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count.c
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count.c
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/*********************************************************************************************\
*
* Phase 2 of FastK: For each set of the NTHREADS files for a each partition bucket produced
* by the split.c module, do the following:
* * Sort the super-mers.
* * Sort the k-mers from each super-mer weighted by the # of times that super-mer occurs.
* * During the 2nd sort accumulate the histogram of k-mer frequencies.
* Output this to <source_root>.K<kmer>.
* * if requesteda (-t) produce a table of all the k-mers with counts >= -t in NTHREADSs
* pieces in files SORT_PATH/<root>.<bucket>.L<thread>
* * if requested (-p) invert the first two sorts to produce a profile for every super-mer
* in the order in the source in files SORT_PATH/<root>.<bucket>.P<thread>.[0-3]
* * if requested (-h) print the histogram of k-mer frequencies.
*
* Author: Gene Myers
* Date : October, 2020
*
*********************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <dirent.h>
#include <pthread.h>
#include <sys/stat.h>
#include <fcntl.h>
#include "libfastk.h"
#include "FastK.h"
#undef DEBUG_COMPRESS
#undef DEBUG_SLIST
#undef DEBUG_KLIST
#undef DEBUG_CANONICAL
#undef DEBUG_TABOUT
#undef DEBUG_CLIST
#undef DEBUG_CMERGE
#undef EQUAL_MERGE
#undef DEBUG_PLIST
#undef SHOW_RUN
#undef DEBUG_PWRITE
#define THREAD pthread_t
/*******************************************************************************************
*
* static void *supermer_list_thread(Slist_Arg *arg)
* Each thread reads a file containing a part of the bit encoded super-mers for a given
* bucket and unpacks them into an array for sorting. If -p each entry also contains
* it super-mer ordinal number in the input.
*
********************************************************************************************/
// Unstuff ints and reads from a bit packed buffer
uint8 Comp[256];
#if defined(DEBUG_CANONICAL) || defined(DEBUG_KLIST) || defined(DEBUG_SLIST) \
|| defined(DEBUG_TABOUT) || defined(DEBUG_CMERGE) || defined(EQUAL_MERGE)
static char DNA[4] = { 'a', 'c', 'g', 't' };
static char *fmer[256], _fmer[1280];
#endif
#if defined(DEBUG_SLIST) || defined(DEBUG_TABOUT) || defined(DEBUG_CMERGE) || defined(EQUAL_MERGE)
static void write_Ascii(uint8 *bytes, int len)
{ int i;
for (i = 0; i < len; i += 4)
printf("%s",fmer[*bytes++]);
}
#endif
static inline IO_UTYPE *Unstuff_Int(int64 *val, int nbits, IO_UTYPE mask, IO_UTYPE *buf, int *bitp)
{ int rem;
rem = *bitp;
if (nbits < rem)
{ rem -= nbits;
*val = ((*buf) >> rem) & mask;
#ifdef DEBUG_COMPRESS
printf(" b = %2d/%016llx -%d-> v = %lld\n",rem,*buf,nbits,*val);
#endif
}
else if (nbits == rem)
{ *val = (*buf++) & mask;
rem = IO_UBITS;
#ifdef DEBUG_COMPRESS
printf(" b = %2d/%016llx -%d-> v = %lld\n",rem,buf[-1],nbits,*val);
#endif
}
else
{ IO_UTYPE x = (*buf++) << (nbits-rem);
rem += IO_UBITS - nbits;
*val = (x | (*buf >> rem)) & mask;
#ifdef DEBUG_COMPRESS
