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GIXmake.c
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GIXmake.c
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/*******************************************************************************************
*
* Produce a k-mer index of genome's contigs suitable for finding adaptamer seed matches.
* As such only k-mers whose count is less than the adaptamer frequency cutoff are in
* the index which consists of a FASTK k-mer table and an associated position list that
* contains the positions at which each k-mer occurs in order of the k-mers of the table.
* What would normally be the count field for a k-mer contains the lcp of the k-mer with
* its predecessor, and the # of positions at which the k-mer occurs, each in a byte.
*
* Author: Gene Myers
* Date : February 2023
*
*******************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <sys/uio.h>
#include <unistd.h>
#include <math.h>
#include <pthread.h>
#include <sys/resource.h>
#include "libfastk.h"
#include "GDB.h"
static char *Usage[] =
{ "[-v] [-T<int(8)>] [-P<dir(/tmp)>] [-k<int(40)] [-f<int(10)>]",
"( <source:path>[.1gdb] | <source:path>[<fa_extn>|<1_extn>] [<target:path>[.gix]] )"
};
static int FREQ; // -f
static int VERBOSE; // -v
static char *SORT_PATH; // -P
static char *TPATH;
static char *TROOT;
static char *POST_NAME;
static int NTHREADS; // by default 8
static int KMER; // by default 40, must be >= 12 and divisible by 4
static int KBYTES; // Bytes for 2-bit compress k-mer (KMER/4)
#undef DEBUG_MAP
#undef DEBUG_THREADS
#undef DEBUG_SORT
#define BUFFER_LEN 1000000
static int *Perm; // Size sorted permutation of contigs
static int *InvP; // Inverse of Perm
static int PostBytes; // # of bytes needed for a position
static int ContBytes; // # of bytes for a contig + sign bit
static int Comp[256]; // DNA complement of packed byte
static int Select[256]; // 1st k-mer byte -> block (of NTHREAD)
// For p in [0,NTHREADS):
static int *DBsplit; // DB split: contig [DBsplit[p],DBsplit[p+1])
static int64 *DBpost; // DB post: post of start of contig DBsplit[p] is DBpost[p]
static int *Ksplit; // Kmer split: 1st bytes [Ksplit[p],Ksplit[p+1])
static int64 **Buckets; // NTHREADS x 256 array:
// B[i][j] = # of posts whose canonical k-mer's 1st byte
// is j from block DBsplit[i],DBsplit[i+1]
// Also used as "fingers" for loading initial sort array.
static int *Units; // NTHREADS^2 IO units for distribution and import & k-mer table parts
static int *Pnits; // NTHREADS^2 extra IO units for post parts
typedef struct
{ int beg;
int end;
int64 off;
} Range;
extern void msd_sort(uint8 *array, int64 nelem, int rsize, int ksize,
int64 *part, int nthreads, Range *range);
/***********************************************************************************************
*
* DISTRIBUTION PHASE: Output signed posts for each 1/NTHREAD of the data and the k-mers
* At completion file ._post.<jobid>.<i*NTHREADS+j>.idx contains the signed posts from
* contigs (DBsplit[j],DBplist[j+1]) whose k-mers 1st byte is in Ksplit[i],Ksplit[i+1].
*
**********************************************************************************************/
typedef struct
{ int beg;
int end;
uint8 *seq;
uint8 *neq;
uint8 *ceq;
int64 buck[256];
} BP;
// Thread computes neq[beg..end-1] and ceq[beg..end-1] given seq
static void *pack_thread(void *args)
{ BP *parm = (BP *) args;
int beg = parm->beg;
int end = parm->end;
uint8 *seq = parm->seq;
uint8 *neq = parm->neq;
uint8 *ceq = parm->ceq;
int i, k;
uint8 *s1, *s2, *s3, *n1;
s1 = seq+1;
s2 = seq+2;
s3 = seq+3;
for (i = beg; i < end; i += 4)
{ neq[i] = (seq[i] << 6) | (s1[i] << 4) | (s2[i] << 2) | s3[i];
ceq[i] = Comp[neq[i]];
}
n1 = neq-1;
for (k = 1; k < 4; k++)
for (i = beg+k; i < end; i += 4)
{ neq[i] = (n1[i] << 2) | s3[i];
ceq[i] = Comp[neq[i]];
}
return (NULL);
}
// Given neq & ceq, upon completion, for i in [beg,end), seq[i] = file k-mer starting at i should
// go to and whether it should be complemented or not (0x80 flag) in order to be canonical.
