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filter.c
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/* vim: set et ts=2 sts=2 sw=2 : */
/*******************************************************************************************
*
* Fast local alignment filter for long, noisy reads based on "dumbing down" of my RECOMB 2005
* filter with Jens Stoye, and a "smarting up" of the k-mer matching by turning it into
* a threaded sort and merge paradigm using a super cache coherent radix sort. Local
* alignment is accomplised with dynamically-banded O(nd) algorithm that terminates when
* it fails to find a e-matching patch for a significant distance, and polishes the match
* to the last e-prefix-positive 32-mer.
*
* Author : Gene Myers
* First : June 2013
* Current: June 1, 2014
*
********************************************************************************************/
// 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 "filter.h"
#include "align.h"
#define THREAD pthread_t
#define MAX_BIAS 2 // In -b mode, don't consider tuples with specificity
// <= 4 ^ -(kmer-MAX_BIAS)
#define MAXGRAM 10000 // Cap on k-mer count histogram (in count_thread, merge_thread)
#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 expected number of hits between two reads
#define TRACE_CHUNK 20000 // Max expected 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;
typedef struct
{ int diag;
int apos;
int aread;
int bread;
} SeedPair;
#else
typedef struct
{ uint64 code;
int read;
int rpos;
} KmerPos;
typedef struct
{ int apos;
int diag;
int bread;
int aread;
} SeedPair;
#endif
/*******************************************************************************************
*
* PARAMETER SETUP
*
********************************************************************************************/
static int Kmer;
static int Hitmin;
static int Binshift;
static int Suppress;
static int Kshift; // 2*Kmer
static uint64 Kmask; // 4^Kmer-1
static int TooFrequent; // (Suppress != 0) ? Suppress : INT32_MAX
static int NTHREADS; // Adjusted downward to nearest power of 2
static int NSHIFT; // NTHREADS = 1 << NSHIFT
int Set_Filter_Params(int kmer, int binshift, int suppress, int hitmin, int nthread)
{ if (kmer <= 1)
return (1);
Kmer = kmer;
Binshift = binshift;
Suppress = suppress;
Hitmin = hitmin;
Kshift = 2*Kmer;
if (Kmer == 32)
Kmask = 0xffffffffffffffffllu;
else
Kmask = (0x1llu << Kshift) - 1;
if (Suppress == 0)
TooFrequent = INT32_MAX;
else
TooFrequent = Suppress;
NTHREADS = 1;
NSHIFT = 0;
while (2*NTHREADS <= nthread)
{ 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;
#define VERY_VERBOSE 0
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 (VERY_VERBOSE)
{ printf("\n ----");
printf("\n shift=%d, LEX_last=%d, n=%lld", shift, LEX_last, n);
fflush(stdout);
}
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]++;
if (VERY_VERBOSE)
{ printf("\n @=%p+%lld i=%6lld,c&=%3lld,x=%3lld,c=%lld ", (void*)trg, (sizeof(Double)*x), i, (c&BMASK), x, c);
fflush(stdout);
}
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;
}
if (VERY_VERBOSE)
{ printf("\n Finished @%p n=%lld", (void*)trg, n);
fflush(stdout);
}
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 int *NormShift = NULL;
static int LogNorm, LogThresh;
static int LogBase[4];
