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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"
#undef DEBUG_MAP
#undef DEBUG_THREADS
#undef DEBUG_SORT
// These constants determine the syncmer (TMER,SMER) and whether to add a spaced seed
#define TMER 12 // Syncmer len
#define SMER 8 // S-mer len (4-8 only)
#define SRES 4 // SMER-4
#define SOFF 4 // TMER-SMER
#undef SPACER // Single spaced-seed?
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)
#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].
*
**********************************************************************************************/
#ifdef GEN_HASH // Code to generate hash map
#include <stdio.h>
#include <stdlib.h>
int main(int argc, char *argv[])
{ int i1, i2, i3, i4;
int i;
int hash[256];
for (i1 = 0; i1 < 4; i1++)
for (i2 = 0; i2 < 4; i2++)
for (i3 = 0; i3 < 4; i3++)
for (i4 = 0; i4 < 4; i4++)
hash[(i1<<6)|(i2<<4)|(i3<<2)|i4] = (i1<<6)|(((i2+1)&0x3)<<4)|(((i3+2)&0x3)<<2)|((i4+3)&0x3);
printf("static int hash[256] =\n { %02x",hash[0]);
for (i = 1; i < 256; i++)
if (i%8 == 0)
printf(",\n %02x",hash[i]);
else
printf(", %02x",hash[i]);
printf("\n };\n");
exit (0);
}
#endif
static int hash[256] =
{ 0x1b, 0x18, 0x19, 0x1a, 0x1f, 0x1c, 0x1d, 0x1e, 0x13, 0x10, 0x11, 0x12, 0x17, 0x14, 0x15, 0x16,
0x2b, 0x28, 0x29, 0x2a, 0x2f, 0x2c, 0x2d, 0x2e, 0x23, 0x20, 0x21, 0x22, 0x27, 0x24, 0x25, 0x26,
0x3b, 0x38, 0x39, 0x3a, 0x3f, 0x3c, 0x3d, 0x3e, 0x33, 0x30, 0x31, 0x32, 0x37, 0x34, 0x35, 0x36,
0x0b, 0x08, 0x09, 0x0a, 0x0f, 0x0c, 0x0d, 0x0e, 0x03, 0x00, 0x01, 0x02, 0x07, 0x04, 0x05, 0x06,
0x5b, 0x58, 0x59, 0x5a, 0x5f, 0x5c, 0x5d, 0x5e, 0x53, 0x50, 0x51, 0x52, 0x57, 0x54, 0x55, 0x56,
0x6b, 0x68, 0x69, 0x6a, 0x6f, 0x6c, 0x6d, 0x6e, 0x63, 0x60, 0x61, 0x62, 0x67, 0x64, 0x65, 0x66,
0x7b, 0x78, 0x79, 0x7a, 0x7f, 0x7c, 0x7d, 0x7e, 0x73, 0x70, 0x71, 0x72, 0x77, 0x74, 0x75, 0x76,
0x4b, 0x48, 0x49, 0x4a, 0x4f, 0x4c, 0x4d, 0x4e, 0x43, 0x40, 0x41, 0x42, 0x47, 0x44, 0x45, 0x46,
0x9b, 0x98, 0x99, 0x9a, 0x9f, 0x9c, 0x9d, 0x9e, 0x93, 0x90, 0x91, 0x92, 0x97, 0x94, 0x95, 0x96,
0xab, 0xa8, 0xa9, 0xaa, 0xaf, 0xac, 0xad, 0xae, 0xa3, 0xa0, 0xa1, 0xa2, 0xa7, 0xa4, 0xa5, 0xa6,
0xbb, 0xb8, 0xb9, 0xba, 0xbf, 0xbc, 0xbd, 0xbe, 0xb3, 0xb0, 0xb1, 0xb2, 0xb7, 0xb4, 0xb5, 0xb6,
0x8b, 0x88, 0x89, 0x8a, 0x8f, 0x8c, 0x8d, 0x8e, 0x83, 0x80, 0x81, 0x82, 0x87, 0x84, 0x85, 0x86,
0xdb, 0xd8, 0xd9, 0xda, 0xdf, 0xdc, 0xdd, 0xde, 0xd3, 0xd0, 0xd1, 0xd2, 0xd7, 0xd4, 0xd5, 0xd6,
0xeb, 0xe8, 0xe9, 0xea, 0xef, 0xec, 0xed, 0xee, 0xe3, 0xe0, 0xe1, 0xe2, 0xe7, 0xe4, 0xe5, 0xe6,
0xfb, 0xf8, 0xf9, 0xfa, 0xff, 0xfc, 0xfd, 0xfe, 0xf3, 0xf0, 0xf1, 0xf2, 0xf7, 0xf4, 0xf5, 0xf6,
0xcb, 0xc8, 0xc9, 0xca, 0xcf, 0xcc, 0xcd, 0xce, 0xc3, 0xc0, 0xc1, 0xc2, 0xc7, 0xc4, 0xc5, 0xc6
};
#ifdef DEBUG_SYNCMERS
static int is_syncmer(int x)
{ int y, z, m, b;
int q, s;
b = 256;
q = 16;
for (s = 16; s >= 0; s -= 2)
{ y = (x>>s) & 0xff;
z = Comp[y];
if (hash[y] < hash[z])
m = hash[y];
else
m = hash[z];
if (m < b)
{ q = s;
b = m;
}
}
return (q == 16 || m <= b);
}
#endif
static void split_4bits(GDB *gdb, int64 *buck)