// Also accumulates # of these k-mers with a given 1st byte in buck.
static void *map_thread(void *args)
{ BP *parm = (BP *) args;
int beg = parm->beg;
int end = parm->end;
uint8 *seq = parm->seq;
uint8 *neq = parm->neq;
uint8 *ceq = parm->ceq;
int64 *buck = parm->buck;
int kspn = KMER-4;
int i, u, v;
for (i = beg; i < end; i++)
{ for (u = i, v = i+kspn; neq[u] == ceq[v]; u += 4, v -= 4)
if (u >= v)
break;
if (ceq[v] < neq[u])
{ u = ceq[i+kspn];
seq[i] = Select[u] | 0x80;
}
else
{ u = neq[i];
seq[i] = Select[u];
}
buck[u] += 1;
}
return (NULL);
}
typedef struct
{ int tid;
int inum;
uint8 *seq;
int len;
int out;
uint8 *buffer;
uint8 *bend;
int64 post;
int64 last;
} DP;
// The thread scans seq and sends those posts assigned to file tid*Nthreads + ? to their
// designated file relative to the last emission in compressed form:
// x0 -> byte, 6-bit post delta with sign x
// x10 -> short, 13-bit ...
// x110 -> short, 28-bit ...
// x111 -> 0x10000000 spacer
static void *distribute_thread(void *args)
{ DP *parm = (DP *) args;
int tid = parm->tid;
uint8 *seq = parm->seq;
int len = parm->len;
int out = parm->out;
uint8 *buffer = parm->buffer;
uint8 *bend = parm->bend;
int64 post, last;
uint8 *lust = (uint8 *) (&last);
uint8 *b;
int i, u;
b = buffer;
last = parm->last;
post = parm->post;
for (i = 0; i < len; i++, post++)
{ u = seq[i];
if ((u & 0x7f) == tid)
{ last = post-last;
if (last < 0x3f)
{ if (u & 0x80)
*b++ = 0x80 | last;
else
*b++ = last;
}
else if (last < 0x1fff)
{ if (u & 0x80)
last |= 0xc000;
else
last |= 0x4000;
*b++ = lust[1];
*b++ = lust[0];
}
else
{ while (last >= 0x10000000)
{ if (u & 0x80)
*b++ = 0xf0;
else
*b++ = 0x70;
if (b >= bend)
{ if (write(out,buffer,b-buffer) < 0)
{ fprintf(stderr,"%s: IO write to file %s%d.idx failed\n",
Prog_Name,POST_NAME,parm->inum);
exit (1);
}
b = buffer;
}
last -= 0x10000000;
}
if (u & 0x80)
last |= 0xe0000000;
else
last |= 0x60000000;
*b++ = lust[3];
*b++ = lust[2];
*b++ = lust[1];
*b++ = lust[0];
}
if (b >= bend)
{ if (write(out,buffer,b-buffer) < 0)
{ fprintf(stderr,"%s: IO write to file %s%d.idx failed\n",
Prog_Name,POST_NAME,parm->inum);
exit (1);
}
b = buffer;
}
last = post;
}
}
if (b > buffer)
if (write(out,buffer,b-buffer) < 0)
{ fprintf(stderr,"%s: IO write to file %s%d.idx failed\n",
Prog_Name,POST_NAME,parm->inum);
exit (1);
}
parm->last = last;
parm->post = post;
return (NULL);
}
// Distribute posts to the appropriate NTHREADS^2 files based on section of the DB and 1st byte
// of its canonical k-mer
void distribute(GDB *gdb)
{ uint8 *seq;
int len, ren;
uint8 *neq, *ceq;
int p, r, i, j;
DP parm[NTHREADS];
BP barm[NTHREADS];
#ifndef DEBUG_THREADS
pthread_t threads[NTHREADS];
#endif
seq = (uint8 *) New_Contig_Buffer(gdb); // Allocate work vectorss and set up fixed parts of
neq = (uint8 *) New_Contig_Buffer(gdb); // of the thread records
ceq = (uint8 *) New_Contig_Buffer(gdb);
if (seq == NULL || neq == NULL || ceq == NULL)
exit (1);
parm[0].buffer = Malloc(BUFFER_LEN*NTHREADS,"Allocating IO buffer");
for (i = 0; i < NTHREADS; i++)
{ parm[i].tid = i;
parm[i].seq = seq;
parm[i].buffer = parm[0].buffer + BUFFER_LEN*i;
parm[i].bend = parm[i].buffer + (BUFFER_LEN-4);
parm[i].post = 0;
parm[i].last = 0;
}
for (i = 0; i < NTHREADS; i++)
{ barm[i].seq = seq;
barm[i].neq = neq;
barm[i].ceq = ceq;
bzero(barm[i].buck,256*sizeof(int64));
}
// For each segment of the input ...