static HITS_DB *TA_block;
static KmerPos *TA_list;
static HITS_TRACK *TA_track;
typedef struct
{ int tnum;
int64 *kptr;
int fill;
} 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;
if (TA_track != NULL)
{ HITS_READ *reads = TA_block->reads;
int64 *anno1 = ((int64 *) (TA_track->anno)) + 1;
int *point = (int *) (TA_track->data);
int64 a, b, f;
int q = 0;
f = anno1[i-1];
for (m = (c * (tnum+1)) >> NSHIFT; i < m; i++)
{ b = f;
f = anno1[i];
for (a = b; a <= f; a += 2)
{ if (a == b)
p = 0;
else
p = point[a-1];
if (a == f)
q = reads[i].rlen;
else
q = point[a];
if (p+Kmer <= q)
{ c = 0;
for (x = 1; x < Kmer; x++)
c = (c << 2) | s[p++];
while (p < q)
{ x = s[p];
c = ((c << 2) | x) & Kmask;
list[n].read = i;
list[n].rpos = p++;
list[n].code = c;
n += 1;
kptr[c & BMASK] += 1;
}
}
}
s += (q+1);
}
m = TA_block->reads[m].boff - Kmer*m;
kptr[BMASK] += (data->fill = m-n);
while (n < m)
{ list[n].code = 0xffffffffffffffffllu;
list[n].read = 0xffffffff;
list[n].rpos = 0xffffffff;
n += 1;
}
}
else
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 void *biased_tuple_thread(void *arg)
{ Tuple_Arg *data = (Tuple_Arg *) arg;
int tnum = data->tnum;
int64 *kptr = data->kptr;
KmerPos *list = TA_list;
int n, i, m;
int x, a, k, p;
uint64 d, c;
char *s, *t;
c = TA_block->nreads;
i = (c * tnum) >> NSHIFT;
n = TA_block->reads[i].boff;
s = ((char *) (TA_block->bases)) + n;
n -= Kmer*i;
if (TA_track != NULL)
{ HITS_READ *reads = TA_block->reads;
int64 *anno1 = ((int64 *) (TA_track->anno)) + 1;
int *point = (int *) (TA_track->data);
int64 j, b, f;
int q = 0;
f = anno1[i-1];
for (m = (c * (tnum+1)) >> NSHIFT; i < m; i++)
{ b = f;
f = anno1[i];
t = s+1;
for (j = b; j <= f; j += 2)
{ if (j == b)
p = 0;
else
p = point[j-1];
if (j == f)
q = reads[i].rlen;
else
q = point[j];
if (p+Kmer <= q)
{ c = 0;
a = 0;
k = 1;
while (p < q)
{ x = s[p];
a += LogBase[x];
c = ((c << 2) | x);
while (a < LogNorm && k < Kmer)
{ if (++p >= q)
break;
k += 1;
x = s[p];
a += LogBase[x];
c = ((c << 2) | x);
}
while (1)
{ int u = a-LogBase[(int) t[p-k]];
if (u < LogNorm) break;
a = u;
k -= 1;
}
if (a > LogThresh)
{ d = ((c << NormShift[k]) & Kmask);
list[n].read = i;
list[n].rpos = p;
list[n].code = d;
n += 1;
kptr[d & BMASK] += 1;
}
p += 1;
a -= LogBase[(int) s[p-k]];
}
}
}
s += (q+1);
}
}
else
for (m = (c * (tnum+1)) >> NSHIFT; i < m; i++)
{ t = s+1;
c = 0;
p = a = 0;
k = 1;
while ((x = s[p]) != 4)
{ a += LogBase[x];
c = ((c << 2) | x);
while (a < LogNorm && k < Kmer)
{ if ((x = s[++p]) == 4)
goto eoread2;
k += 1;
a += LogBase[x];
c = ((c << 2) | x);
}
while (1)
{ int u = a-LogBase[(int) t[p-k]];
if (u < LogNorm) break;
a = u;
k -= 1;
}
if (a > LogThresh)
{ d = ((c << NormShift[k]) & Kmask);
list[n].read = i;
list[n].rpos = p;
list[n].code = d;
n += 1;
kptr[d & BMASK] += 1;
}
p += 1;
a -= LogBase[(int) s[p-k]];
}
eoread2:
s += (p+1);
}
m = TA_block->reads[m].boff - Kmer*m;
kptr[BMASK] += (data->fill = m-n);
while (n < m)
{ list[n].code = 0xffffffffffffffffllu;
list[n].read = 0xffffffff;
list[n].rpos = 0xffffffff;
n += 1;
}
return (NULL);
}
static KmerPos *FR_src;
static KmerPos *FR_trg;
typedef struct
{ int beg;
int end;
int kept;
} Comp_Arg;
static void *compsize_thread(void *arg)
{ Comp_Arg *data = (Comp_Arg *) arg;
int end = data->end;
KmerPos *src = FR_src;
int n, i, c, p;
