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merge.c
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merge.c
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/*******************************************************************************************
*
* Phase 4 of FastK: Given NPARTS sorted super-mer profiles for ITHREADS in NPANELS
* parts per thread, merge the super-mer NPARTS x NPANELS files for each thread
* (in subdirectory SORT_PATH) into single compressed read-profile files (in
* subdirectory "path").
*
* Author: Gene Myers
* Date : Oectober 2020
*
*******************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <ctype.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <dirent.h>
#include <fcntl.h>
#include <pthread.h>
#include <errno.h>
#include "libfastk.h"
#include "FastK.h"
#undef DEBUG
#undef DEBUG_SEGS
#undef SHOW_RUN
#define THREAD pthread_t
// IO block data structure and block fetcher
static int64 BUFLEN_UINT8;
static int64 BUFLEN_INT64;
static int64 BUFLEN_IBYTE;
typedef struct
{ int stream;
int panel;
uint8 *block;
uint8 *ptr;
uint8 *top;
int64 rid;
int lst;
} IO_block;
static void reload(IO_block *in)
{ int64 del;
del = in->top - in->ptr;
if (del > 0)
memmove(in->block, in->ptr, del);
in->ptr = in->block;
in->top = in->block + del;
in->top += read(in->stream,in->top,BUFLEN_UINT8-del);
}
// Thread to merge files of super-mer profiles
static int PAN_SIZE; // # of profile runs to output as a block
typedef struct
{ int len; // length of super-mer profile (including length bytes)
int lst; // ends a read
uint8 *frag; // encoding of super-mer profile
} Entry;
typedef struct
{ char *root; // Path & prefix of each part file
IO_block *io; // input & output buffers
Entry *chord; // super-mer profiles vector
int wch; // Number of this thread
int afile; // A-file output
char *aname;
int dfile; // D-file output
char *dname;
int64 nreads; // # of reads seen by this thread
int64 nbase; // First rid for thread
} Track_Arg;
static int64 totin; // Total bytes for part 0, thread 0
static void *merge_profile_thread(void *arg)
{ Track_Arg *data = (Track_Arg *) arg;
int afile = data->afile;
int dfile = data->dfile;
IO_block *io = data->io;
Entry *chord = data->chord;
int64 nbase = data->nbase;
int maxS = 2*MAX_SUPER + 2 + PLEN_BYTES + RUN_BYTES;
uint8 *dbuf;
int64 *abuf, *aptr, *atop;
int64 offset;
int nreads;
char *fname;
int64 panel, nanel;
int naval, wlast;
uint16 lcont, d;
uint8 *db = (uint8 *) &d;
int n;
int64 nidx = 0;
FILE *nfile; // Invalid k-mers file
int64 iridx;
int ileng, ilast = 0;
int64 pct1, partin, nextin;
int CLOCK;
int len = 0;
int64 rid = 0;
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
uint8 *lb = ((uint8 *) &len) - 1;