for (p = 0; p < NTHREADS; p++)
// Open the NTHREAD files to recieve posts from this segment
{ for (i = 0; i < NTHREADS; i++)
{ parm[i].out = Units[i*NTHREADS+p];
parm[i].inum = i*NTHREADS+p;
}
// For each contig in the segment ...
ren = DBsplit[p+1];
for (r = DBsplit[p]; r < ren; r++)
{ if (gdb->contigs[r].boff < 0)
continue;
len = gdb->contigs[r].clen;
Get_Contig(gdb,r,NUMERIC,(char *) seq); // Load the contig
#ifdef DEBUG_MAP
printf("Src:");
for (i = 0; i < len; i++)
printf(" %d",seq[i]);
printf("\n");
#endif
// In segments each thread computes neq and ceq from seq
len -= 3;
barm[0].beg = 0;
for (i = 1; i < NTHREADS; i++)
barm[i-1].end = barm[i].beg = (((int64) i)*len)/NTHREADS;
barm[NTHREADS-1].end = len;
#ifdef DEBUG_THREADS
for (i = 0; i < NTHREADS; i++)
pack_thread(barm+i);
#else
for (i = 1; i < NTHREADS; i++)
pthread_create(threads+i,NULL,pack_thread,barm+i);
pack_thread(barm);
for (i = 1; i < NTHREADS; i++)
pthread_join(threads[i],NULL);
#endif
#ifdef DEBUG_MAP
printf("Neq:");
for (i = 0; i < len; i++)
printf(" %02x",neq[i]);
printf("\n");
printf("Ceq:");
for (i = 0; i < len; i++)
printf(" %02x",ceq[i]);
printf("\n");
#endif
// In segments each thread computes processed seq array from neq,ceq
len -= (KMER-4);
if (len < 0)
{ for (i = 0; i < NTHREADS; i++)
parm[i].post += len + (KMER-1);
continue;
}
barm[0].beg = 0;
for (i = 1; i < NTHREADS; i++)
barm[i-1].end = barm[i].beg = (((int64) i)*len)/NTHREADS;
barm[NTHREADS-1].end = len;
#ifdef DEBUG_THREADS
for (i = 0; i < NTHREADS; i++)
map_thread(barm+i);
#else
for (i = 1; i < NTHREADS; i++)
pthread_create(threads+i,NULL,map_thread,barm+i);
map_thread(barm);
for (i = 1; i < NTHREADS; i++)
pthread_join(threads[i],NULL);
#endif
#ifdef DEBUG_MAP
printf("Out:");
for (i = 0; i < len; i++)
printf(" (%d)%d %02x %02x\n",(seq[i]&0x80)!=0,seq[i]&0x7f,neq[i],ceq[i+KMER-4]);
printf("\n");
#endif
// Each thread scans *all* of seq, writing the k-mers assigned to "its" file
for (i = 0; i < NTHREADS; i++)
parm[i].len = len;
#ifdef DEBUG_THREADS
for (i = 0; i < NTHREADS; i++)
distribute_thread(parm+i);
#else
for (i = 1; i < NTHREADS; i++)
pthread_create(threads+i,NULL,distribute_thread,parm+i);
distribute_thread(parm);
for (i = 1; i < NTHREADS; i++)
pthread_join(threads[i],NULL);
#endif
for (i = 0; i < NTHREADS; i++)
parm[i].post += (KMER-1);
}
// Accumulate bucket counts into Bucket vector for data panel
{ int64 *buck;
buck = Buckets[p];
for (i = 0; i < NTHREADS; i++)
{ for (j = 0; j < 256; j++)
buck[j] += barm[i].buck[j];
parm[i].last = parm[i].post;
}
}
}
free(parm[0].buffer);
free(seq-1);
free(neq-1);
free(ceq-1);
// Complete the bucket array by accumulating counts across k-mer 1st bytes
{ int i, j;
int64 cum;
cum = 0;
for (i = 0; i < 256; i++)
{ for (j = 0; j < NTHREADS; j++)
Buckets[j][i] += cum;
if (i < 255 && Select[i] == Select[i+1])
cum = Buckets[NTHREADS-1][i];
else
cum = 0;
}
}
}
/***********************************************************************************************
*
* SORT PHASE: Read in posts for a given k-mer 1st byte range, recompute their 2-bit compressed
* canonical k-mer, and place them and their k-mer in a sort array in order of 1st byte
* using the Bucket array as a set of "fingers". Then complete the sort with a min-first
* radix sort. Finally output the k-mer table and index for each k-mer range.
