void freeSeqInfo(SeqInfo *si)
/*
*
*/
{
#define FREE(F) \
if (si->F != NULL) {\
xfree(si->F);\
si->F = NULL;\
}
if (si != NULL) {
if(si->e != NULL) { exp_destroy_info(si->e); si->e = NULL; }
FREE(confidence);
FREE(origpos);
xfree(si);
}
}
/*
* Write a sequence to a FILE *fp of format "format". If "format" is 0,
* we choose our favourite - SCF.
*
* Returns:
* 0 for success
* -1 for failure
*/
int mfwrite_reading(mFILE *fp, Read *read, int format) {
int r = -1;
int no_compress = 0;
#ifdef _WIN32
/*
* jkb 09/06/00 comment below
*
* On windows "prog > file.scf" will work wrongly (compared to
* "prog file.scf") because windows is rather stupid. It treats ascii
* and binary streams differently, it considers stdout to be ascii unless
* told otherwise, and it can only be told otherwise by using non-ansi
* windows-specific function calls.
*/
if (format != TT_EXP && format != TT_PLN && fp->fp)
_setmode(_fileno(fp->fp), _O_BINARY);
#endif
switch (format) {
default:
/* Defaults to ZTR type */
#ifdef IOLIB_ZTR
case TT_ZTR:
case TT_ZTR2: {
ztr_t *ztr;
ztr = read2ztr(read);
compress_ztr(ztr, 2);
r = mfwrite_ztr(fp, ztr);
delete_ztr(ztr);
no_compress = 1;
break;
}
case TT_ZTR1: {
ztr_t *ztr;
ztr = read2ztr(read);
compress_ztr(ztr, 1);
r = mfwrite_ztr(fp, ztr);
delete_ztr(ztr);
break;
}
case TT_ZTR3: {
ztr_t *ztr;
ztr = read2ztr(read);
compress_ztr(ztr, 3);
r = mfwrite_ztr(fp, ztr);
delete_ztr(ztr);
no_compress = 1;
break;
}
#endif
#ifdef IOLIB_SCF
case TT_SCF: {
Scf *scf;
scf = read2scf(read);
r = mfwrite_scf(scf, fp);
scf_deallocate(scf);
break;
}
#endif
#ifdef IOLIB_CTF
case TT_CTF:
r = mfwrite_ctf(fp, read);
break;
#endif
#ifdef IOLIB_ABI
case TT_ABI:
/*return mfwrite_abi(fp, read); */
break;
#endif
#ifdef IOLIB_ALF
case TT_ALF:
/* return mfwrite_alf(fp, read); */
break;
#endif
#ifdef IOLIB_EXP
case TT_EXP: {
Exp_info *e = read2exp(read, read->ident ? read->ident : "unknown");
if (NULL == e) {
fprintf(stderr, "Failed to create experiment file.\n");
r = -1;
} else {
exp_print_mfile(fp, e);
exp_destroy_info(e);
r = 0;
}
break;
}
#endif
#ifdef IOLIB_PLN
case TT_PLN:
r = mfwrite_pln(fp, read);
break;
#endif
}
mftruncate(fp, -1);
if (r == 0 && !no_compress) {
fcompress_file(fp);
}
mfflush(fp);
return r;
}
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;
}