printf(" b = %2d/%016llx|%016llx -%d-> v = %lld\n",rem,buf[-1],*buf,nbits,*val);
#endif
}
*bitp = rem;
return (buf);
}
static inline IO_UTYPE *Unstuff_Code(uint8 *s, int len, IO_UTYPE *buf, int *bitp)
{ int i, rem;
IO_UTYPE x;
rem = *bitp;
len <<= 1;
for (i = 8; i < len; i += 8)
if (rem > 8)
{ rem -= 8;
*s++ = ((*buf) >> rem) & 0xff;
}
else if (rem == 8)
{ *s++ = *buf++ & 0xff;
rem = IO_UBITS;
}
else
{ x = (*buf++) << (8-rem);
rem += IO_UBITS - 8;
*s++ = (x | (*buf >> rem)) & 0xff;
}
i = len - (i-8);
if (i > 0)
{ if (rem > i)
{ rem -= i;
x = ((*buf) >> rem);
}
else if (rem == i)
{ x = *buf++;
rem = IO_UBITS;
}
else
{ x = (*buf++) << (i-rem);
rem += IO_UBITS - i;
x |= ((*buf) >> rem);
}
*s++ = (x << (8-i)) & 0xff;
}
*bitp = rem;
return (buf);
}
// Read smers stuffed super-mers from tfile producing kmer list, loading at fill
static int Fixed_Reload[IO_UBITS+1];
static int Runer_Reload[IO_UBITS+1];
static int *Super_Reload[IO_UBITS+1];
typedef struct
{ int tfile; // Bit compressed super-mer input streaam for thread
int64 nmers; // # of super-mers in the input
int64 nbase; // if DO_PROFILE then start of indices for this thread
int64 nidxs; // total number of super-mers for this thread slice
uint8 *fours[256]; // finger for filling list sorted on first super-mer byte
} Slist_Arg;
static void *supermer_list_thread(void *arg)
{ Slist_Arg *data = (Slist_Arg *) arg;
int64 nmers = data->nmers;
int64 nbase = data->nbase;
int in = data->tfile;
uint8 **fours = data->fours;
uint8 *fill, *prev;
int64 f, *fb = &f;
int64 rmask, rlim;
int N, i, rbits;
int64 r = 0;
int64 n = 0;
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
uint8 *nb = ((uint8 *) &n) - 1;
uint8 *rb = ((uint8 *) &r) - 1;
#else
uint8 *nb = ((uint8 *) &n) + (sizeof(int64)-SLEN_BYTES);
uint8 *rb = ((uint8 *) &r) + (sizeof(int64)-RUN_BYTES);
#endif
IO_UTYPE iobuf[IO_BUF_LEN], *ioend, *ptr;
int bit, clen;
int64 k;
read(in,iobuf,IO_UBYTES*IO_BUF_LEN);
ioend = iobuf + IO_BUF_LEN;
ptr = iobuf;
bit = IO_UBITS;
rbits = 17;
rlim = 0x10000ll;
rmask = 0x1ffffll;
#ifdef DEBUG_SLIST
printf("Index at %d(%llx)\n",rbits,rmask);
#endif
prev = fours[0];
for (k = 0; k < nmers; k++)
{ while (1)
{ if (ptr + Fixed_Reload[bit] >= ioend)
{ int res = 0;
while (ptr < ioend)
iobuf[res++] = *ptr++;
read(in,iobuf+res,IO_UBYTES*(IO_BUF_LEN-res));
ptr = iobuf;
}
ptr = Unstuff_Int(&n,SLEN_BITS,SLEN_BIT_MASK,ptr,&bit);
if (n < MAX_SUPER)
break;
*prev |= 0x80;
#ifdef DEBUG_SLIST
printf("+++\n");
#endif
}
if (ptr + Super_Reload[bit][n] >= ioend)
{ int res = 0;
while (ptr < ioend)
iobuf[res++] = *ptr++;
read(in,iobuf+res,IO_UBYTES*(IO_BUF_LEN-res));
ptr = iobuf;
}
N = n+KMER;
ptr = Unstuff_Int(fb,8,0xffllu,ptr,&bit);
fill = fours[f];
fours[f] += SMER_WORD;
*fill++ = 0;
ptr = Unstuff_Code(fill,N-4,ptr,&bit);
clen = ((N-1)>>2);
fill += clen;
for (i = clen+1; i < SMER_BYTES; i++)
*fill++ = 0;
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
for (i = SLEN_BYTES; i > 0; i--)
*fill++ = nb[i];
#else
for (i = 0; i < SLEN_BYTES; i++)
*fill++ = nb[i];
#endif
if (DO_PROFILE)
{ while (1)
{ if (ptr + Runer_Reload[bit] >= ioend)
{ int res = 0;