*
**********************************************************************************************/
#ifdef DEBUG_SORT
static void print_table(uint8 *array, int swide, int64 nelem)
{ static char DNA[4] = { 'a', 'c', 'g', 't' };
static char *fmer[256], _fmer[1280];
static int first = 1;
int64 x, post, cont, flag, end;
int k;
uint8 *pust = (uint8 *) &post;
uint8 *cust = (uint8 *) &cont;
if (first)
{ char *t;
int i, l3, l2, l1, l0;
first = 0;
i = 0;
t = _fmer;
for (l3 = 0; l3 < 4; l3++)
for (l2 = 0; l2 < 4; l2++)
for (l1 = 0; l1 < 4; l1++)
for (l0 = 0; l0 < 4; l0++)
{ fmer[i] = t;
*t++ = DNA[l3];
*t++ = DNA[l2];
*t++ = DNA[l1];
*t++ = DNA[l0];
*t++ = 0;
i += 1;
}
}
flag = (0x1ll << (8*ContBytes-1));
post = 0;
cont = 0;
end = nelem * swide;
for (x = 0; x < end; x += swide)
{ printf(" %10lld %2d: ",x,array[x]);
for (k = 1; k < KBYTES; k++)
printf("%s",fmer[array[x+k]]);
for (k = 0; k < PostBytes; k++)
pust[k] = array[x+KBYTES+k];
for (k = 0; k < ContBytes; k++)
cust[k] = array[x+KBYTES+PostBytes+k];
if (cont & flag)
printf(" - %11lld (%d)\n",post,cont-flag);
else
printf(" + %11lld (%d)\n",post,cont);
fflush(stdout);
}
}
#endif
typedef struct
{ GDB gdb;
int tid;
int inum;
int in;
int swide;
uint8 *sarr;
uint8 *buff;
} SP;
// Read post file, uncompressing it, recomputing the canonical k-mer at its absolute
// position and loading the k-mer and the signed post into the initial soring array
// for the current 1st byte panel.
static void *setup_thread(void *args)
{ SP *parm = (SP *) args;
int in = parm->in;
int tid = parm->tid;
int swide = parm->swide;
uint8 *sarr = parm->sarr;
uint8 *buffer = parm->buff;
GDB *gdb = &(parm->gdb);
int64 *buck = Buckets[tid];
int iamt;
uint8 *seq;
int len;
uint8 *neq, *ceq, *keq;
int ncntg, inv;
int64 post, bost, last;
int64 cont, nont, flag;
uint8 *lust = (uint8 *) (&last);
uint8 *bust = (uint8 *) (&bost);
uint8 *cust = (uint8 *) (&cont);
uint8 *nust = (uint8 *) (&nont);
int64 nextpost, basepost;
uint8 *bend, *btop, *b;
seq = (uint8 *) New_Contig_Buffer(gdb);
neq = (uint8 *) New_Contig_Buffer(gdb);
ceq = (uint8 *) New_Contig_Buffer(gdb);
if (seq == NULL || neq == NULL || ceq == NULL)
exit (1);
keq = ceq+(KMER-4);
flag = (0x1ll << (8*ContBytes-1));
if (lseek(in,0,SEEK_SET) < 0)
{ fprintf(stderr,"%s: Rewind of file %s%d.idx failed\n",
Prog_Name,POST_NAME,parm->inum);
exit (1);
}
iamt = read(in,buffer,BUFFER_LEN);
if (iamt < 0)
{ fprintf(stderr,"%s: IO read to file %s%d.idx failed\n",
Prog_Name,POST_NAME,parm->inum);
exit (1);
}
bend = buffer + iamt;
if (bend-buffer < BUFFER_LEN)
btop = bend;
else
btop = bend-4;
b = buffer;
if (btop <= buffer) // Nothing to do
{ close(in);
return (NULL);
}
