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/*******************************************************************************************
*
* Load a file U.las of overlaps into memory, sort them all by A,B index,
* and then output the result to U.S.las
*
* Author: Gene Myers
* Date : July 2013
*
*******************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>
#include "DB.h"
#include "align.h"
static char *Usage = "[-va] <align:las> ...";
#define MEMORY 1000 // How many megabytes for output buffer
static char *IBLOCK;
static int SORT_OVL(const void *x, const void *y)
{ int64 l = *((int64 *) x);
int64 r = *((int64 *) y);
Overlap *ol, *or;
int al, ar;
int bl, br;
int cl, cr;
int pl, pr;
ol = (Overlap *) (IBLOCK+l);
or = (Overlap *) (IBLOCK+r);
al = ol->aread;
ar = or->aread;
if (al != ar)
return (al-ar);
bl = ol->bread;
br = or->bread;
if (bl != br)
return (bl-br);
cl = COMP(ol->flags);
cr = COMP(or->flags);
if (cl != cr)
return (cl-cr);
pl = ol->path.abpos;
pr = or->path.abpos;
if (pl != pr)
return (pl-pr);
pl = ol->path.aepos;
pr = or->path.aepos;
if (pl != pr)
return (pl-pr);
pl = ol->path.bbpos;
pr = or->path.bbpos;
if (pl != pr)
return (pl-pr);
pl = ol->path.bepos;
pr = or->path.bepos;
if (pl != pr)
return (pl-pr);
pl = ol->path.diffs;
pr = or->path.diffs;
if (pl != pr)
return (pl-pr);
if (ol < or)
return (-1);
else if (ol > or)
return (1);
else
return (0);
}
static int SORT_MAP(const void *x, const void *y)
{ int64 l = *((int64 *) x);
int64 r = *((int64 *) y);
Overlap *ol, *or;
int al, ar;
int bl, br;
int cl, cr;
int pl, pr;
ol = (Overlap *) (IBLOCK+l);
or = (Overlap *) (IBLOCK+r);
al = ol->aread;
ar = or->aread;
if (al != ar)
return (al-ar);
pl = ol->path.abpos;
pr = or->path.abpos;
if (pl != pr)
return (pl-pr);
bl = ol->bread;
br = or->bread;
if (bl != br)
return (bl-br);
cl = COMP(ol->flags);
cr = COMP(or->flags);
if (cl != cr)
return (cl-cr);
pl = ol->path.aepos;
pr = or->path.aepos;
if (pl != pr)
return (pl-pr);
pl = ol->path.bbpos;
pr = or->path.bbpos;
if (pl != pr)
return (pl-pr);
pl = ol->path.bepos;
pr = or->path.bepos;
if (pl != pr)
return (pl-pr);
pl = ol->path.diffs;
pr = or->path.diffs;
if (pl != pr)
return (pl-pr);
if (ol < or)
return (-1);
else if (ol > or)
return (1);
else
return (0);
}
static int EQUAL(Overlap *ol, Overlap *or)
{ int al, ar;
int bl, br;
int cl, cr;
int pl, pr;
al = ol->aread;
ar = or->aread;
if (al != ar)
return (0);
bl = ol->bread;
br = or->bread;
if (bl != br)
return (0);
cl = COMP(ol->flags);
cr = COMP(or->flags);
if (cl != cr)
return (0);
pl = ol->path.abpos;
pr = or->path.abpos;
if (pl != pr)
return (0);
pl = ol->path.aepos;
pr = or->path.aepos;
if (pl != pr)
return (0);
pl = ol->path.bbpos;
pr = or->path.bbpos;
if (pl != pr)
return (0);
pl = ol->path.bepos;
pr = or->path.bepos;
if (pl != pr)
return (0);
return (1);
}
int main(int argc, char *argv[])
{ char *iblock, *fblock, *iend;
int64 isize, osize;
int64 ovlsize, ptrsize;
int tspace, tbytes;
int i;
int VERBOSE;
int MAP_ORDER;
// Process options
{ int j, k;
int flags[128];
ARG_INIT("LAsort")
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
{ ARG_FLAGS("va") }
else
argv[j++] = argv[i];
argc = j;
VERBOSE = flags['v'];
MAP_ORDER = flags['a'];
if (argc <= 1)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage);
fprintf(stderr,"\n");
fprintf(stderr," -v: Verbose mode, output statistics as proceed.\n");
fprintf(stderr," -a: sort .las by A-read,A-position pairs for map usecase\n");
fprintf(stderr," off => sort .las by A,B-read pairs for overlap piles\n");
exit (1);
}
}
