size_t load_rectangle_to_file(int rect_id, struct cseq **sequences, int cseq_count)
{
int i;
size_t size;
char tmpfilename[255];
FILE *tmpfile;
size = 0;
sprintf(tmpfilename, "%s/rect%03d.cfa", outdirname, rect_id);
tmpfile = fopen(tmpfilename, "w");
if(!tmpfile)
return 0;
for(i = 0; i < cseq_count; i++) {
cseq_write(tmpfile, sequences[i]);
size += cseq_size(sequences[i]);
}
fclose(tmpfile);
return size;
}
int main(int argc, char ** argv)
{
const char *progname = "sand_compress_reads";
FILE * infile;
FILE * outfile;
int quiet_mode = 0;
struct seq *s;
struct cseq *c;
signed char d;
int clip = 0;
int internal = 0;
char tmp_id[128];
int count = 0;
while((d=getopt(argc,argv,"cvqhi")) > -1) {
switch(d) {
case 'c':
clip = 1;
break;
case 'i':
internal = 1;
break;
case 'q':
quiet_mode = 1;
break;
case 'v':
cctools_version_print(stdout, progname);
exit(0);
break;
case 'h':
default:
show_help(progname);
exit(0);
break;
}
}
cctools_version_debug(D_DEBUG, argv[0]);
if( optind<argc ) {
infile = fopen(argv[optind], "r");
if(!infile) {
fprintf(stderr,"%s: couldn't open %s: %s\n",progname,argv[optind],strerror(errno));
return 1;
}
optind++;
} else {
infile = stdin;
}
if( optind<argc ) {
outfile = fopen(argv[optind],"w");
if(!outfile) {
fprintf(stderr,"%s: couldn't open %s: %s\n",progname,argv[optind],strerror(errno));
return 1;
}
optind++;
} else {
outfile = stdout;
}
while((s = seq_read(infile))) {
if(clip != 0 || internal != 0){
strcpy(tmp_id, s->name);
strcpy(s->name, strtok(tmp_id,","));
if(internal != 0){
strcpy(s->name, strtok(NULL,","));
}
}
c = seq_compress(s);
cseq_write(outfile,c);
cseq_free(c);
seq_free(s);
count++;
}
if(!quiet_mode) {
fprintf(stderr,"%d sequences compressed.\n",count);
}
fclose(infile);
fclose(outfile);
return 0;
}