uint8 *rb = ((uint8 *) &rid) - 1;
#else
uint8 *lb = ((uint8 *) &len) + (sizeof(int)-PLEN_BYTES);
uint8 *rb = ((uint8 *) &rid)) + (sizeof(int64)-RUN_BYTES);
#endif
#ifdef DEBUG
printf("THREAD %d\n",data->wch);
#endif
fname = Malloc(strlen(data->root) + 100,"File name buffer");
if (fname == NULL)
Clean_Exit(1);
// Set up clock if required
nextin = pct1 = partin = 0;
if (VERBOSE && data->wch == 0)
{ nextin = pct1 = totin/100;
fprintf(stderr,"\n 0%%");
fflush(stderr);
CLOCK = 1;
}
else
CLOCK = 0;
// Setup A-file and D-file buffers
abuf = (int64 *) io[NPARTS].block;
aptr = abuf;
atop = abuf + BUFLEN_INT64;
dbuf = chord[0].frag;
// Open invalid interval file
sprintf(fname,"%s.NS.T%d",data->root,data->wch);
nfile = fopen(fname,"r");
if (nfile == NULL)
{ fprintf(stderr,"\n%s: Cannot open external file %s in %s\n",
Prog_Name,fname,SORT_PATH);
Clean_Exit(1);
}
if (fread(&iridx,sizeof(int64),1,nfile) < 1)
iridx = 0x7fffffffffffffffll;
else
{ if ((iridx & 0x8000000000000000ll) != 0)
{ ilast = 1;
iridx &= 0x7fffffffffffffffll;
}
else
ilast = 0;
fread(&ileng,sizeof(int),1,nfile);
}
// Read the first run-id for each part
offset = 0;
nreads = 0;
wlast = 1;
lcont = 0;
naval = NPARTS;
for (n = 0; n < NPARTS; n++)
{ IO_block *src;
uint8 *sptr;
int f;
src = io+n;
sptr = src->block;
src->ptr = src->top = sptr;
src->panel = -1;
// Open panels until get to a non-empty one or all are exhausted
while (sptr >= src->top)
{ if (src->panel >= 0)
{ close(src->stream);
#ifndef DEVELOPER
sprintf(fname,"%s.%d.P%d.%d",data->root,n,data->wch,src->panel);
unlink(fname);
#endif
#ifdef DEBUG
printf("Closing Panel %d:%d.%d\n",n,data->wch,src->panel);
#endif
}
src->panel += 1;
if (src->panel >= NPANELS)
break;
#ifdef DEBUG
printf("Starting Panel %d:%d.%d\n",n,data->wch,src->panel);
fflush(stdout);
#endif
sprintf(fname,"%s.%d.P%d.%d",data->root,n,data->wch,src->panel);
f = open(fname,O_RDONLY);
if (f == -1)
{ fprintf(stderr,"\n%s: Cannot open external file %s in %s\n",
Prog_Name,fname,SORT_PATH);
Clean_Exit(1);
}
#ifdef DEVELOPER
if (src->panel == 0)
{ if (data->wch == 0)
lseek(f,3*sizeof(int),SEEK_SET);
read(f,&nidx,sizeof(int64));
}
#else
nidx = NUM_RID[data->wch];
#endif
src->stream = f;
src->top = sptr + read(f,sptr,BUFLEN_UINT8);
}
// If panels exhausted then part is exhausted (has no data)
if (src->panel >= NPANELS)
{ naval -= 1;
src->rid = 0x7fffffffffffffffll;
continue;
}
// Scan run-id
if (*sptr & 0x80)
{ src->lst = 1;
*sptr &= 0x7f;
}
else
src->lst = 0;
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
for (f = RUN_BYTES; f > 0; f--)
rb[f] = *sptr++;
#else
for (f = 0; f < RUN_BYTES; f++)
rb[f] = *sptr++;
#endif
src->rid = rid;
src->ptr = sptr;
}
// For each run of PAN_SIZE consecutive super-mer profiles do
