static int convert(char *in, mFILE *ofp, char *out, int format, int prec,
int comp, int normalise) {
Read *r;
if (NULL == (r = read_reading(in, format))) {
fprintf(stderr, "%s: failed to read\n", in);
return 1;
}
if (normalise) {
subtract_background(r);
reset_max_called_height(r);
rescale_heights(r);
}
add_comments(r, in, format);
if (prec == 1)
scale_trace8(r);
if (comp != -1)
set_compression_method(comp);
if (0 != (mfwrite_reading(ofp, r, TT_SCF))) {
fprintf(stderr, "%s: failed to write\n", out);
read_deallocate(r);
return 1;
}
read_deallocate(r);
return 0;
}
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;
}