uint64 h, g;
i = data->beg;
h = src[i].code;
n = 0;
while (i < end)
{ p = i++;
while ((g = src[i].code) == h)
i += 1;
if ((c = (i-p)) < TooFrequent)
n += c;
h = g;
}
data->kept = n;
return (NULL);
}
static void *compress_thread(void *arg)
{ Comp_Arg *data = (Comp_Arg *) arg;
int end = data->end;
KmerPos *src = FR_src;
KmerPos *trg = FR_trg;
int n, i, p;
uint64 h, g;
i = data->beg;
h = src[i].code;
n = data->kept;
while (i < end)
{ p = i++;
while ((g = src[i].code) == h)
i += 1;
if (i-p < TooFrequent)
{ while (p < i)
trg[n++] = src[p++];
}
h = g;
}
return (NULL);
}
void *Sort_Kmers(HITS_DB *block, int *len)
{ THREAD threads[NTHREADS];
Tuple_Arg parmt[NTHREADS];
Comp_Arg parmf[NTHREADS];
Lex_Arg parmx[NTHREADS];
int mersort[16];
KmerPos *src, *trg, *rez;
int kmers, nreads;
int i, j, x, z;
uint64 h;
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;
if (NormShift == NULL && BIASED)
{ double scale;
NormShift = (int *) Malloc(sizeof(int)*(Kmer+1),"Allocating Sort_Kmers bias shift");
if (NormShift == NULL)
exit (1);
for (i = 0; i <= Kmer; i++)
NormShift[i] = Kshift - 2*i;
LogNorm = 10000 * Kmer;
LogThresh = 10000 * (Kmer-MAX_BIAS);
scale = -10000. / log(4.);
for (i = 0; i < 4; i++)
LogBase[i] = (int) ceil( scale * log(block->freq[i]) );
}
nreads = block->nreads;
kmers = block->reads[nreads].boff - Kmer * nreads;
if (kmers <= 0)
goto no_mers;
if (VERBOSE)
{
printf("\n Kshift=%d", Kshift);
printf("\n BSHIFT=%d", BSHIFT);
printf("\n TooFrequent=%d", TooFrequent);
printf("\n (Kshift-1)/BSHIFT + (TooFrequent < INT32_MAX)=%d", ((Kshift-1)/BSHIFT + (TooFrequent < INT32_MAX)));
printf("\n sizeof(KmerPos)=%ld", sizeof(KmerPos));
printf("\n nreads=%d", nreads);
printf("\n Kmer=%d", Kmer);
printf("\n block->reads[nreads].boff=%lld", (block->reads[nreads].boff));
printf("\n kmers=%d", kmers);
printf("\n sizeof(KmerPos)*(kmers+1)=%ld", (sizeof(KmerPos)*(kmers+1)));
fflush(stdout);
}
if (( (Kshift-1)/BSHIFT + (TooFrequent < INT32_MAX) ) & 0x1)
{ trg = (KmerPos *) Malloc(sizeof(KmerPos)*(kmers+2),"Allocating Sort_Kmers vectors");
src = (KmerPos *) Malloc(sizeof(KmerPos)*(kmers+2),"Allocating Sort_Kmers vectors");
}
else
{ src = (KmerPos *) Malloc(sizeof(KmerPos)*(kmers+2),"Allocating Sort_Kmers vectors");
trg = (KmerPos *) Malloc(sizeof(KmerPos)*(kmers+2),"Allocating Sort_Kmers vectors");
}
if (VERBOSE) printf("\n Allocated %d of %ld (%lu bytes) at %p", (kmers+1), sizeof(KmerPos), (sizeof(KmerPos)*(kmers+1)), (void*)trg);
if (src == NULL || trg == NULL)
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;
TA_track = block->tracks;
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;
}
if (BIASED)
for (i = 0; i < NTHREADS; i++)
pthread_create(threads+i,NULL,biased_tuple_thread,parmt+i);
else
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 (BIASED || TA_track != NULL)
for (i = 0; i < NTHREADS; i++)
kmers -= parmt[i].fill;
if (TooFrequent < INT32_MAX && kmers > 0)
{ parmf[0].beg = 0;
for (i = 1; i < NTHREADS; i++)
{ x = (((int64) i)*kmers) >> NSHIFT;
h = rez[x-1].code;
while (rez[x].code == h)
x += 1;
parmf[i-1].end = parmf[i].beg = x;
}
parmf[NTHREADS-1].end = kmers;
if (rez[kmers-1].code == 0xffffffffffffffffllu)
rez[kmers].code = 0;
else
rez[kmers].code = 0xffffffffffffffffllu;
if (src == rez)
{ FR_src = src;
FR_trg = rez = trg;