{ int KM4 = KMER-(4+SRES);
int counter;
uint8 *seq;
int len;
uint8 *neq, *ceq;
uint8 *npl, *cpl;
uint16 *mzr;
int r, i;
seq = (uint8 *) New_Contig_Buffer(gdb);
neq = (uint8 *) New_Contig_Buffer(gdb);
ceq = (uint8 *) New_Contig_Buffer(gdb);
mzr = (uint16 *) Malloc(sizeof(uint16)*(gdb->maxctg+4),"Allocating minimizer array") + 1;
if (seq == NULL || neq == NULL || ceq == NULL || mzr == NULL)
exit (1);
npl = neq + SRES;
cpl = ceq + SRES;
counter = 0;
for (r = 0; r < gdb->ncontig; r++)
{ if (gdb->contigs[r].boff < 0)
continue;
len = gdb->contigs[r].clen;
if (len < TMER)
continue;
Get_Contig(gdb,r,NUMERIC,(char *) seq); // Load the contig
// compute neq, ceq, and mzr from seq for contig
len -= 3;
{ uint8 *s1, *s2, *s3, *n1;
int n, c, k;
s1 = seq+1;
s2 = seq+2;
s3 = seq+3;
for (i = 0; i < len; 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 = k; i < len; i += 4)
{ neq[i] = (n1[i] << 2) | s3[i];
ceq[i] = Comp[neq[i]];
}
len -= SRES;
for (i = 0; i < len; i++)
#if SRES == 0
{ n = hash[neq[i]];
c = hash[ceq[i]];
#else
{ n = hash[neq[i]] * 251 + hash[npl[i]];
c = hash[ceq[i]] * 251 + hash[cpl[i]];
#endif
if (n < c)
mzr[i] = n;
else
mzr[i] = c;
}
}
// Compute processed seq array from neq,ceq
{ int min4, pos4;
int w, j;
min4 = mzr[0];
pos4 = 0;
for (i = 1; i < SOFF; i++)
if (mzr[i] < min4)
{ min4 = mzr[i];
pos4 = i;
}
for (i = SOFF; i < len; i++)
{ if (mzr[i] < min4) // right-end of 12-syncmer
{ min4 = mzr[i];
pos4 = i;
}
else if (pos4 == i-SOFF) // left-end of 12-syncmer
{ min4 = mzr[++pos4];
for (j = pos4+1; j <= i; j++)
if (mzr[j] < min4)
{ min4 = mzr[j];
pos4 = j;
}
}
else if (mzr[i] > min4)
continue;
j = i-SOFF;
if (j+KM4 < len)
{ w = neq[j];
buck[w] += 1;
counter += 1;
}
if (i >= KM4)
{ w = cpl[i];
buck[w] += 1;
counter += 1;
}
if (counter >= 1000000)
goto enough;
}
}
}
enough:
{ int64 t;
int r;
for (i = 1; i < 256; i++)
buck[i] = buck[i-1] + buck[i];
Ksplit[0] = 0;
r = 1;
t = buck[255]/NTHREADS;
for (i = 0; i < 256; i++)
{ if (buck[i] >= t)
{ if (buck[i]-t > t-buck[i-1])
{ Select[i] = r;
Ksplit[r] = i;
}
else
{ Select[i] = r-1;
Ksplit[r] = i+1;
}
r += 1;
t = (r*buck[255])/NTHREADS;
}
else
Select[i] = r-1;
}
Ksplit[NTHREADS] = 256;
}
#ifdef EXAMINE_TRIAL
printf("Prepatory %lld %d\n",buck[255],counter);
for (i = 0; i <= NTHREADS; i++)
printf(" %3d: %3d\n",i,Ksplit[i]);
for (i = 0; i < 256; i++)
printf(" %3d: %8lld %d\n",i,buck[i],Select[i]);
fflush(stdout);
#endif
free(seq-1);
free(neq-1);
free(ceq-1);
free(mzr-1);
}
typedef struct
{ int tid;
int64 *buck;
GDB gdb;
} DP;
typedef struct
{ uint8 *ptr;
uint8 *end;
uint8 *buffer;
uint64 last;
int out;
int inum;
} Packet;
// 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
void push(Packet *pack, int64 post, int comp)
{ uint8 *b = pack->ptr;
uint8 *p;
uint32 x;
uint8 *xbyte = (uint8 *) &x;
x = post - pack->last;
if (x < 0x3f)
{ if (comp)
*b++ = 0x80 | x;
else
*b++ = x;
}
else if (x < 0x1fff)
{ if (comp)
x |= 0xc000;
else
x |= 0x4000;
*b++ = xbyte[1];
*b++ = xbyte[0];
}
else
{ while (x >= 0x10000000)
{ if (comp)
*b++ = 0xf0;
