n",LEX_shift);
if (LEX_shift >= 64)
{ x = (1 << ((LEX_shift-64)+BSHIFT))-1;
for (i = 0; i < len; i++)
{ printf("%6d: %8llx %8llx %8llx %8llx : %4llx",
i,LEX_src[i].p2>>32,(LEX_src[i].p2)&0xffffffffll,LEX_src[i].p1>>32,
LEX_src[i].p1&0xffffffffll,LEX_src[i].p2&x);
if (i > 0 && (LEX_src[i].p1 < LEX_src[i].p1 ||
(LEX_src[i].p1 == LEX_src[i].p1 &&
(LEX_src[i].p2 & x) < (LEX_src[i-1].p2 & x))))
printf(" OO");
printf("\n");
}
}
else
{ x = (1 << (LEX_shift+BSHIFT))-1;
for (i = 0; i < len; i++)
{ printf("%6d: %8llx %8llx %8llx %8llx : %4llx",
i,LEX_src[i].p2>>32,(LEX_src[i].p2)&0xffffffffll,LEX_src[i].p1>>32,
LEX_src[i].p1&0xffffffffll,LEX_src[i].p1&x);
if (i > 0 && (LEX_src[i].p1 & x) < (LEX_src[i-1].p1 & x))
printf(" OO");
printf("\n");
}
}
#endif
}
return (LEX_src);
}
/*******************************************************************************************
*
* INDEX BUILD
*
********************************************************************************************/
static DAZZ_DB *TA_block;
static KmerPos *TA_list;
typedef struct
{ int tnum;
int64 *kptr;
} Tuple_Arg;
static void *tuple_thread(void *arg)
{ Tuple_Arg *data = (Tuple_Arg *) arg;
int tnum = data->tnum;
int64 *kptr = data->kptr;
KmerPos *list = TA_list;
int i, m, n, x, p;
uint64 c;
char *s;
c = TA_block->nreads;
i = (c * tnum) >> NSHIFT;
n = TA_block->reads[i].boff;
s = ((char *) (TA_block->bases)) + n;
n -= Kmer*i;
for (m = (c * (tnum+1)) >> NSHIFT; i < m; i++)
{ c = p = 0;
for (x = 1; x < Kmer; x++)
c = (c << 2) | s[p++];
while ((x = s[p]) != 4)
{ c = ((c << 2) | x) & Kmask;
list[n].read = i;
list[n].rpos = ++p;
list[n].code = c;
n += 1;
kptr[c & BMASK] += 1;
}
s += (p+1);
}
return (NULL);
}
static KmerPos *Sort_Kmers(DAZZ_DB *block, int *len, KmerPos **buffer)
{ THREAD threads[NTHREADS];
Tuple_Arg parmt[NTHREADS];
Lex_Arg parmx[NTHREADS];
int mersort[16];
KmerPos *src, *trg, *rez;
int kmers, nreads;
int i, j, x;
for (i = 0; i < NTHREADS; i++)
parmx[i].sptr = (int64 *) alloca(NTHREADS*BPOWR*sizeof(int64));
for (i = 0; i < 16; i++)
mersort[i] = 0;
for (i = 0; i < Kshift; i += 8)
mersort[i>>3] = 1;
nreads = block->nreads;
kmers = block->reads[nreads].boff - Kmer * nreads;
if (kmers <= 0)
goto no_mers;
if (((Kshift-1)/BSHIFT) & 0x1)
{ trg = (KmerPos *) Malloc(sizeof(KmerPos)*(kmers+1),"Allocating Sort_Kmers vectors");
src = (KmerPos *) Malloc(sizeof(KmerPos)*(kmers+1),"Allocating Sort_Kmers vectors");
}
else
{ src = (KmerPos *) Malloc(sizeof(KmerPos)*(kmers+1),"Allocating Sort_Kmers vectors");
trg = (KmerPos *) Malloc(sizeof(KmerPos)*(kmers+1),"Allocating Sort_Kmers vectors");
}
if (src == NULL || trg == NULL)
Clean_Exit(1);
if (VERBOSE)
{ printf("\n Kmer count = ");
Print_Number((int64) kmers,0,stdout);
printf("\n Using %.2fGb of space\n",(1. * kmers) / 33554432);
fflush(stdout);
}
TA_block = block;
TA_list = src;