nidx += nbase;
for (panel = nbase; naval > 0; panel = nanel)
{ nanel = panel + PAN_SIZE;
if (nanel > nidx)
nanel = nidx;
#ifdef DEBUG_SEGS
printf("Panning %lld - %lld\n",panel,nanel);
#endif
for (n = 0; n < PAN_SIZE; n++)
chord[n].len = 0;
// Load profiles in current run range [panel,nanel) from the parts part so as to fill range
for (n = 0; n < NPARTS; n++)
{ IO_block *src;
uint8 *sptr;
int f;
src = io+n;
sptr = src->ptr;
rid = src->rid;
while (rid < nanel) // While next profile is in range
{
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
for (f = PLEN_BYTES; f > 0; f--)
lb[f] = *sptr++;
#else
for (f = 0; f < PLEN_BYTES; f++)
lb[f] = *sptr++;
#endif
if (len > 2)
len += 2;
#ifdef DEBUG_SEGS
printf(" %lld: %d(%d) %d\n",rid,len,src->lst,n);
#endif
rid -= panel;
chord[rid].len = len;
chord[rid].lst = src->lst;
memcpy(chord[rid].frag,sptr,len);
sptr += len;
// Fetch more data from panel if needed
if (sptr + maxS >= src->top && src->top - src->block >= BUFLEN_UINT8)
{ src->ptr = sptr;
if (CLOCK && n == 0)
{ partin += src->ptr - src->block;
reload(src);
}
else
reload(src);
sptr = src->ptr;
}
// If panel EOF then open next panel(s) to get next run-id
while (sptr >= src->top)
{ int f;
if (CLOCK && n == 0 && src->top - src->block < BUFLEN_UINT8)
partin += src->top - src->block;
close(src->stream);
#ifndef DEVELOPER
sprintf(fname,"%s.%d.P%d.%d",data->root,n,data->wch,src->panel);
unlink(fname);
#endif
src->panel += 1;
if (src->panel >= NPANELS)
break;
#ifdef DEBUG
printf("Starting Panel %d:%d.%d\n",n,data->wch,src->panel);
fflush(stdout);
#endif
sprintf(fname,"%s.%d.P%d.%d",data->root,n,data->wch,src->panel);
f = open(fname,O_RDONLY);
if (f == -1)
{ fprintf(stderr,"\n%s: A Cannot open external file %s in %s\n",
Prog_Name,fname,SORT_PATH);
Clean_Exit(1);
}
sptr = src->block;
src->stream = f;
src->top = sptr + read(f,sptr,BUFLEN_UINT8);
}
// If all panels exhausted then thread is exhausted
if (src->panel >= NPANELS)
{ naval -= 1;
rid = 0x7fffffffffffffffll;
break;
}
// Scan run-id
if (*sptr & 0x80)
{ src->lst = 1;
*sptr &= 0x7f;
}
else
src->lst = 0;
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
for (f = RUN_BYTES; f > 0; f--)
rb[f] = *sptr++;
#else
for (f = 0; f < RUN_BYTES; f++)
rb[f] = *sptr++;
#endif
#ifdef DEBUG_SEGS
printf(" %lld(%d) <%d> [%d]\n",rid,src->lst,n,data->wch);
fflush(stdout);
#endif
}
src->rid = rid;
src->ptr = sptr;
}
#ifdef DEBUG_SEGS
if (nanel-panel < PAN_SIZE)
{ printf("Loaded %lld (%d)\n",nanel-panel,data->wch);
for (n = 0; n < PAN_SIZE; n++)
if (chord[n].len > 0)
printf(" %d -- %lld\n",n,panel+n);
}
fflush(stdout);
#endif
// Compress and join the profile fragments in the current range and output
{ uint8 *o, *ptr;
int64 p;