else
*b++ = 0x70;
if (b >= pack->end)
{ p = pack->buffer;
if (write(pack->out,p,b-p) < 0)
{ fprintf(stderr,"%s: IO write to file %s%d.idx failed\n",
Prog_Name,POST_NAME,pack->inum);
exit (1);
}
b = p;
}
x -= 0x10000000;
}
if (comp)
x |= 0xe0000000;
else
x |= 0x60000000;
*b++ = xbyte[3];
*b++ = xbyte[2];
*b++ = xbyte[1];
*b++ = xbyte[0];
}
if (b >= pack->end)
{ p = pack->buffer;
if (write(pack->out,p,b-p) < 0)
{ fprintf(stderr,"%s: IO write to file %s%d.idx failed\n",
Prog_Name,POST_NAME,pack->inum);
exit (1);
}
b = p;
}
pack->ptr = b;
pack->last = post;
}
static void *scan_thread(void *args)
{ DP *parm = (DP *) args;
int tid = parm->tid;
int64 *buck = parm->buck;
GDB *gdb = &parm->gdb;
int KM4 = KMER-(4+SRES);
Packet packs[NTHREADS];
uint8 *seq, *buffer;
int len, ren;
uint8 *neq, *ceq;
uint8 *npl, *cpl;
uint16 *mzr;
int r, i;
int64 post;
buffer = malloc(NTHREADS*BUFFER_LEN);
for (i = 0; i < NTHREADS; i++)
{ packs[i].buffer = buffer+i*BUFFER_LEN;
packs[i].ptr = packs[i].buffer;
packs[i].end = packs[i].buffer + (BUFFER_LEN-4);
packs[i].out = Units[i*NTHREADS+tid];
packs[i].inum = NTHREADS*tid+i;
packs[i].last = DBpost[tid];
}
seq = (uint8 *) New_Contig_Buffer(gdb);
neq = (uint8 *) New_Contig_Buffer(gdb);
ceq = (uint8 *) New_Contig_Buffer(gdb);
mzr = (uint16 *) Malloc(sizeof(uint16)*(gdb->maxctg+4),"Allocating minimizer array") + 1;
if (seq == NULL || neq == NULL || ceq == NULL || mzr == NULL)
exit (1);
npl = neq + SRES;
cpl = ceq + SRES;
post = DBpost[tid];
ren = DBsplit[tid+1];
for (r = DBsplit[tid]; r < ren; r++)
{ if (gdb->contigs[r].boff < 0)
continue;
len = gdb->contigs[r].clen;
if (len < TMER)
{ post += len;
continue;
}
Get_Contig(gdb,r,NUMERIC,(char *) seq); // Load the contig
#ifdef DEBUG_MAP
printf("Src:");
for (i = 0; i < 50; i++)
printf(" %2d",seq[i]);
printf("\n");
fflush(stdout);
#endif
// compute neq, ceq, and mzr from seq for contig
len -= 3;
{ uint8 *s1, *s2, *s3, *n1;
int n, c, k;
s1 = seq+1;
s2 = seq+2;
s3 = seq+3;
for (i = 0; i < len; 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 = k; i < len; i += 4)
{ neq[i] = (n1[i] << 2) | s3[i];
ceq[i] = Comp[neq[i]];
}
len -= SRES;
for (i = 0; i < len; i++)
#if SRES == 0
{ n = hash[neq[i]];
c = hash[ceq[i]];
#else
{ n = hash[neq[i]] * 251 + hash[npl[i]];
c = hash[ceq[i]] * 251 + hash[cpl[i]];
#endif
if (n < c)
mzr[i] = n;
else
mzr[i] = c;
}
}
#ifdef DEBUG_MAP
printf("Neq:");
for (i = 0; i < 50; i++)
printf(" %02x",neq[i]);
printf("\n");
printf("Ceq:");
for (i = 0; i < 50; i++)
printf(" %02x",ceq[i]);
printf("\n");
printf("Mzr:");
for (i = 0; i < 50; i++)
printf(" %02x",mzr[i]);
printf("\n");
printf(" ");
for (i = 0; i < 50; i++)
printf(" %2d",i);
printf("\n");
fflush(stdout);
#endif
// Compute processed seq array from neq,ceq
#ifdef LINEAR_TIME_CODE
{ int min4[16];
int pos4[16];
bot = 0;
min4[bot] = mzr[0];
pos4[bot] = 0;
for (i = 1; i < len; i++)
{ while (mzr[i] <= min4[top])
{ if (top == bot)
{ min4[top] = mzr[i];
pos4[top] = i;
goto hit;
}
top = ((top-1) & 0xf);
}
top = ((top+1) & 0xff);
min4[top] = mzr[i];
pos4[top] = i;