for (i = 0; i < NTHREADS; i++)
{ parmt[i].tnum = i;
parmt[i].kptr = parmx[i].tptr;
for (j = 0; j < BPOWR; j++)
parmt[i].kptr[j] = 0;
}
for (i = 0; i < NTHREADS; i++)
pthread_create(threads+i,NULL,tuple_thread,parmt+i);
for (i = 0; i < NTHREADS; i++)
pthread_join(threads[i],NULL);
x = 0;
for (i = 0; i < NTHREADS; i++)
{ parmx[i].beg = x;
j = (int) ((((int64) nreads) * (i+1)) >> NSHIFT);
parmx[i].end = x = block->reads[j].boff - j*Kmer;
}
rez = (KmerPos *) lex_sort(mersort,(Double *) src,(Double *) trg,parmx);
if (rez[kmers-1].code == 0xffffffffffffffffllu)
rez[kmers].code = 0;
else
rez[kmers].code = 0xffffffffffffffffllu;
rez[kmers].read = nreads;
if (src != rez)
*buffer = src;
else
*buffer = trg;
#ifdef TEST_KSORT
{ int i;
printf("\nKMER SORT:\n");
for (i = 0; i < HOW_MANY && i < kmers; i++)
{ KmerPos *c = rez+i;
printf(" %5d / %5d / %10lld\n",c->read,c->rpos,c->code);
}
fflush(stdout);
}
#endif
if (VERBOSE)
{ printf(" Index occupies %.2fGb\n",(1. * kmers) / 67108864);
fflush(stdout);
}
if (kmers <= 0)
{ free(rez);
goto no_mers;
}
*len = kmers;
return (rez);
no_mers:
*len = 0;
return (NULL);
}
/*******************************************************************************************
*
* FILTER MATCH
*
********************************************************************************************/
// After the initial sort, all equal K-tuples are contiguous, and for a given K-tuple read,rpos
// is in sorted order because the sort is stable. For a given read, record the distance between
// consecutive positions with the same K-mer in the .code field. Afterwords, the array is
// stably resorted on read,rpos so that for each read one has effectively a "linked list" of
// positions with equal K-mers.
static KmerPos *MG_alist;
typedef struct
{ int abeg, aend;
int64 *kptr;
} Merge_Arg;
static void *count_thread(void *arg)
{ Merge_Arg *data = (Merge_Arg *) arg;
int64 *kptr = data->kptr;
KmerPos *asort = MG_alist;
int aend = data->aend;
uint64 ca, da;
int ia;
int ar, nr;
int ap, np;
ia = data->abeg;
da = asort[ia].code;
while (ia < aend)
{ ca = da;
ar = asort[ia].read;
ap = asort[ia].rpos;
kptr[ap & BMASK] += 1;
while ((da = asort[++ia].code) == ca)
{ np = asort[ia].rpos;
if ((nr = asort[ia].read) == ar)
asort[ia].code = np - ap;
else
{ asort[ia].code = 0;
ar = nr;
}
ap = np;
kptr[ap & BMASK] += 1;
}
asort[ia].code = 0;
}
return (NULL);
}
// Report threads: using the linked lists of consereved K-mers find likely seeds and then check
// for alignments as per "daligner".
static DAZZ_DB *MR_ablock;
static Align_Spec *MR_spec;
static int MR_tspace;
typedef struct
{ uint64 max;
uint64 top;
uint16 *trace;
} Trace_Buffer;
// Determine if the minimum B-distance between the overlapping trace points of jpath and kpath
// Return this minimum and also the A-coordinate of a trace point where it is acheived.