ncntg = DBsplit[tid];
post = DBpost[tid];
nextpost = post;
basepost = post;
while (1)
{ { int v;
int64 extra;
v = *b++; // Get next encoded post, uncompress it and "un-delta"
inv = ((v & 0x80) != 0);
if (v & 0x40)
if (v & 0x20)
{ extra = 0;
while (v & 0x1)
{ extra -= 0x10000000;
v = *b++;
}
last = 0;
lust[3] = (v & 0x0f);
lust[2] = *b++;
lust[1] = *b++;
lust[0] = *b++;
last += extra;
}
else
{ last = 0;
lust[1] = (v & 0x1f);
lust[0] = *b++;
}
else
last = (v & 0x3f);
post += last;
}
if (post >= nextpost) // if position is not in current contig, then fetch the next one
{ int i, k, l;
uint8 *s1, *s2, *s3, *n1;
do
{ len = gdb->contigs[ncntg].clen;
basepost = nextpost;
if (gdb->contigs[ncntg].boff >= 0)
nextpost += len;
ncntg += 1;
}
while (post >= nextpost);
Get_Contig(gdb,ncntg-1,NUMERIC,(char *) seq);
cont = InvP[ncntg-1];
nont = cont | flag;
s1 = seq+1;
s2 = seq+2;
s3 = seq+3;
n1 = neq-1;
l = len-3;
for (i = 0; i < l; i += 4)
{ neq[i] = (seq[i] << 6) | (s1[i] << 4) | (s2[i] << 2) | s3[i];
ceq[i] = Comp[neq[i]];
}
for (k = 1; k < 4; k++)
for (i = k; i < l; i += 4)
{ neq[i] = (n1[i] << 2) | s3[i];
ceq[i] = Comp[neq[i]];
}
}
{ int i; // load the k-mer / post pair into the next available slot in the
uint8 *n, *x; // initial sort array using the bucket index
bost = post-basepost;
if (inv)
{ n = keq+bost;
x = sarr + swide * buck[*n]++;
*x++ = 0;
for (i = 4; i < KMER; i += 4)
*x++ = n[-i];
for (i = 0; i < PostBytes; i++)
*x++ = bust[i];
for (i = 0; i < ContBytes; i++)
*x++ = nust[i];
}
else
{ n = neq+bost;
x = sarr + swide * buck[*n]++;
*x++ = 0;
for (i = 4; i < KMER; i += 4)
*x++ = n[i];
for (i = 0; i < PostBytes; i++)
*x++ = bust[i];
for (i = 0; i < ContBytes; i++)
*x++ = cust[i];
}
}
if (b >= btop) // refill input buffer if needed
{ int ex = bend-b;
memcpy(buffer,b,ex);
bend = buffer+ex;
iamt = read(in,bend,BUFFER_LEN-ex);
if (iamt < 0)
{ fprintf(stderr,"%s: IO read to file %s%d.idx failed\n",
Prog_Name,POST_NAME,parm->inum);
exit (1);
}
bend += iamt;
if (bend == buffer)
break;
if (bend-buffer < BUFFER_LEN)
btop = bend;
else
btop = bend-4;
b = buffer;
}
}
free(seq-1);
free(neq-1);
free(ceq-1);
close(in);
return (NULL);
}
typedef struct
{ int inum;
int swide;
int64 *panel;
uint8 *sarr;
uint8 *buff;
Range *range;
int tout;
int pout;
int64 *prefix;
int64 *posfix;
int64 nelim;
int64 nbase;
int64 nkmer;
int64 npost;
} RP;
// for 1st k-mer byte range [beg,end), find each group of equal k-mers and if < FREQ, then
// write to FastK table under construtions and output (signed) posts of each equal
// k-mer to the associated post list. K-mer 2byte payloads contain the count in the
// first byte and the lcp with its predecessor in the 2nd byte.