while (ptr < ioend)
iobuf[res++] = *ptr++;
read(in,iobuf+res,IO_UBYTES*(IO_BUF_LEN-res));
ptr = iobuf;
}
ptr = Unstuff_Int(&r,rbits,rmask,ptr,&bit);
if (r < rlim)
break;
rbits += 1;
rlim <<= 1;
rmask = (rmask << 1) + 1;
#ifdef DEBUG_SLIST
printf("Index bumped to %d(%llx) r = %llu\n",rbits,rmask,r);
#endif
}
r += nbase;
prev = fill;
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
for (i = RUN_BYTES; i > 0; i--)
*fill++ = rb[i];
#else
for (i = 0; i < RUN_BYTES; i++)
*fill++ = rb[i];
#endif
}
#ifdef DEBUG_SLIST
if (DO_PROFILE)
printf(" %5lld: ",r);
printf("[%02llx] %s ",f,fmer[f]);
write_Ascii(fill-(SMER_WORD-1),N-4);
printf(" : %d\n",N);
printf(" ");
for (i = -SMER_WORD; i < 0; i++)
printf(" %02x",fill[i]);
printf("\n");
#endif
}
if (ptr + Fixed_Reload[bit] >= ioend)
{ int res = 0;
while (ptr < ioend)
iobuf[res++] = *ptr++;
read(in,iobuf+res,IO_UBYTES*(IO_BUF_LEN-res));
ptr = iobuf;
}
ptr = Unstuff_Int(&n,SLEN_BITS,SLEN_BIT_MASK,ptr,&bit);
if (n >= MAX_SUPER)
{ *prev |= 0x80;
#ifdef DEBUG_SLIST
printf("+++\n");
#endif
}
return (NULL);
}
/*******************************************************************************************
*
* static void *kmer_list_thread(Klist_Arg *arg)
* Each thread takes the now sorted super-mers, counts the # of each unique super-mer,
* and places the canonical k-mers of each with weights in an array for sorting.
* If the -p option is set then each k-mer entry also has the ordinal number of the
* k-mer in order of generation.
*
********************************************************************************************/
typedef struct
{ uint8 *sort;
int64 *parts;
int beg;
int end;
int64 off;
uint8 *fours[256];
int64 kidx;
int64 overflow;
} Klist_Arg;
static int kclip[4] = { 0xff, 0xc0, 0xf0, 0xfc };
static void *kmer_list_thread(void *arg)
{ Klist_Arg *data = (Klist_Arg *) arg;
int beg = data->beg;
int end = data->end;
int64 *part = data->parts;
uint8 **fours = data->fours;
int64 overflow;
int KMp3 = KMER+3;
int KRS = ((KMER-1)&0x3)<<1;
int KMd2 = (KMER_BYTES+1)>>1;
int fptr[SMER_BYTES+1], rptr[SMER_BYTES+1];
int *FPT = fptr-1;
int *RPT = rptr-(KMER_BYTES-1);
int KCLIP = kclip[KMER&0x3];
uint8 *sptr, *send, *lptr;
int x, ct, sbytes;
uint8 *asp, *fill;
#ifdef DEBUG_KLIST
int64 ridx = 0;
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
uint8 *rbx = ((uint8 *) &ridx) - 1;
#else
uint8 *rbx = ((uint8 *) &ridx) + (sizeof(int64)-RUN_BYTES);
#endif
#endif
int i, o;
int *f, *r;
int fb, rb;
int fs, rs;
int kb, hb;
int kf, hf;
int sln = 0;
int64 idx = 0;
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
uint8 *sb = ((uint8 *) &sln) - 1;
uint8 *ib = ((uint8 *) &idx) - 1;
#else
uint8 *sb = ((uint8 *) &sln) + (sizeof(int)-SLEN_BYTES);
uint8 *ib = ((uint8 *) &idx) + (sizeof(int64)-KMAX_BYTES);
#endif
overflow = 0;
idx = data->kidx;
sptr = data->sort + data->off;
for (x = beg; x < end; x++)
for (send = sptr + part[x]; sptr < send; sptr = lptr)
{ asp = sptr + SMER_BYTES;
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
for (i = SLEN_BYTES; i > 0; i--)
sb[i] = *asp++;
#else
for (i = 0; i < SLEN_BYTES; i++)