// For each file do
ptrsize = sizeof(void *);
ovlsize = sizeof(Overlap) - ptrsize;
isize = 0;
iblock = NULL;
osize = MEMORY * 1000000ll;
fblock = Malloc(osize,"Allocating LAsort output block");
for (i = 1; i < argc; i++)
{ int64 *perm;
FILE *input, *foutput;
int64 novl, sov;
Block_Looper *parse;
parse = Parse_Block_LAS_Arg(argv[i]);
while ((input = Next_Block_Arg(parse)) != NULL)
{
// Read in the entire file and output header
{ int64 size;
struct stat info;
char *root, *path;
path = Block_Arg_Path(parse);
root = Block_Arg_Root(parse);
stat(Catenate(path,"/",root,".las"),&info);
size = info.st_size;
if (fread(&novl,sizeof(int64),1,input) != 1)
SYSTEM_READ_ERROR
if (fread(&tspace,sizeof(int),1,input) != 1)
SYSTEM_READ_ERROR
if (tspace <= TRACE_XOVR && tspace != 0)
tbytes = sizeof(uint8);
else
tbytes = sizeof(uint16);
if (VERBOSE)
{ printf(" %s: ",root);
Print_Number(novl,0,stdout);
printf(" records ");
Print_Number(size-novl*ovlsize,0,stdout);
printf(" trace bytes\n");
fflush(stdout);
}
foutput = Fopen(Catenate(path,"/",root,".S.las"),"w");
if (foutput == NULL)
exit (1);
if (fwrite(&novl,sizeof(int64),1,foutput) != 1)
SYSTEM_WRITE_ERROR
if (fwrite(&tspace,sizeof(int),1,foutput) != 1)
SYSTEM_WRITE_ERROR
if (size > isize)
{ if (iblock == NULL)
iblock = Malloc(size+ptrsize,"Allocating LAsort input block");
else
iblock = Realloc(iblock-ptrsize,size+ptrsize,"Allocating LAsort input block");
if (iblock == NULL)
exit (1);
iblock += ptrsize;
isize = size;
}
size -= (sizeof(int64) + sizeof(int));
if (size > 0)
{ if (fread(iblock,size,1,input) != 1)
SYSTEM_READ_ERROR
}
fclose(input);
iend = iblock + (size - ptrsize);
free(root);
free(path);
}
if (novl == 0)
{ fclose(foutput);
continue;
}
// Set up unsorted permutation array
perm = (int64 *) Malloc(sizeof(int64)*novl,"Allocating LAsort permutation vector");
if (perm == NULL)
exit (1);
{ int64 off;
int j;
if (CHAIN_START(((Overlap *) (iblock-ptrsize))->flags))
{ sov = 0;
off = -ptrsize;
for (j = 0; j < novl; j++)
{ if (CHAIN_START(((Overlap *) (iblock+off))->flags))
perm[sov++] = off;
off += ovlsize + ((Overlap *) (iblock+off))->path.tlen*tbytes;
}
}
else
{ off = -ptrsize;
for (j = 0; j < novl; j++)
{ perm[j] = off;
off += ovlsize + ((Overlap *) (iblock+off))->path.tlen*tbytes;
}
sov = novl;
}
}
// Sort permutation array of ptrs to records
IBLOCK = iblock;
if (MAP_ORDER)
qsort(perm,sov,sizeof(int64),SORT_MAP);
else
qsort(perm,sov,sizeof(int64),SORT_OVL);
// Output the records in sorted order
{ int j, equal;
Overlap *w, *x, y;
int64 tsize, span;
char *fptr, *ftop, *wo;
y.aread = ((Overlap *) (iblock+perm[0]))->aread+1;
x = &y;
fptr = fblock;
ftop = fblock + osize;
for (j = 0; j < sov; j++)
{ w = (Overlap *) (wo = iblock+perm[j]);
do
{ equal = EQUAL(w,x);
tsize = w->path.tlen*tbytes;
span = ovlsize + tsize;
if (fptr + span > ftop)
{ if (fwrite(fblock,1,fptr-fblock,foutput) != (size_t) (fptr-fblock))
SYSTEM_WRITE_ERROR
fptr = fblock;
}
if (equal)
{ fptr += (ovlsize + tsize);
novl -= 1;
}
else
{ memmove(fptr,((char *) w)+ptrsize,ovlsize);
fptr += ovlsize;
memmove(fptr,(char *) (w+1),tsize);
fptr += tsize;
}
x = w;
w = (Overlap *) (wo += span);
}
while (wo < iend && CHAIN_NEXT(w->flags));
}
if (fptr > fblock)
{ if (fwrite(fblock,1,fptr-fblock,foutput) != (size_t) (fptr-fblock))
SYSTEM_WRITE_ERROR
}
}
rewind(foutput);
if (fwrite(&novl,sizeof(int64),1,foutput) != 1)
SYSTEM_WRITE_ERROR
free(perm);
fclose(foutput);
}
Free_Block_Arg(parse);
}
if (iblock != NULL)
free(iblock - ptrsize);
free(fblock);
exit (0);
}
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