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/*******************************************************************************************
*
* Merge together in index order, overlap files <XXX>.1.las, <XXX>.2.las, ... into a
* single overlap file and output to the standard output
*
* 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 = "[-v] <source:las> > <target>.las";
#define MEMORY 1000 // How many megabytes for output buffer
int main(int argc, char *argv[])
{ char *iblock, *oblock;
FILE *input;
int64 novl, bsize, ovlsize, ptrsize;
int tspace, tbytes;
char *pwd, *root, *root2;
int VERBOSE;
// Process options
{ int i, j, k;
int flags[128];
ARG_INIT("LAcat")
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
{ ARG_FLAGS("v") }
else
argv[j++] = argv[i];
argc = j;
VERBOSE = flags['v'];
if (argc <= 1)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage);
exit (1);
}
}
ptrsize = sizeof(void *);
ovlsize = sizeof(Overlap) - ptrsize;
bsize = MEMORY * 1000000ll;
oblock = (char *) Malloc(bsize,"Allocating output block");
iblock = (char *) Malloc(bsize + ptrsize,"Allocating input block");
if (oblock == NULL || iblock == NULL)
exit (1);
iblock += ptrsize;
pwd = PathTo(argv[1]);
root = Root(argv[1],".las");
root2 = index(root,'#');
if (root2 == NULL)
{ fprintf(stderr,"%s: No #-sign in source name '%s'\n",Prog_Name,root);
exit (1);
}
if (index(root2+1,'#') != NULL)
{ fprintf(stderr,"%s: Two or more occurences of #-sign in source name '%s'\n",Prog_Name,root);
exit (1);
}
*root2++ = '\0';
{ int64 povl;
int i, mspace;
novl = 0;
tspace = 0;
mspace = 0;
tbytes = 0;
for (i = 0; 1; i++)
{ char *name = Catenate(pwd,"/",Numbered_Suffix(root,i+1,root2),".las");
if ((input = fopen(name,"r")) == NULL) break;
if (fread(&povl,sizeof(int64),1,input) != 1)
SYSTEM_ERROR
novl += povl;
if (fread(&mspace,sizeof(int),1,input) != 1)
SYSTEM_ERROR
if (i == 0)
{ tspace = mspace;
if (tspace <= TRACE_XOVR)
tbytes = sizeof(uint8);
else
tbytes = sizeof(uint16);
}
else if (tspace != mspace)
{ fprintf(stderr,"%s: PT-point spacing conflict (%d vs %d)\n",Prog_Name,tspace,mspace);
exit (1);
}
fclose(input);
}
fwrite(&novl,sizeof(int64),1,stdout);
fwrite(&tspace,sizeof(int),1,stdout);
}
{ int i, j;
Overlap *w;
int64 tsize, povl;
int mspace;
char *iptr, *itop;
char *optr, *otop;
optr = oblock;
otop = oblock + bsize;
for (i = 0; 1; i++)
{ char *name = Catenate(pwd,"/",Numbered_Suffix(root,i+1,root2),".las");
if ((input = fopen(name,"r")) == NULL) break;
if (fread(&povl,sizeof(int64),1,input) != 1)
SYSTEM_ERROR
if (fread(&mspace,sizeof(int),1,input) != 1)
SYSTEM_ERROR
if (VERBOSE)
fprintf(stderr," Concatenating %s: %lld la\'s\n",Numbered_Suffix(root,i+1,root2),povl);
iptr = iblock;
itop = iblock + fread(iblock,1,bsize,input);
for (j = 0; j < povl; j++)
{ if (iptr + ovlsize > itop)
{ int64 remains = itop-iptr;
if (remains > 0)
memcpy(iblock,iptr,remains);
iptr = iblock;
itop = iblock + remains;
itop += fread(itop,1,bsize-remains,input);
}
w = (Overlap *) (iptr - ptrsize);
tsize = w->path.tlen*tbytes;
if (optr + ovlsize + tsize > otop)
{ fwrite(oblock,1,optr-oblock,stdout);
optr = oblock;
}
memcpy(optr,iptr,ovlsize);
optr += ovlsize;
iptr += ovlsize;
if (iptr + tsize > itop)
{ int64 remains = itop-iptr;
if (remains > 0)
memcpy(iblock,iptr,remains);
iptr = iblock;
itop = iblock + remains;
itop += fread(itop,1,bsize-remains,input);
}
memcpy(optr,iptr,tsize);
optr += tsize;
iptr += tsize;
}
fclose(input);
}
if (optr > oblock)
fwrite(oblock,1,optr-oblock,stdout);
}
if (VERBOSE)
fprintf(stderr," Totalling %lld la\'s\n",novl);
free(pwd);
free(root);
free(oblock);
free(iblock-ptrsize);
exit (0);
}
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