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#include <stdlib.h>
#include <stdio.h>
#include "DB.h"
#include "align.h"
int main(int argc, char *argv[])
{ char code, which;
int64 total;
int aread, bread;
char orient, chain;
int alen, blen;
int ab, ae, bb, be;
int diffs;
int len;
int tspace, small;
uint8 *tbuffer = NULL;
uint16 *sbuffer = NULL;
(void) argv;
// Process arguments
if (argc > 1)
{ fprintf(stderr,"Usage: LAa2b <(ascii) >(binary)\n");
exit (1);
}
if (fread(&code,sizeof(char),1,stdin) == 0)
code = 0;
while (code == '@' || code == '+' || code == '%')
{ fread(&which,sizeof(char),1,stdin);
fread(&total,sizeof(int64),1,stdin);
printf("%c %c %lld\n",code,which,total);
if (code == '@')
{ tbuffer = (uint8 *) malloc(2*total*sizeof(uint16));
sbuffer = (uint16 *) tbuffer;
}
if (fread(&code,sizeof(char),1,stdin) == 0)
code = 0;
}
small = 0;
if (tbuffer != NULL && code != 0)
{ if (code != 'X')
{ fprintf(stderr,"LAb2a: .las dump has traces but no X-info\n");
exit (1);
}
fread(&tspace,sizeof(int),1,stdin);
small = (tspace <= TRACE_XOVR && tspace != 0);
printf("X %d\n",tspace);
}
while (code != 0) // For each data item do
{ switch (code)
{ case 'P': // Alignment pair
fread(&aread,sizeof(int),1,stdin);
fread(&bread,sizeof(int),1,stdin);
fread(&orient,sizeof(char),1,stdin);
fread(&chain,sizeof(char),1,stdin);
printf("%c %d %d %c %c\n",code,aread,bread,orient,chain);
break;
case 'L': // Read lengths
scanf(" %d %d",&alen,&blen);
fread(&len,sizeof(int),1,stdin);
fread(&blen,sizeof(int),1,stdin);
printf("%c %d %d\n",code,alen,blen);
break;
case 'C': // Coordinate intervals
fread(&ab,sizeof(int),1,stdin);
fread(&ae,sizeof(int),1,stdin);
fread(&bb,sizeof(int),1,stdin);
fread(&be,sizeof(int),1,stdin);
printf("%c %d %d %d %d\n",code,ab,ae,bb,be);
break;
case 'D': // Differences
fread(&diffs,sizeof(int),1,stdin);
printf("%c %d\n",code,diffs);
break;
case 'T': // Mask
if (tbuffer == NULL)
{ fprintf(stderr,"LAb2a: .las dump has traces but no @ T-info\n");
exit (1);
}
fread(&len,sizeof(int),1,stdin);
printf("%c %d\n",code,len);
len *= 2;
if (small)
{ fread(tbuffer,sizeof(uint8),len,stdin);
for (int i = 0; i < len; i += 2)
printf(" %d %d\n",tbuffer[i],tbuffer[i+1]);
}
else
{ fread(sbuffer,sizeof(uint16),len,stdin);
for (int i = 0; i < len; i += 2)
printf(" %d %d\n",sbuffer[i],sbuffer[i+1]);
}
}
if (fread(&code,sizeof(char),1,stdin) == 0)
code = 0;
}
exit (0);
}
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