sb[i] = *asp++;
#endif
#ifdef DEBUG_KLIST
printf("Run ids:");
lptr = sptr;
do
{ lptr += SMER_WORD;
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
for (i = RUN_BYTES; i > 0; i--)
rbx[i] = lptr[-i];
rbx[RUN_BYTES] &= 0x7ff;
#else
for (i = 0; i < RUN_BYTES; i++)
rbx[i] = lptr[i-RUN_BYTES];
rbx[0] &= 0x7ff;
#endif
printf(" %c%lld",lptr[-RUN_BYTES]&0x8?'+':' ',ridx);
}
while (*lptr == 0);
printf("\n");
#endif
lptr = sptr + SMER_WORD;
ct = 1;
while (*lptr == 0)
{ lptr += SMER_WORD;
ct += 1;
}
*sptr = x;
sbytes = (KMp3 + sln) >> 2;
#ifdef DEBUG_KLIST
printf("%02x/%lld: l=%d c=%d\n ",x,idx,sln+1,ct);
for (i = 0; i < sbytes; i++)
printf(" %s",fmer[sptr[i]]);
printf("\n");
fflush(stdout);
#endif
for (o = sbytes, i = 0; i <= sbytes; i++, o--)
{ fptr[i] = (sptr[i] << 8) | sptr[i+1];
rptr[i] = (Comp[sptr[o]] << 8) | Comp[sptr[o-1]];
}
#ifdef DEBUG_CANONICAL
printf(" F = ");
for (i = 0; i < sbytes; i++)
printf(" %s%s",fmer[fptr[i]>>8],fmer[fptr[i]&0xff]);
printf("\n R = ");
for (i = 0; i < sbytes; i++)
printf(" %s%s",fmer[rptr[i]>>8],fmer[rptr[i]&0xff]);
printf("\n");
fflush(stdout);
#endif
if (ct >= 0x8000)
{ overflow += ((int64) (ct-0x7fff))*(sln+1);
ct = 0x7fff;
}
f = FPT;
fs = 2;
fb = 0;
r = RPT + sbytes;
rs = KRS;
rb = *r;
for (o = 0; o <= sln; o++)
{ fs -= 2;
rs += 2;
if (fs == 0)
{ fb = *++f;
fs = 8;
}
kb = kf = (fb >> fs) & 0xff;
if (rs == 8)
{ rb = *--r;
rs = 0;
}
hb = hf = (rb >> rs) & 0xff;
#ifdef DEBUG_CANONICAL
printf(" + %d / %s%s / %s\n",fs, fmer[fb>>8], fmer[fb&0xff], fmer[kb]);
printf(" - %d / %s%s / %s\n",rs, fmer[rb>>8], fmer[rb&0xff], fmer[hb]);
fflush(stdout);
#endif
if (kb == hb)
{ for (i = 1; i < KMd2; i++)
{ kb = (f[i] >> fs) & 0xff;
hb = (r[i] >> rs) & 0xff;
#ifdef DEBUG_CANONICAL
printf(" @ %d: %s vs %s\n",i,fmer[kb],fmer[hb]);
fflush(stdout);
#endif
if (kb != hb)
break;
}
}
if (kb < hb)
{ fill = fours[kf];
fours[kf] = fill+KMER_WORD;
*fill++ = 0;
for (i = 1; i < KMER_BYTES; i++)
*fill++ = (f[i] >> fs) & 0xff;
}
else
{ fill = fours[hf];
fours[hf] = fill+KMER_WORD;
*fill++ = 0;
for (i = 1; i < KMER_BYTES; i++)
*fill++ = (r[i] >> rs) & 0xff;
}
fill[-1] &= KCLIP;
*((uint16 *) fill) = ct;
fill += 2;
if (DO_PROFILE)
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
{ for (i = KMAX_BYTES; i > 0; i--)
*fill++ = ib[i];
#else
{ for (i = 0; i < KMAX_BYTES; i++)
*fill++ = ib[i];
#endif
idx += 1;
}
#ifdef DEBUG_KLIST
printf(" [%02x/%s]:",kf < hf ? kf : hf,fmer[kf < hf ? kf : hf]);
for (i = 1-KMER_WORD; i < KMER_BYTES-KMER_WORD; i++)
printf(" %s",fmer[fill[i]]);
for (i = KMER_BYTES-KMER_WORD; i < 0; i++)
printf(" %02x",fill[i]);
printf("\n");
fflush(stdout);
#endif
}
*sptr = 1;
}
data->overflow = overflow;
return (NULL);
}
/*******************************************************************************************
*
* static void *table_write_thread(Twrite_Arg *arg)
* Each thread takes the now sorted weighted k-mers, adds together the wgt.s of each
* unique k-mer, and outputs to a "L" file each k-mer and count pair that has weight
* greater thaan DO_TABLE (the -t option value, called only if set).