uint8 lz;
lz = 0;
o = dbuf;
for (n = 0, p = panel; p < nanel; n++, p++)
{ len = chord[n].len;
ptr = chord[n].frag;
if (len == 0)
{ if (iridx+nbase != p) // read < KMER bp long
{ if (aptr >= atop)
{ if (write(afile,abuf,BUFLEN_IBYTE) < 0)
{ fprintf(stderr,"%s: Cannot write to %s. Enough disk space?\n",
Prog_Name,data->aname);
Clean_Exit(1);
}
aptr = abuf;
}
*aptr++ = offset + (o-dbuf);
#ifdef SHOW_RUN
if (wlast)
printf("READ %d\n %5d:: SHORT\n",nreads,n);
else
printf(" %5d:: SHORT\n",n);
#endif
nreads += 1;
}
else
{ if (wlast)
{ *o++ = 0;
lz = 0;
#ifdef SHOW_RUN
printf("READ %d\n %5d:: N=%d {0} [%02x]",nreads,n,ileng,o[-1]);
#endif
}
else
{ d = -lcont;
#ifdef SHOW_RUN
printf(" %5d:: N=%d {0}",n,ileng);
#endif
if (d == 0)
{ lz += 1;
if (lz >= 63)
{ *o++ = 63;
lz = 0;
#ifdef SHOW_RUN
printf(" @");
#endif
}
}
else
{ if (lz)
{ *o++ = lz;
#ifdef SHOW_RUN
printf(" %02x",lz);
#endif
lz = 0;
}
if (d > 0xffe1 || d < 32)
{ *o++ = 0x40 | (d & 0x3f);
#ifdef SHOW_RUN
printf(" %02x",o[-1]);
#endif
}
else
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
{ *o++ = db[1] | 0x80;
*o++ = db[0];
#else
{ *o++ = db[0] | 0x80;
*o++ = db[1];
#endif
#ifdef SHOW_RUN
printf(" %02x.%02x",o[-2],o[-1]);
#endif
}
}
}
if (ileng > 1)
{ ileng += lz;
for (ileng -= 1; ileng >= 63; ileng -= 63)
{ *o++ = 63;
#ifdef SHOW_RUN
printf(" @");
#endif
}
lz = ileng;
#ifdef SHOW_RUN
printf(" {0} <%d>\n",lz);
#endif
}
#ifdef SHOW_RUN
else
printf(" {0} <%d>\n",lz);
#endif
lcont = 0;
if (ilast)
{ if (lz)
{ *o++ = lz;
#ifdef SHOW_RUN
printf(" TAILI:: %02x\n",lz);
#endif
lz = 0;
}
if (aptr >= atop)
{ if (write(afile,abuf,BUFLEN_IBYTE) < 0)
{ fprintf(stderr,"%s: Cannot write to %s. Enough disk space?\n",
Prog_Name,data->aname);
Clean_Exit(1);
}
aptr = abuf;
}
*aptr++ = offset + (o-dbuf);
nreads += 1;
wlast = 1;
}
else
wlast = 0;
if (fread(&iridx,sizeof(int64),1,nfile) < 1)
iridx = 0x7fffffffffffffffll;
else
{ if ((iridx & 0x8000000000000000ll) != 0)
{ ilast = 1;
iridx &= 0x7fffffffffffffffll;
}
else
ilast = 0;
fread(&ileng,sizeof(int),1,nfile);
}
}
continue;
}
// Get 1st count of profile n
d = *((uint16 *) ptr);
ptr += 2;
// If start of read then encode as absolute
if (wlast)
{ if (d < 128)
{ *o++ = d;
#ifdef SHOW_RUN
printf("READ %d\n %5d:: %3d: {%hu} [%02x]",nreads,n,len,d,o[-1]);
#endif
}
else
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
{ *o++ = db[1] | 0x80;
*o++ = db[0];
#else
{ *o++ = db[0] | 0x80;
*o++ = db[1];
#endif
#ifdef SHOW_RUN
printf("READ %d\n %5d:: %3d: {%hu} [%02x.%02x]",nreads,n,len,d,o[-2],o[-1]);
#endif
}
lcont = d;
lz = 0;
}
// Otherwise encode 1st forward difference
else
{
#ifdef SHOW_RUN
printf(" %5d:: %3d: {%hd}",n,len,d);
#endif
d -= lcont;
if (d == 0)
{ lz += 1;
if (lz >= 63)