static void *output_thread(void *args)
{ RP *parm = (RP *) args;
int swide = parm->swide;
int64 *panel = parm->panel;
uint8 *sarray = parm->sarr;
Range *range = parm->range;
int beg = range->beg;
int end = range->end;
int tout = parm->tout;
int pout = parm->pout;
int64 *prefix = parm->prefix;
int64 *posfix = parm->posfix;
uint8 *buf1 = parm->buff;
uint8 *buf2 = buf1 + 500000;
uint8 *bed1 = (buf1 + 500000) - (KBYTES-1);
uint8 *bed2 = (buf2 + 500000) - (PostBytes+ContBytes);
int64 nelim, nkmer, nbase;
int64 x, e, y;
int o, w, k, z, lcp, idx;
uint8 *_w = (uint8 *) &w;
uint8 *b, *c;
nelim = nkmer = nbase = 0;
o = KMER;
b = buf1;
c = buf2;
x = range->off;
lcp = sarray[x];
prefix += (beg << 16);
posfix += (beg << 8);
for (o = beg; o < end; o++, prefix += 0x10000, posfix += 0x100)
{ e = x + panel[o];
z = (sarray[e] == 0); // Caution: end of panel can have 0 lcp
if (z)
sarray[e] = 1;
for (e = x + panel[o]; x < e; )
{ y = x+swide;
w = 1;
while (sarray[y] == 0)
{ y += swide;
w += 1;
}
// sorted w entries in [x,y) are all equal
if (w >= FREQ)
{ x = y;
if (sarray[x] < lcp)
lcp = sarray[x];
nelim += 1;
nbase += w;
continue;
}
// if < FREQ then output to k-mer table and post list
idx = sarray[x+1];
posfix[idx] += (y-x)/swide;
idx = ((idx << 8) | sarray[x+2]);
prefix[idx] += 1;
for (k = 3; k < KBYTES; k++)
*b++ = sarray[x+k];
*b++ = _w[0];
*b++ = lcp;
if (b >= bed1)
{ if (write(tout,buf1,b-buf1) < 0)
{ fprintf(stderr,"%s: IO write to file %s%d.ktb failed\n",
Prog_Name,POST_NAME,parm->inum);
exit (1);
}
b = buf1;
}
nkmer += 1;
while (x < y)
{ for (k = KBYTES; k < swide; k++)
*c++ = sarray[x+k];
if (c >= bed2)
{ if (write(pout,buf2,c-buf2) < 0)
{ fprintf(stderr,"%s: IO write to file %s%d.pst failed\n",
Prog_Name,POST_NAME,parm->inum);
exit (1);
}
c = buf2;
}
x += swide;
}
lcp = sarray[x];
}
if (z)
lcp = sarray[e] = 0;
}
if (b > buf1)
if (write(tout,buf1,b-buf1) < 0)
{ fprintf(stderr,"%s: IO write to file %s%d.ktb failed\n",
Prog_Name,POST_NAME,parm->inum);
exit (1);
}
if (c > buf2)
if (write(pout,buf2,c-buf2) < 0)
{ fprintf(stderr,"%s: IO write to file %s%d.pst failed\n",
Prog_Name,POST_NAME,parm->inum);
exit (1);
}
parm->npost = (x-range->off)/swide - nbase;
parm->nelim = nelim;
parm->nbase = nbase;
parm->nkmer = nkmer;
return (NULL);
}
typedef struct
{ int tid;
uint8 *bufr;
int64 nkmer;
int64 npost;
int fail;
int tout, pout;
} CP;
static void *catenate_thread(void *args)
{ CP *parm = (CP *) args;
uint8 *bufr = parm->bufr;
int tid = parm->tid;
int tout = parm->tout;
int pout = parm->pout;
int tin, pin;
int p, x;
parm->fail = 1;
if (write(tout,&KMER,sizeof(int)) < 0) goto tout_write_fail;
if (write(tout,&parm->nkmer,sizeof(int64)) < 0) goto tout_write_fail;
for (p = tid*NTHREADS; p < (tid+1)*NTHREADS; p++)
{ tin = Units[p];
if (lseek(tin,0,SEEK_SET) < 0)
{ fprintf(stderr,"%s: Rewind of file %s%d.ktb failed\n",Prog_Name,POST_NAME,p);