*
********************************************************************************************/
typedef struct
{ uint8 *sort;
int64 *parts;
int beg;
int end;
int64 off;
int kfile;
char *kname;
int64 tmers;
} Twrite_Arg;
static void *table_write_thread(void *arg)
{ Twrite_Arg *data = (Twrite_Arg *) arg;
int beg = data->beg;
int end = data->end;
int64 *part = data->parts;
int kfile = data->kfile;
uint8 bufr[0x10000];
uint8 *fill, *bend;
int x, ct;
uint8 *kptr, *lptr, *kend;
int64 tmer;
fill = bufr;
bend = bufr + (0x10000 - TMER_WORD);
tmer = 0;
kptr = data->sort + data->off;
for (x = beg; x < end; x++)
for (kend = kptr + part[x]; kptr < kend; kptr = lptr)
{ ct = *((uint16 *) (kptr+KMER_BYTES));
lptr = kptr+KMER_WORD;
while (*lptr == 0)
lptr += KMER_WORD;
if (ct >= DO_TABLE)
{ if (fill >= bend)
{ if (write(kfile,bufr,fill-bufr) < 0)
{ fprintf(stderr,"%s: Cannot write to %s. Enough disk space?\n",
Prog_Name,data->kname);
Clean_Exit(1);
}
fill = bufr;
}
*kptr = x;
memcpy(fill,kptr,TMER_WORD);
#ifdef DEBUG_TABOUT
write_Ascii(kptr,KMER);
printf(" %hd\n",*((uint16 *) (kptr+KMER_BYTES)));
#endif
fill += TMER_WORD;
tmer += 1;
}
}
if (fill > bufr)
if (write(kfile,bufr,fill-bufr) < 0)
{ fprintf(stderr,"%s: Cannot write to %s. Enough disk space?\n",Prog_Name,data->kname);
Clean_Exit(1);
}
data->tmers = tmer;
return (NULL);
}
/*******************************************************************************************
*
* static void *cmer_list_thread(Clist_Arg *arg)
* Each thread takes the now sorted weighted k-mers entries and reduces each to
* an entry containg the count and k-mer ordinal index, in preparation for the
* first of two "inverting" sorts to realize the -p option.
*
********************************************************************************************/
typedef struct
{ uint8 *sort;
int64 *parts;
int beg;
int end;
int64 off;
uint8 *fours[256];
Kmer_Stream *stm; // used only by cmer_merge_thread
} Clist_Arg;
static void *cmer_list_thread(void *arg)
{ Clist_Arg *data = (Clist_Arg *) arg;
int beg = data->beg;
int end = data->end;
int64 *part = data->parts;
uint8 **fours = data->fours;
int KM1 = KMER_WORD-1;
int x, d, k;
uint8 *kptr, *kend;
uint8 *fill;
kptr = data->sort + data->off;
for (x = beg; x < end; x++)
for (kend = kptr + part[x]; kptr < kend; kptr += KMER_WORD)
{ d = kptr[KM1];
fill = fours[d];
for (k = KMER_BYTES; k < KM1; k++)
*fill++ = kptr[k];
fours[d] = fill;
}
return (NULL);
}
/*******************************************************************************************
*
* static void *cmer_merge_thread(Clist_Arg *arg)
* Each thread takes the now sorted weighted k-mers entries and reduces each to
* an entry containg the count and k-mer ordinal index, in preparation for the
* first of two "inverting" sorts to realize the -p option.
