int convert(FILE *infp, FILE *outfp, char *infname, char *outfname,
struct opts *opts) {
Read *r;
if (NULL == (r = fread_reading(infp, infname, opts->in_format))) {
fprintf(stderr, "failed to read file %s\n", infname);
return 1;
}
if (opts->sub_background) {
/*
trace_freq(r->traceA, r->NPoints);
trace_freq(r->traceC, r->NPoints);
trace_freq(r->traceG, r->NPoints);
trace_freq(r->traceT, r->NPoints);
*/
subtract_background(r);
/*
separate_dyes(r, matrix);
trace_freq(r->traceA, r->NPoints);
trace_freq(r->traceC, r->NPoints);
trace_freq(r->traceG, r->NPoints);
trace_freq(r->traceT, r->NPoints);
*/
reset_max_called_height(r);
}
if (opts->normalise) {
rescale_heights(r);
}
if (opts->scale) {
rescale_trace(r, opts->scale);
}
if (opts->name)
r->ident = strdup(opts->name);
else if (0 == strcmp(outfname, "(stdout)"))
r->ident = strdup(infname);
else
r->ident = strdup(outfname);
if (opts->compress_mode != -1)
set_compression_method(opts->compress_mode);
if (0 != (fwrite_reading(outfp, r, opts->out_format))) {
fprintf(stderr, "failed to write file %s\n", outfname);
read_deallocate(r);
return 1;
}
read_deallocate(r);
return 0;
}
Read *fread_pln(FILE *fp) {
return fread_reading(fp, NULL, TT_PLN);
}
Read *fread_ctf(FILE *fp) {
return fread_reading(fp, NULL, TT_CTF);
}
Read *fread_alf(FILE *fp) {
return fread_reading(fp, NULL, TT_ALF);
}
Read *fread_abi(FILE *fp) {
return fread_reading(fp, NULL, TT_ABI);
}
int convert(char *file, int format, mFILE *ofp, char *name, int output_conf) {
Read *r;
Exp_info *e;
char buf[50];
double aq;
if (format == TT_BIO) {
if (NULL == (r = read_reading(file, format))) {
fprintf(stderr, "%s: failed to read\n", file);
return 1;
}
} else {
FILE *infp;
if (NULL == (infp = open_trace_file(file, NULL))) {
perror(file);
return 1;
}
if (NULL == (r = fread_reading(infp, file, format))) {
fprintf(stderr, "%s: failed to read\n", file);
return 1;
}
fclose(infp);
}
e = read2exp(r, name);
if (NULL == e) {
fprintf(stderr, "Failed to create experiment file.\n");
read_deallocate(r);
return 1;
}
sprintf(buf, "%f", aq = avg_qual(r));
exp_set_entry(e, EFLT_AQ, buf);
exp_print_mfile(ofp, e);
if (output_conf && aq != 0) {
char *cstr;
int1 *conf;
int i;
conf = xmalloc(r->NBases * sizeof(*conf));
cstr = xmalloc(5 * r->NBases+2);
for (i = 0; i < r->NBases; i++) {
switch (r->base[i]) {
case 'a':
case 'A':
conf[i] = r->prob_A[i];
break;
case 'c':
case 'C':
conf[i] = r->prob_C[i];
break;
case 'g':
case 'G':
conf[i] = r->prob_G[i];
break;
case 't':
case 'T':
conf[i] = r->prob_T[i];
break;
default:
conf[i] = (r->prob_A[i] +
r->prob_C[i] +
r->prob_G[i] +
r->prob_T[i]) / 4;
break;
}
}
conf2str(conf, r->NBases, cstr);
exp_set_entry(e, EFLT_AV, cstr);
xfree(cstr);
xfree(conf);
}
read_deallocate(r);
exp_destroy_info(e);
mfflush(ofp);
return 0;
}