return (NULL);
}
while (1)
{ x = read(tin,bufr,BUFFER_LEN);
if (x < 0)
{ fprintf(stderr,"%s: IO read from file %s%d.ktb failed\n",Prog_Name,POST_NAME,p);
return (NULL);
}
if (x == 0)
break;
if (write(tout,bufr,x) < 0) goto tout_write_fail;
}
close(tin);
}
close(tout);
if (write(pout,&PostBytes,sizeof(int)) < 0) goto pout_write_fail;
if (write(pout,&ContBytes,sizeof(int)) < 0) goto pout_write_fail;
if (write(pout,&parm->npost,sizeof(int64)) < 0) goto pout_write_fail;
for (p = tid*NTHREADS; p < (tid+1)*NTHREADS; p++)
{ pin = Pnits[p];
if (lseek(pin,0,SEEK_SET) < 0)
{ fprintf(stderr,"%s: Rewind of file %s%d.pst failed\n",Prog_Name,POST_NAME,p);
return (NULL);
}
while (1)
{ x = read(pin,bufr,BUFFER_LEN);
if (x < 0)
{ fprintf(stderr,"%s: IO read from file %s%d.pst failed\n",Prog_Name,POST_NAME,p);
return (NULL);
}
if (x == 0)
break;
if (write(pout,bufr,x) < 0) goto pout_write_fail;
}
close(pin);
}
close(pout);
parm->fail = 0;
return (NULL);
tout_write_fail:
fprintf(stderr,"%s: IO error writing to part file %s/.%s.ktab.%d\n",Prog_Name,TPATH,TROOT,tid+1);
return (NULL);
pout_write_fail:
fprintf(stderr,"%s: IO error writing to part file %s/.%s.post.%d\n",Prog_Name,TPATH,TROOT,tid+1);
return (NULL);
}
void k_sort(GDB *gdb)
{ uint8 *sarray;
uint8 *buffer;
int p, part, swide;
int64 panel[256];
Range range[NTHREADS];
SP sarm[NTHREADS];
RP rarm[NTHREADS];
CP carm[NTHREADS];
int64 nelim, nbase, nkmer;
int64 *prefix;
int64 *posfix;
#ifndef DEBUG_THREADS
pthread_t threads[NTHREADS];
#endif
{ int64 x, nelmax;
nelmax = 0;
for (p = 0; p < NTHREADS; p++)
{ x = Buckets[NTHREADS-1][Ksplit[p+1]-1];
if (nelmax < x)
nelmax = x;
}
swide = KBYTES + PostBytes + ContBytes;
prefix = Malloc(sizeof(int64)*0x1000000,"Allocating prefix array");
posfix = Malloc(sizeof(int64)*0x10000,"Allocating postfix array");
sarray = Malloc(nelmax*swide+1,"Allocating sort array");
buffer = Malloc(NTHREADS*BUFFER_LEN,"Allocating input buffers");
bzero(prefix,sizeof(int64)*0x1000000);
bzero(posfix,sizeof(int64)*0x10000);
}
{ int i, j;
for (i = 255; i >= 0; i--)
{ for (j = NTHREADS-1; j >= 1; j--)
Buckets[j][i] = Buckets[j-1][i];
if (i == 0 || Select[i] != Select[i-1])
Buckets[0][i] = 0;
else
Buckets[0][i] = Buckets[NTHREADS-1][i-1];
}
}
// Must open a separate file descriptor to DB bases for each setup thread !!!
for (p = 0; p < NTHREADS; p++)
{ sarm[p].tid = p;
sarm[p].swide = swide;
sarm[p].sarr = sarray;
sarm[p].buff = buffer + p*BUFFER_LEN;
sarm[p].gdb = *gdb;
if (p > 0)
{ sarm[p].gdb.seqs = fopen(gdb->seqpath,"r");
if (sarm[p].gdb.seqs == NULL)
{ fprintf(stderr,"%s: Cannot open another copy of GDB\n",Prog_Name);
exit (1);
}
}
}
for (p = 0; p < NTHREADS; p++)
{ rarm[p].swide = swide;
rarm[p].sarr = sarray;
rarm[p].buff = buffer + p*BUFFER_LEN;
rarm[p].range = range + p;
rarm[p].panel = panel;
rarm[p].prefix = prefix;
rarm[p].posfix = posfix;
}
for (p = 0; p < NTHREADS; p++)