static int Entwine(Path *jpath, Path *kpath, Trace_Buffer *tbuf, int *where)
{ int ac, b2, y2, ae;
int i, j, k;
int num, den, min;
#ifdef SEE_ENTWINE
int strt, iflare, oflare;
#endif
uint16 *ktrace = tbuf->trace + (uint64) (kpath->trace);
uint16 *jtrace = tbuf->trace + (uint64) (jpath->trace);
min = 10000;
num = 0;
den = 0;
#ifdef SEE_ENTWINE
strt = 1;
printf("\n");
#endif
y2 = jpath->bbpos;
j = jpath->abpos/MR_tspace;
b2 = kpath->bbpos;
k = kpath->abpos/MR_tspace;
if (jpath->abpos == kpath->abpos)
{ min = abs(y2-b2);
if (min == 0)
*where = kpath->abpos;
}
if (j < k)
{ ac = k*MR_tspace;
j = 1 + 2*(k-j);
k = 1;
for (i = 1; i < j; i += 2)
y2 += jtrace[i];
}
else
{ ac = j*MR_tspace;
k = 1 + 2*(j-k);
j = 1;
for (i = 1; i < k; i += 2)
b2 += ktrace[i];
}
ae = jpath->aepos;
if (ae > kpath->aepos)
ae = kpath->aepos;
while (1)
{ ac += MR_tspace;
if (ac >= ae)
break;
y2 += jtrace[j];
b2 += ktrace[k];
j += 2;
k += 2;
#ifdef SEE_ENTWINE
printf(" @ %5d : %5d %5d = %4d\n",ac,y2,b2,abs(b2-y2));
#endif
i = abs(y2-b2);
if (i <= min)
{ min = i;
if (i == 0)
*where = ac;
}
num += i;
den += 1;
#ifdef SEE_ENTWINE
if (strt)
{ strt = 0;
iflare = i;
}
oflare = i;
#endif
}
if (jpath->aepos == kpath->aepos)
{ i = abs(jpath->bepos-kpath->bepos);
if (i <= min)
{ min = i;
if (i == 0)
*where = kpath->aepos;
}
}
#ifdef SEE_ENTWINE
if (den == 0)
printf("Nothing\n");
else
printf("MINIM = %d AVERAGE = %d IFLARE = %d OFLARE = %d\n",min,num/den,iflare,oflare);
#endif
if (den == 0)
return (-1);
else
return (min);
}
// Produce the concatentation of path1 and path2 where they are known to meet at
// the trace point with coordinate ap. Place this result in a big growing buffer,
// that gets reset when fusion is called with path1 = NULL
static void Fusion(Path *path1, int ap, Path *path2, Trace_Buffer *tbuf)
{ int k, k1, k2;
int len, diff;
uint16 *trace;
k1 = 2 * ((ap/MR_tspace) - (path1->abpos/MR_tspace));
k2 = 2 * ((ap/MR_tspace) - (path2->abpos/MR_tspace));
len = k1+(path2->tlen-k2);
if (tbuf->top + len >= tbuf->max)
{ tbuf->max = 1.2*(tbuf->top+len) + 1000;
tbuf->trace = (uint16 *) Realloc(tbuf->trace,sizeof(uint16)*tbuf->max,"Allocating paths");
if (tbuf->trace == NULL)
Clean_Exit(1);
}
trace = tbuf->trace + tbuf->top;
tbuf->top += len;
diff = 0;
len = 0;
if (k1 > 0)
{ uint16 *t = tbuf->trace + (uint64) (path1->trace);
for (k = 0; k < k1; k += 2)
{ trace[len++] = t[k];
trace[len++] = t[k+1];
diff += t[k];
}
}
if (k2 < path2->tlen)
{ uint16 *t = tbuf->trace + (uint64) (path2->trace);
for (k = k2; k < path2->tlen; k += 2)
{ trace[len++] = t[k];
trace[len++] = t[k+1];
diff += t[k];
}
}
path1->aepos = path2->aepos;
path1->bepos = path2->bepos;
path1->diffs = diff;
path1->trace = (void *) (trace - tbuf->trace);
path1->tlen = len;
}
// Given all the LA's for a given read in amatch[0..novls-1], merge any overlapping LA's and
// remove any redundant ones.