*
********************************************************************************************/
static void *cmer_merge_thread(void *arg)
{ Clist_Arg *data = (Clist_Arg *) arg;
int beg = data->beg;
int end = data->end;
int64 *part = data->parts;
uint8 **fours = data->fours;
Kmer_Stream *S = data->stm;
int hbyte = S->hbyte;
int KM1 = KMER_WORD-1;
int x, d, k, c;
uint8 *kptr, *lptr, *kend;
uint8 *fill;
int ct;
#ifdef EQUAL_MERGE
int skip = 0;
#endif
if (beg > 0)
S = Clone_Kmer_Stream(S);
kptr = data->sort + data->off;
*kptr = beg;
GoTo_Kmer_Entry(S,kptr);
#ifdef DEBUG_CMERGE
printf("\n\nStart: x = %s k = ",fmer[beg]);
write_Ascii(kptr,KMER);
printf(" e = %s",fmer[S->cpre]);
write_Ascii(S->csuf,KMER-4);
printf(" %lld\n",S->cidx);
#endif
for (x = beg; x < end; x++)
{ while (S->cpre < x)
Next_Kmer_Entry(S);
for (kend = kptr + part[x]; kptr < kend; )
{ lptr = kptr+KMER_WORD;
while (*lptr == 0)
lptr += KMER_WORD;
while (1)
{ if (S->cpre > x)
{ c = 5000;
break;
}
c = memcmp(S->csuf,kptr+1,hbyte);
if (c >= 0)
break;
Next_Kmer_Entry(S);
#ifdef EQUAL_MERGE
printf("Skip?\n"); fflush(stdout);
skip = 1;
#endif
}
#ifdef EQUAL_MERGE
if (c != 0 || skip)
{ int u;
printf("\nx = %02x kptr = %ld start = %ld\n",
x,kptr-data->sort,(kend-part[x])-data->sort);
write_Ascii(kptr+1,KMER-4);
printf("\n");
write_Ascii(S->csuf,KMER-4);
printf("\n");
GoTo_Kmer_Index(S,S->cidx-3);
kptr -= 3*KMER_WORD;
for (u = 0; u < 7; u++)
{ printf("c = %4d k = ",c);
write_Ascii(kptr,KMER);
printf(" %d e = %s",*((uint16 *) (kptr+KMER_BYTES)),fmer[S->cpre]);
write_Ascii(S->csuf,KMER-4);
printf(" %d %lld\n",*((uint16 *) (S->csuf+hbyte)),S->cidx);
kptr += KMER_WORD;
Next_Kmer_Entry(S);
}
kptr -= 4*KMER_WORD;
GoTo_Kmer_Index(S,S->cidx-4);
printf("\n");
}
#endif
#ifdef DEBUG_CMERGE
*kptr = x;
printf("c = %4d k = ",c);
write_Ascii(kptr,KMER);
printf(" %d e = %s",*((uint16 *) (kptr+KMER_BYTES)),fmer[S->cpre]);
write_Ascii(S->csuf,KMER-4);
printf(" %d %lld\n",*((uint16 *) (S->csuf+hbyte)),S->cidx);
#endif
if (c != 0)
ct = 0;
else // c == 0
{ ct = *((uint16 *) (S->csuf+hbyte));
Next_Kmer_Entry(S);
}
while (kptr < lptr)
{ d = kptr[KM1];
fill = fours[d];
*((uint16 *) fill) = ct;
fill += 2;
for (k = TMER_WORD; k < KM1; k++)
*fill++ = kptr[k];
fours[d] = fill;
kptr += KMER_WORD;
}
}
}
#ifndef DEVELOPER
if (beg > 0)
Free_Kmer_Stream(S);
#endif
return (NULL);
}
/*******************************************************************************************
*
* static void *profile_list_thread(Plist_Arg *arg)
* Each thread takes the now "un"sorted weighted k-mers entries that are now in order
* of the k-mers along each super-mer. Produce a profile for each unique super-mer
* in place and build an array of entries consisting of a pointer to the profile fragment
* and the ordinal super-mer id of each of the equall super-mers with that profile.
* This array will be "un"sorted on super-mer id.