{ *o++ = 63;
lz = 0;
#ifdef SHOW_RUN
printf(" @");
#endif
}
}
else
{ if (lz)
{ *o++ = lz;
#ifdef SHOW_RUN
printf(" %02x",lz);
#endif
lz = 0;
}
if (d > 0xffe1 || d < 32)
{ *o++ = 0x40 | (d & 0x3f);
#ifdef SHOW_RUN
printf(" %02x",o[-1]);
#endif
}
else
#if __ORDER_LITTLE_ENDIAN__ == __BYTE_ORDER__
{ *o++ = db[1] | 0x80;
*o++ = db[0];
#else
{ *o++ = db[0] | 0x80;
*o++ = db[1];
#endif
#ifdef SHOW_RUN
printf(" %02x.%02x",o[-2],o[-1]);
#endif
}
}
lcont += d;
}
// Transfer remainder of super-mer profile
if (len > 2)
{ len -= 4;
lcont = *((uint16 *) (ptr+len));
if (lz)
{ while (len > 0 && *ptr < 64)
{ lz += *ptr;
if (lz >= 63)
{ *o++ = 63;
#ifdef SHOW_RUN
printf(" @");
#endif
lz -= 63;
}
ptr += 1;
len -= 1;
}
}
if (len > 0)
{ if (lz)
{ *o++ = lz;
#ifdef SHOW_RUN
printf(" %02x",lz);
#endif
lz = 0;
}
{ int u, one;
one = 1;
for (u = 0; u < len; u++)
if ((ptr[u] & 0x80) != 0)
{ one = 0;
u += 1;
}
else
one = 1;
if (one)
{ lz = ptr[len-1];
if (lz < 63)
len -= 1;
else
lz = 0;
}
}
memmove(o,ptr,len);
#ifdef SHOW_RUN
{ int u;
for (u = 0; u < len; u++)
if ((ptr[u] & 0x80) != 0)
{ printf(" %02x.%02x",ptr[u],ptr[u+1]);
u += 1;
}
else
printf(" %02x",ptr[u]);
}
#endif
o += len;
}
}
#ifdef SHOW_RUN
printf(" {%d}",lcont);
if (lz)
printf(" <%d>",lz);
printf("\n");
#endif
// If last profile of a read, then add to A-file index
wlast = chord[n].lst;
if (wlast)
{ if (lz)
{ *o++ = lz;
#ifdef SHOW_RUN
printf(" TAILZ:: %02x\n",lz);
#endif
lz = 0;
}
if (aptr >= atop)
{ if (write(afile,abuf,BUFLEN_IBYTE) < 0)
{ fprintf(stderr,"%s: Cannot write to %s. Enough disk space?\n",
Prog_Name,data->aname);
Clean_Exit(1);
}
aptr = abuf;
}
*aptr++ = offset + (o-dbuf);
nreads += 1;
}
}
// Write the merged, compressed profiles for the range
if (lz)
{ *o++ = lz;
#ifdef SHOW_RUN
printf(" TAILE:: %02x\n",lz);
#endif
}
if (write(dfile,dbuf,o-dbuf) < 0)
{ fprintf(stderr,"%s: Cannot write to %s. Enough disk space?\n",
Prog_Name,data->dname);
Clean_Exit(1);
}
offset += o-dbuf;
// Check clock
if (CLOCK && partin + (io->ptr - io->block) > nextin)
{ nextin = partin + (io->ptr - io->block);
fprintf(stderr,"\r %3d%%",(int) ((100.*nextin)/totin));
fflush(stderr);
nextin += pct1;
}
}
}
// Flush the A-file buffer
if (aptr > abuf)
if (write(afile,abuf,(aptr-abuf)*sizeof(int64)) < 0)
{ fprintf(stderr,"%s: Cannot write to %s. Enough disk space?\n",
Prog_Name,data->aname);
Clean_Exit(1);
}
data->nreads = nreads;
fclose(nfile);
#ifndef DEVELOPER
sprintf(fname,"%s.NS.T%d",data->root,data->wch);
unlink(fname);
#endif
free(fname);
if (CLOCK)
fprintf(stderr,"\r \r");
return (NULL);
}
void Merge_Profiles(char *dpwd, char *dbrt)
{ char *fname;
IO_block *io;
uint8 *blocks;
Entry *chord;
uint8 *_chord;
Track_Arg *parmk;
#ifndef DEBUG