if (i-8 == pos4[bot])
bot = ((bot+1) & 0xf);
else
continue;
hit:
Hit at i-8
}
}
#endif
{ int min4, pos4;
int w, j;
min4 = mzr[0];
pos4 = 0;
for (i = 1; i < SOFF; i++)
if (mzr[i] < min4)
{ min4 = mzr[i];
pos4 = i;
}
for (i = SOFF; i < len; i++)
{
#ifdef DEBUG_MAP
printf("%3d: %02x %02x %d\n",i,mzr[i],min4,pos4);
#endif
if (mzr[i] < min4) // right-end of 12-syncmer
{ min4 = mzr[i];
pos4 = i;
#ifdef DEBUG_MAP
printf(" Hit R");
#endif
}
else if (pos4 == i-SOFF) // left-end of 12-syncmer
{ min4 = mzr[++pos4];
for (j = pos4+1; j <= i; j++)
if (mzr[j] < min4)
{ min4 = mzr[j];
pos4 = j;
}
#ifdef DEBUG_MAP
printf(" Hit L");
#endif
}
else if (mzr[i] > min4)
continue;
#ifdef DEBUG_MAP
else
printf(" Hit RE");
#endif
j = i-SOFF;
if (j+KM4 < len)
{ w = neq[j];
buck[w] += 1;
#ifdef DEBUG_MAP
printf(" %02x %d ::",w,Select[w]);
#endif
push(packs+Select[w],post+j,0);
}
if (i >= KM4)
{ w = cpl[i];
buck[w] += 1;
#ifdef DEBUG_MAP
printf(" %02x %d",w,Select[w]);
#endif
push(packs+Select[w],post+j,1);
}
#ifdef DEBUG_MAP
printf("\n");
#endif
}
}
post += len + SRES + 3;
}
for (i = 0; i < NTHREADS; i++)
if (packs[i].ptr > packs[i].buffer)
write(packs[i].out,packs[i].buffer,packs[i].ptr-packs[i].buffer);
free(buffer);
free(seq-1);
free(neq-1);
free(ceq-1);
free(mzr-1);
return (NULL);
}
// Create a thread for each DB section, and have it distribute syncmer posts to NTHREAD files
// according to the 1st byte of its k-mer.
void distribute(GDB *gdb)
{ int i;
DP parm[NTHREADS];
#ifndef DEBUG_THREADS
pthread_t threads[NTHREADS];
#endif
Buckets = malloc(NTHREADS*sizeof(int64 *));
Buckets[0] = malloc(sizeof(int64)*256*NTHREADS);
for (i = 0; i < NTHREADS; i++)
{ parm[i].tid = i;
parm[i].buck = Buckets[i] = Buckets[0] + i*256;
parm[i].gdb = *gdb;
if (i > 0)
{ parm[i].gdb.seqs = fopen(gdb->seqpath,"r");
if (parm[i].gdb.seqs == NULL)
{ fprintf(stderr,"%s: Cannot open another copy of GDB\n",Prog_Name);
exit (1);
}
}
}
bzero(Buckets[0],sizeof(int64)*256*NTHREADS);
split_4bits(gdb,Buckets[0]); // Empirically sets up Ksplit,Select based on 1st 1Mbp
bzero(Buckets[0],sizeof(int64)*256);
#ifdef DEBUG_THREADS
for (i = 0; i < NTHREADS; i++)
scan_thread(parm+i);
#else
for (i = 1; i < NTHREADS; i++)
pthread_create(threads+i,NULL,scan_thread,parm+i);
scan_thread(parm);
for (i = 1; i < NTHREADS; i++)
pthread_join(threads[i],NULL);
#endif
for (i = 1; i < NTHREADS; i++)
fclose(parm[i].gdb.seqs);
}
/***********************************************************************************************
*
* 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+8;
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;
bost += 12;
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];
#ifdef SPACER
buck[*n] += 1;
*x++ = 0;
*x++ = n[-4];
for (i = 9; 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];
#endif
}
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];
#ifdef SPACER
buck[*n] += 1;
*x++ = 0;
*x++ = n[4];
for (i = 9; 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];
#endif
}
}
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)