*
********************************************************************************************/
typedef struct
{ uint8 *sort;
int64 *parts;
int beg;
int end;
int64 off;
uint8 *prol;
int64 cnts;
uint8 *fill; // profile list uses this (basaed on the counts)
} Plist_Arg;
static void *profile_list_thread(void *arg)
{ Plist_Arg *data = (Plist_Arg *) arg;
int beg = data->beg;
int end = data->end;
int64 *part = data->parts;
uint8 *cnts, *fill, *prof;
uint8 *sptr, *send;
int i, x;
uint8 *asp;
uint8 b[2*MAX_SUPER+2];
uint64 pidx;
int STOT = SMER_BYTES + SLEN_BYTES;
int sln = 0;
int len = 0;
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
uint8 *sb = ((uint8 *) &sln) - 1;
uint8 *lb = ((uint8 *) &len) - 1;
#else
uint8 *sb = ((uint8 *) &sln) + (sizeof(int)-SLEN_BYTES);
uint8 *lb = ((uint8 *) &len) + (sizeof(int)-PLEN_BYTES);
#endif
#ifdef SHOW_RUN
int64 ridx = 0;
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
uint8 *rbx = ((uint8 *) &ridx) - 1;
#else
uint8 *rbx = ((uint8 *) &ridx) + (sizeof(int64)-RUN_BYTES);
#endif
#endif
prof = data->prol;
pidx = CMER_WORD*data->cnts;
cnts = data->prol + pidx;
sptr = data->sort + data->off;
fill = data->fill;
for (x = beg; x < end; x++)
for (send = sptr + part[x]; sptr < send; )
{ asp = sptr + SMER_BYTES;
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
for (i = SLEN_BYTES; i > 0; i--)
sb[i] = *asp++;
#else
for (i = 0; i < SLEN_BYTES; i++)
sb[i] = *asp++;
#endif
{ int j, p, c, d;
int run;
uint8 *db = (uint8 *) &d;
p = *((uint16 *) cnts);
cnts += CMER_WORD;
*((uint16 *) b) = p;
len = 2;
#ifdef SHOW_RUN
printf(" {%d}",p);
#endif
run = 0;
for (j = 1; j <= sln; j++)
{ c = *((uint16 *) cnts);
cnts += CMER_WORD;
if (c == p)
if (run > 0)
{ if (run >= 63)
{ b[len++] = run;
#ifdef SHOW_RUN
printf(" [%d]",run);
#endif
run = 1;
}
else
run += 1;
}
else
run = 1;
else
{ if (run > 0)
{ b[len++] = run;
#ifdef SHOW_RUN
printf(" [%d]",run);
#endif
run = 0;
}
d = c-p;
#ifdef SHOW_RUN
printf(" %d",d);
#endif
if (abs(d) < 32)
b[len++] = 0x40 | (d & 0x3f);
else
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
{ b[len++] = db[1] | 0x80;
b[len++] = db[0];
#else
{ b[len++] = db[0] | 0x80;
b[len++] = db[1];
#endif
#ifdef SHOW_RUN
printf("+");
#endif
}
}
p = c;
}
if (run > 0)
{ b[len++] = run;
#ifdef SHOW_RUN
printf(" [%d]",run);
#endif
}
if (len > 2)
{ *((uint16 *) (b+len)) = p;
#ifdef SHOW_RUN
printf(" {%d}",p);
#endif
}
#ifdef SHOW_RUN
printf(" += %d / %d\n",len,sln+1);
#endif
}
#ifdef SHOW_RUN
printf("Run ids:");
#endif
do
{ if (sptr[STOT] & 0x80)
{ *((uint64 *) fill) = (pidx<<1) | 0x1;
sptr[STOT] &= 0x7f;
#ifdef SHOW_RUN
printf(" +");
#endif
}
else
{ *((uint64 *) fill) = (pidx<<1);
#ifdef SHOW_RUN
printf(" ");
#endif
}
fill += sizeof(uint64);
for (i = STOT; i < SMER_WORD; i++)
*fill++ = sptr[i];
#ifdef SHOW_RUN
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
for (i = RUN_BYTES; i > 0; i--)
rbx[i] = sptr[SMER_WORD-i];
#else
for (i = 0; i < PLEN_BYTES; i++)
rbx[i] = sptr[STOT+i];
#endif
printf("%lld",ridx);
#endif
sptr += SMER_WORD;
}
while (*sptr == 0);
#ifdef SHOW_RUN
printf(" <%ld>\n",(sptr-asp)/SMER_WORD+1);
#endif
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
for (i = PLEN_BYTES; i > 0; i--)
prof[pidx++] = lb[i];
#else
for (i = 0; i < PLEN_BYTES; i++)
prof[pidx++] = lb[i];
#endif
if (len > 2)
len += 2;
for (i = 0; i < len; i++)
prof[pidx++] = b[i];