THREAD *threads;
#endif
if (VERBOSE)
{ fprintf(stderr,"\nPhase 4 (-p option): Merging Profile Fragments\n");
fflush(stderr);
}
// Chek that input files are at sort path and determine the number of panels,
// threads, and partitions
fname = Malloc(3*(strlen(dpwd) + strlen(SORT_PATH) + strlen(dbrt)) + 100,"File name buffer");
if (fname == NULL)
Clean_Exit(1);
// Allocate all working data structures
parmk = Malloc(sizeof(Track_Arg)*ITHREADS,"Allocating control data");
if (parmk == NULL)
Clean_Exit(1);
#ifndef DEBUG
threads = Malloc(sizeof(THREAD)*ITHREADS,"Allocating control data");
if (threads == NULL)
Clean_Exit(1);
#endif
{ int t;
int64 o, n;
o = 0;
for (t = 0; t < ITHREADS; t++)
{ int f, i;
struct stat info;
sprintf(fname,"%s/%s.0.P%d.0",SORT_PATH,dbrt,t);
f = open(fname,O_RDONLY);
if (f == -1)
{ fprintf(stderr,"%s: A Cannot find file %s.0.P%d.0 in directory %s\n",
Prog_Name,dbrt,t,SORT_PATH);
Clean_Exit(1);
}
#ifdef DEVELOPER
if (t == 0)
{ read(f,&RUN_BYTES,sizeof(int));
read(f,&PLEN_BYTES,sizeof(int));
read(f,&MAX_SUPER,sizeof(int));
}
read(f,&n,sizeof(int64));
#else
n = NUM_RID[t];
#endif
parmk[t].nbase = o;
o += n;
if (VERBOSE && t == 0)
{ fstat(f,&info);
totin = info.st_size;
for (i = 1; i < NPANELS; i++)
{ sprintf(fname,"%s/%s.0.P0.%d",SORT_PATH,dbrt,i);
stat(fname,&info);
totin += info.st_size;
}
}
close(f);
}
}
BUFLEN_UINT8 = SORT_MEMORY/((NPARTS+1)*ITHREADS);
if (BUFLEN_UINT8 > 0x7fffffffll)
BUFLEN_UINT8 = 0x7ffffff8ll;
if (BUFLEN_UINT8 < 2*MAX_SUPER)
BUFLEN_UINT8 = 2*MAX_SUPER;
BUFLEN_INT64 = BUFLEN_UINT8 / sizeof(int64);
BUFLEN_IBYTE = BUFLEN_INT64 * sizeof(int64);
PAN_SIZE = 1024*NPARTS;
io = (IO_block *) Malloc(sizeof(IO_block)*(NPARTS+1)*ITHREADS,"Allocating IO buffers");
blocks = (uint8 *) Malloc(BUFLEN_UINT8*(NPARTS+1)*ITHREADS,"Allocating IO buffers");
chord = (Entry *) Malloc(PAN_SIZE*sizeof(Entry)*ITHREADS,"Allocating IO buffers");
_chord = (uint8 *) Malloc(PAN_SIZE*2*(MAX_SUPER+1)*ITHREADS,"Allocating IO buffers");
if (io == NULL || blocks == NULL || chord == NULL || _chord == NULL)
Clean_Exit(1);
// Remove previous profile result if any
sprintf(fname,"rm -f %s/%s.prof %s/.%s.pidx.* %s/.%s.prof.*",dpwd,dbrt,dpwd,dbrt,dpwd,dbrt);
system(fname);
// Create new stub file
{ int f;
sprintf(fname,"%s/%s.prof",dpwd,dbrt);
f = open(fname,O_WRONLY|O_CREAT|O_TRUNC,S_IRWXU|S_IRWXG|S_IRWXO);
if (f == -1)
{ fprintf(stderr,"%s: Cannot open external file %s for writing\n",Prog_Name,fname);
Clean_Exit(1);
}
write(f,&KMER,sizeof(int));
if (write(f,&ITHREADS,sizeof(int)) < 0)
{ fprintf(stderr,"%s: Cannot write to %s. Enough disk space?\n",Prog_Name,fname);
Clean_Exit(1);
}
close(f);
}
// Open up A- and D-files, assign blocks for the inputs, and setup thread params