static int Handle_Redundancies(Path *amatch, int novls, Trace_Buffer *tbuf)
{ Path *jpath, *kpath;
int j, k, no;
int dist, awhen = 0;
#ifdef TEST_CONTAIN
for (j = 0; j < novls; j++)
printf(" %3d: [%5d,%5d] x [%5d,%5d]\n",j,amatch[j].abpos,amatch[j].aepos,
amatch[j].bbpos,amatch[j].bepos);
#endif
for (j = 1; j < novls; j++)
{ jpath = amatch+j;
for (k = j-1; k >= 0; k--)
{ kpath = amatch+k;
if (kpath->abpos < 0)
continue;
if (jpath->abpos < kpath->abpos)
{ if (kpath->abpos <= jpath->aepos && kpath->bbpos <= jpath->bepos)
{ dist = Entwine(jpath,kpath,tbuf,&awhen);
if (dist == 0)
{ if (kpath->aepos > jpath->aepos)
{ Fusion(jpath,awhen,kpath,tbuf);
#ifdef TEST_CONTAIN
printf(" Really 3");
#endif
k = j;
}
kpath->abpos = -1;
#ifdef TEST_CONTAIN
printf(" Fuse! A %d %d\n",j,k);
#endif
}
}
}
else // kpath->abpos <= jpath->abpos
{ if (jpath->abpos <= kpath->aepos && jpath->bbpos <= kpath->bepos)
{ dist = Entwine(kpath,jpath,tbuf,&awhen);
if (dist == 0)
{ if (kpath->abpos == jpath->abpos)
{ if (kpath->aepos > jpath->aepos)
*jpath = *kpath;
}
else if (jpath->aepos > kpath->aepos)
{ Fusion(kpath,awhen,jpath,tbuf);
*jpath = *kpath;
#ifdef TEST_CONTAIN
printf(" Really 6");
#endif
k = j;
}
else
*jpath = *kpath;
kpath->abpos = -1;
#ifdef TEST_CONTAIN
printf(" Fuse! B %d %d\n",j,k);
#endif
}
}
}
}
}
no = 0;
for (j = 0; j < novls; j++)
if (amatch[j].abpos >= 0)
amatch[no++] = amatch[j];
novls = no;
#ifdef TEST_CONTAIN
for (j = 0; j < novls; j++)
printf(" %3d: [%5d,%5d] x [%5d,%5d]\n",j,amatch[j].abpos,amatch[j].aepos,
amatch[j].bbpos,amatch[j].bepos);
#endif
return (novls);
}
// Determine the range of diagonal bins containing trace points of path
void Diagonal_Span(Path *path, int *mind, int *maxd)
{ uint16 *points;
int i, tlen;
int dd, low, hgh;
points = path->trace;
tlen = path->tlen;
dd = path->abpos - path->bbpos;
low = hgh = dd;
dd = path->aepos - path->bepos;
if (dd < low)
low = dd;
else if (dd > hgh)
hgh = dd;
dd = (path->abpos/MR_tspace)*MR_tspace - path->bbpos;
tlen -= 2;
for (i = 1; i < tlen; i += 2)
{ dd += MR_tspace - points[i];
if (dd < low)
low = dd;
else if (dd > hgh)
hgh = dd;
}
*mind = (low >> Binshift)-1;
*maxd = (hgh >> Binshift)+1;
}
typedef struct
{ int64 beg, end;
int *score;
int *lastp;
int *lasta;
Work_Data *work;
FILE *ofile;
int64 nfilt;
int64 ncheck;
} Report_Arg;
static void *report_thread(void *arg)
{ Report_Arg *data = (Report_Arg *) arg;
DAZZ_READ *aread = MR_ablock->reads;
KmerPos *asort = MG_alist;
int *score = data->score;
int *scorp = data->score + 1;
int *scorm = data->score - 1;
int *lastp = data->lastp;
int *lasta = data->lasta;
int maxdiag = ( MR_ablock->maxlen >> Binshift);
int mindiag = (-MR_ablock->maxlen >> Binshift);
