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LAa2b.c
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LAa2b.c
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#include <stdlib.h>
#include <stdio.h>
int main(int argc, char *argv[])
{ char code, which;
long long int total;
int aread, bread;
char orient, chain;
int alen, blen;
int ab, ae, bb, be;
int diffs;
int len;
unsigned char *tbuffer;
(void) argv;
// Process arguments
if (argc > 1)
{ fprintf(stderr,"Usage: LAa2b <(ascii) >(binary)\n");
exit (1);
}
while (scanf(" %c",&code) == 1) // Header lines
if (code == '@' || code == '+' || code == '%')
{ scanf(" %c %lld",&which,&total);
fwrite(&code,sizeof(char),1,stdout);
fwrite(&which,sizeof(char),1,stdout);
fwrite(&total,sizeof(long long int),1,stdout);
if (code == '@')
tbuffer = malloc(2*total*sizeof(unsigned char));
}
else
{ ungetc(code,stdin);
break;
}
while (scanf(" %c",&code) == 1) // For each data line do
{ fwrite(&code,sizeof(char),1,stdout);
switch (code)
{ case 'P': // Alignment pair
scanf(" %d %d %c %c",&aread,&bread,&orient,&chain);
fwrite(&aread,sizeof(int),1,stdout);
fwrite(&bread,sizeof(int),1,stdout);
fwrite(&orient,sizeof(char),1,stdout);
fwrite(&chain,sizeof(char),1,stdout);
break;
case 'L': // Read lengths
scanf(" %d %d",&alen,&blen);
fwrite(&len,sizeof(int),1,stdout);
fwrite(&blen,sizeof(int),1,stdout);
break;
case 'C': // Coordinate intervals
scanf(" %d %d %d %d",&ab,&ae,&bb,&be);
fwrite(&ab,sizeof(int),1,stdout);
fwrite(&ae,sizeof(int),1,stdout);
fwrite(&bb,sizeof(int),1,stdout);
fwrite(&be,sizeof(int),1,stdout);
break;
case 'D': // Differences
scanf(" %d",&diffs);
fwrite(&diffs,sizeof(int),1,stdout);
break;
case 'T': // Mask
scanf(" %d",&len);
fwrite(&len,sizeof(int),1,stdout);
len *= 2;
for (int i = 0; i < len; i += 2)
scanf(" %hhd %hhd",tbuffer+i,tbuffer+(i+1));
fwrite(tbuffer,sizeof(unsigned char),len,stdout);
}
}
exit (0);
}