{ char *root;
char *aname, *dname;
int t, n, p;
root = Malloc(strlen(SORT_PATH) + strlen(dbrt) + 10,"File name buffer");
if (root == NULL)
Clean_Exit(1);
sprintf(root,"%s/%s",SORT_PATH,dbrt);
p = 0;
for (t = 0; t < ITHREADS; t++)
{ int f, g;
int64 zero = 0;
sprintf(fname,"%s/.%s.pidx.%d",dpwd,dbrt,t+1);
f = open(fname,O_WRONLY|O_CREAT|O_TRUNC,S_IRWXU|S_IRWXG|S_IRWXO);
if (f == -1)
{ fprintf(stderr,"%s: Cannot open external file %s\n",Prog_Name,fname);
Clean_Exit(1);
}
aname = Strdup(fname,"Allocating stream names");
sprintf(fname,"%s/.%s.prof.%d",dpwd,dbrt,t+1);
g = open(fname,O_WRONLY|O_CREAT|O_TRUNC,S_IRWXU|S_IRWXG|S_IRWXO);
if (g == -1)
{ fprintf(stderr,"%s: Cannot open external file %s\n",Prog_Name,fname);
Clean_Exit(1);
}
dname = Strdup(fname,"Allocating stream names");
if (aname == NULL || dname == NULL)
Clean_Exit(1);
parmk[t].root = root;
parmk[t].wch = t;
parmk[t].afile = f;
parmk[t].aname = aname;
parmk[t].dfile = g;
parmk[t].dname = dname;
parmk[t].io = io + p;
parmk[t].chord = chord + PAN_SIZE*t;
for (n = 0; n <= NPARTS; n++, p++)
io[p].block = blocks + p*BUFLEN_UINT8;
write(f,&KMER,sizeof(int));
write(f,&zero,sizeof(int64));
if (write(f,&zero,sizeof(int64)) < 0)
{ fprintf(stderr,"%s: Cannot write to %s. Enough disk space?\n",Prog_Name,aname);
Clean_Exit(1);
}
}
// Setup the fragment buffers for each range chord
for (n = 0; n < PAN_SIZE*ITHREADS; n++)
chord[n].frag = _chord + 2*(MAX_SUPER+1)*n;
// In parallel process each of the ITHREADS partitions
#ifdef DEBUG
for (t = 0; t < ITHREADS; t++)
merge_profile_thread(parmk+t);
#else
for (t = 1; t < ITHREADS; t++)
pthread_create(threads+t,NULL,merge_profile_thread,parmk+t);
merge_profile_thread(parmk);
for (t = 1; t < ITHREADS; t++)
pthread_join(threads[t],NULL);
#endif
if (VERBOSE)
{ int64 psize;
psize = 0;
for (t = 0; t < ITHREADS; t++)
psize += lseek(parmk[t].afile,0,SEEK_CUR) + lseek(parmk[t].dfile,0,SEEK_CUR);
if (psize >= 5.e8)
fprintf(stderr," The profiles occupy %.2f GB\n",psize/1.e9);
else if (psize >= 5.e5)
fprintf(stderr," The profiles occupy %.2f MB\n",psize/1.e6);
else
fprintf(stderr," The profiles occupy %.2f KB\n",psize/1.e3);
fflush(stderr);
}
// Rewind and set the header of each A-file
{ int64 nreads;
int f;
nreads = 0;
for (t = 0; t < ITHREADS; t++)
{ f = parmk[t].afile;
lseek(f,sizeof(int),SEEK_SET);
write(f,&nreads,sizeof(int64));
if (write(f,&(parmk[t].nreads),sizeof(int64)) < 0)
{ fprintf(stderr,"%s: Cannot write to %s. Enough disk space?\n",
Prog_Name,parmk[t].aname);
Clean_Exit(1);
}
nreads += parmk[t].nreads;
close(parmk[t].dfile);
close(f);
free(parmk[t].dname);
free(parmk[t].aname);
}
}
// Release working data
free(root);
free(_chord);
free(chord);
free(blocks);
free(io);
#ifndef DEBUG