FILE *ofile = data->ofile;
char *aseq = (char *) (MR_ablock->bases);
Work_Data *work = data->work;
int afirst = MR_ablock->tfirst;
Overlap _ovla, *ovla = &_ovla;
Alignment _align, *align = &_align;
Path *apath = &(ovla->path);
int64 nfilt = 0;
int64 ahits = 0;
int small, tbytes;
int novla;
int AOmax;
Path *amatch;
Trace_Buffer _tbuf, *tbuf = &_tbuf;
int ar, aend;
KmerPos *aoff;
align->flags = ovla->flags = 0;
align->path = apath;
if (MR_tspace <= TRACE_XOVR)
{ small = 1;
tbytes = sizeof(uint8);
}
else
{ small = 0;
tbytes = sizeof(uint16);
}
AOmax = MATCH_CHUNK;
amatch = Malloc(sizeof(Path)*AOmax,"Allocating match vector");
tbuf->max = 2*TRACE_CHUNK;
tbuf->trace = Malloc(sizeof(short)*tbuf->max,"Allocating trace vector");
if (amatch == NULL || tbuf->trace == NULL)
Clean_Exit(1);
fwrite(&ahits,sizeof(int64),1,ofile);
fwrite(&MR_tspace,sizeof(int),1,ofile);
#ifdef TEST_GATHER
printf("\nNEW THREAD %5d(%5lld)-%5d(%5lld)\n",asort[data->beg].read,data->beg,
asort[data->end-1].read,data->end);
fflush(stdout);
#endif
aoff = asort + (data->beg - Kmer);
aend = asort[data->end-1].read;
for (ar = asort[data->beg].read; ar <= aend; ar++)
{ int alen, amarkb, amarke;
int apos, diag;
int setaln;
#ifdef TEST_GATHER
printf("Read %5d\n",ar);
fflush(stdout);
#endif
setaln = 1;
novla = 0;
tbuf->top = 0;
alen = aread[ar].rlen;
amarkb = Kmer;
amarke = PANEL_SIZE;
if (amarke >= alen)
amarke = alen+1;
while (1)
{
// Accumulate diagonal scores
for (apos = amarkb; apos < amarke; apos++)
{ diag = aoff[apos].code;
if (diag == 0) continue;
diag >>= Binshift;
if (apos - lastp[diag] >= Kmer)
score[diag] += Kmer;
else
score[diag] += apos - lastp[diag];
lastp[diag] = apos;
}
// Examine diagonal scores for hits to check out
for (apos = amarkb; apos < amarke; apos++)
{ diag = aoff[apos].code;
if (diag == 0) continue;
diag >>= Binshift;
if (apos > lasta[diag] &&
(score[diag] + scorp[diag] >= Hitmin || score[diag] + scorm[diag] >= Hitmin))
{ int bpos;
bpos = apos - aoff[apos].code;
if (setaln)
{ setaln = 0;
align->aseq = align->bseq = aseq + aread[ar].boff;
align->alen = align->blen = alen;
ovla->aread = ovla->bread = ar + afirst;
}
#ifdef TEST_GATHER
if (scorm[diag] > scorp[diag])
printf(" %5d.. x %5d.. %5d (%3d)",
bpos,apos,apos-bpos,score[diag]+scorm[diag]);
else
printf(" %5d.. x %5d.. %5d (%3d)",
bpos,apos,apos-bpos,score[diag]+scorp[diag]);
fflush(stdout);
#endif
nfilt += 1;
Local_Alignment(align,work,MR_spec,apos-bpos,apos-bpos,apos+bpos,-1,-1);
{ int low, hgh, ae;
Diagonal_Span(apath,&low,&hgh);
if (diag < low)
low = diag;
else if (diag > hgh)
hgh = diag;
ae = apath->aepos;
for (diag = low; diag <= hgh; diag++)
if (ae > lasta[diag])
lasta[diag] = ae;
#ifdef TEST_GATHER