}
else
{ FR_src = trg;
FR_trg = rez = src;
}
for (i = 0; i < NTHREADS; i++)
pthread_create(threads+i,NULL,compsize_thread,parmf+i);
for (i = 0; i < NTHREADS; i++)
pthread_join(threads[i],NULL);
x = 0;
for (i = 0; i < NTHREADS; i++)
{ z = parmf[i].kept;
parmf[i].kept = x;
x += z;
}
kmers = x;
for (i = 0; i < NTHREADS; i++)
pthread_create(threads+i,NULL,compress_thread,parmf+i);
for (i = 0; i < NTHREADS; i++)
pthread_join(threads[i],NULL);
}
rez[kmers].code = 0xffffffffffffffffllu;
rez[kmers+1].code = 0;
if (src != rez)
free(src);
else
free(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)
{ if (TooFrequent < INT32_MAX || BIASED || TA_track != NULL)
{ printf(" Revised kmer count = ");
Print_Number((int64) kmers,0,stdout);
printf("\n");
}
printf(" Index occupies %.2fGb\n",(1. * kmers) / 67108864);
fflush(stdout);
}
if (kmers <= 0)
{ free(rez);
goto no_mers;
}
if (kmers > (int64) (MEM_LIMIT/(4*sizeof(KmerPos))))
{ fprintf(stderr,"Warning: Block size too big, index occupies more than 1/4 of");
if (MEM_LIMIT == MEM_PHYSICAL)
fprintf(stderr," physical memory (%.1fGb)\n",(1.*MEM_LIMIT)/0x40000000ll);
else
fprintf(stderr," desired memory allocation (%.1fGb)\n",(1.*MEM_LIMIT)/0x40000000ll);
fflush(stderr);
}
*len = kmers;
return (rez);
no_mers:
*len = 0;
return (NULL);
}
/*******************************************************************************************
*
* FILTER MATCH
*
********************************************************************************************/
static int find_tuple(uint64 x, KmerPos *a, int n)
{ int l, r, m;
// smallest k s.t. a[k].code >= x (or n if does not exist)
l = 0;
r = n;
while (l < r)
{ m = ((l+r) >> 1);
if (a[m].code < x)
l = m+1;
else
r = m;
}
return (l);
}
// Determine what *will* be the size of the merged list and histogram of sizes for given cutoffs
static KmerPos *MG_alist;
static KmerPos *MG_blist;
static SeedPair *MG_hits;
static int MG_comp;
static int MG_self;
typedef struct
{ int abeg, aend;
int bbeg, bend;
int64 *kptr;
int64 nhits;
int limit;
int64 hitgram[MAXGRAM];
} Merge_Arg;
static void *count_thread(void *arg)
{ Merge_Arg *data = (Merge_Arg *) arg;
KmerPos *asort = MG_alist;
KmerPos *bsort = MG_blist;
int64 *gram = data->hitgram;
int64 nhits = 0;
int aend = data->aend;
int64 ct;
int ia, ib;
int jb, ja;
uint64 ca, cb;
uint64 da, db;
int ar, ap;
int a, b;
ia = data->abeg;
ca = asort[ia].code;
ib = data->bbeg;
cb = bsort[ib].code;
if (MG_self)
{ while (1)
{ while (cb < ca)
cb = bsort[++ib].code;
while (cb > ca)
ca = asort[++ia].code;
if (cb == ca)
{ ja = ia++;
while ((da = asort[ia].code) == ca)
ia += 1;
jb = ib++;
while ((db = bsort[ib].code) == cb)
ib += 1;
if (ia > aend)
{ if (ja >= aend)
break;
da = asort[ia = aend].code;
db = bsort[ib = data->bend].code;
}
ct = 0;
b = jb;
if (IDENTITY)
for (a = ja; a < ia; a++)
{ ar = asort[a].read;
if (MG_comp)
{ while (b < ib && bsort[b].read <= ar)
b += 1;
}
else
{ ap = asort[a].rpos;
while (b < ib && bsort[b].read < ar)
b += 1;
while (b < ib && bsort[b].read == ar && bsort[b].rpos < ap)
b += 1;
}
ct += (b-jb);
}
else
for (a = ja; a < ia; a++)
{ ar = asort[a].read;
while (b < ib && bsort[b].read < ar)
b += 1;
ct += (b-jb);
}
nhits += ct;
ca = da;
cb = db;
if (ct < MAXGRAM)
gram[ct] += 1;
}
}
}
else
{ while (1)
{ while (cb < ca)