/*
* Read the SCF format sequence from FILE *fp into a 'scf' structure.
* A NULL result indicates failure.
*/
Scf *fread_scf(FILE *fp) {
Scf *scf;
Header h;
int err;
float scf_version;
int sections = read_sections(0);
/* Read header */
if (read_scf_header(fp, &h) == -1) {
return NULL;
}
/* Allocate memory */
if (NULL == (scf = scf_allocate(h.samples, h.sample_size,
h.bases, h.comments_size,
h.private_size)))
return NULL;
/* fake things for older style SCF -- SD */
if (h.sample_size != 1 && h.sample_size != 2) h.sample_size = 1;
scf_version = scf_version_str2float(h.version);
memcpy(&scf->header, &h, sizeof(Header));
if (sections & READ_SAMPLES) {
/* Read samples */
if (fseek(fp, (off_t)h.samples_offset, 0 /* SEEK_SET */) != 0) {
scf_deallocate(scf);
return NULL;
}
if ( 2.9 > scf_version ) {
if (h.sample_size == 1) {
err= read_scf_samples1(fp, scf->samples.samples1, h.samples);
}
else {
err= read_scf_samples2(fp, scf->samples.samples2, h.samples);
}
}
else {
if (h.sample_size == 1) {
err= read_scf_samples31(fp, scf->samples.samples1, h.samples);
}
else {
err= read_scf_samples32(fp, scf->samples.samples2, h.samples);
}
}
if (-1 == err) {
scf_deallocate(scf);
return NULL;
}
}
if (sections & READ_BASES) {
/* Read bases */
if (fseek(fp, (off_t)h.bases_offset, 0 /* SEEK_SET */) != 0) {
scf_deallocate(scf);
return NULL;
}
if ( 2.9 > scf_version ) {
if (-1 == read_scf_bases(fp, scf->bases, h.bases)) {
scf_deallocate(scf);
return NULL;
}
}
else {
if (-1 == read_scf_bases3(fp, scf->bases, h.bases)) {
scf_deallocate(scf);
return NULL;
}
}
}
if (sections & READ_COMMENTS) {
/* Read comments */
if (scf->comments) {
if (fseek(fp,(off_t)(h.comments_offset), 0) != 0
|| -1 == read_scf_comment(fp, scf->comments,
h.comments_size)) {
/*
* Was: "scf_deallocate(scf); return NULL;".
* We now simply clear the comments and gracefully continue.
*/
fprintf(stderr, "Warning: SCF file had invalid comment field\n");
xfree(scf->comments);
scf->comments = NULL;
} else {
scf->comments[h.comments_size] = '\0';
}
}
}
/* Read private data */
if (h.private_size) {
if (-1 == fseek(fp, (off_t)(h.private_offset), 0) ||
h.private_size != fread(scf->private_data, 1, h.private_size, fp)){
scf_deallocate(scf);
return NULL;
}
}
return scf;
}
/*
* 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;
}
/*
* Translates a Read structure into a Scf structure.
* The Read structure is left unchanged.
*
* Returns:
* A pointer to an allocated Scf structure upon success.
* NULL upon failure.
*/
Scf *read2scf(Read *read) {
Scf *scf;
register int i, i_end;
int sample_size;
/* allocate */
sample_size = read->maxTraceVal >= 0x100 ? 2 : 1;
scf = scf_allocate(read->NPoints, sample_size, read->NBases, 0, 0);
if (NULL == scf)
return NULL;
/* copy the samples */
i_end = read->NPoints;
scf->header.samples = i_end;
if (sample_size == 1) {
scf->header.sample_size = 1;
for (i = 0; i < i_end; i++) {
scf->samples.samples1[i].sample_A = (uint_1)read->traceA[i];
scf->samples.samples1[i].sample_C = (uint_1)read->traceC[i];
scf->samples.samples1[i].sample_G = (uint_1)read->traceG[i];
scf->samples.samples1[i].sample_T = (uint_1)read->traceT[i];
}
} else {
scf->header.sample_size = 2;
for (i = 0; i < i_end; i++) {
scf->samples.samples2[i].sample_A = read->traceA[i];
scf->samples.samples2[i].sample_C = read->traceC[i];
scf->samples.samples2[i].sample_G = read->traceG[i];
scf->samples.samples2[i].sample_T = read->traceT[i];
}
}
/* copy the bases */
i_end = read->NBases;
scf->header.bases = i_end;
for (i = 0; i < i_end; i++) {
scf->bases[i].peak_index = read->basePos ? read->basePos[i] : i;
scf->bases[i].prob_A = read->prob_A ? read->prob_A[i] : 0;
scf->bases[i].prob_C = read->prob_A ? read->prob_C[i] : 0;
scf->bases[i].prob_G = read->prob_A ? read->prob_G[i] : 0;
scf->bases[i].prob_T = read->prob_A ? read->prob_T[i] : 0;
scf->bases[i].base = read->base ? read->base[i] : '-';
}
/* allocate and copy the comments */
if (read->info) {
scf->header.comments_size = strlen(read->info) + 1;
scf->comments = (char *)xmalloc(scf->header.comments_size);
if (NULL == scf->comments) {
scf_deallocate(scf);
return NULL;
}
memcpy(scf->comments, read->info, scf->header.comments_size - 1);
/* just to make sure */
scf->comments[scf->header.comments_size-1] = '\0';
}
/* other bits and pieces */
scf->header.bases_left_clip = read->leftCutoff;
scf->header.bases_right_clip = read->NBases - read->rightCutoff + 1;
scf->header.code_set = CSET_DEFAULT;
memcpy(scf->header.version, scf_version_float2str(SCF_VERSION), 4);
return scf;
}
/*
* Read a sequence from a FILE *fp of format "format". If "format" is 0
* (ANY_FORMAT), we automatically determine the correct format.
* We still pass a filename 'fn' although this isn't used other than for
* filling in the read->trace_name field.
*
* NB this function should NOT be used when Biolims support is required
* (as biolims readings are not stored in a file)
*
* Returns:
* Read * for success
* NULLRead for failure
*/
Read *mfread_reading(mFILE *fp, char *fn, int format) {
Read *read;
mFILE *newfp;
if (!fn)
fn = "(unknown)";
newfp = freopen_compressed(fp, NULL);
if (newfp != fp) {
fp = newfp;
} else {
newfp = NULL;
}
#ifdef _WIN32
/*
* jkb 16/05/00 comment below
*
* On windows "prog < file.abi" will work wrongly (compared to
* "prog file.abi") because windows is rather stupid. It treats ascii
* and binary streams differently, it considers stdin 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
if (format == TT_ANY) {
format = fdetermine_trace_type(fp);
mrewind(fp);
}
switch (format) {
case TT_UNK:
case TT_ERR:
errout("File '%s' has unknown trace type\n", fn);
read = NULLRead;
break;
#ifdef IOLIB_SCF
case TT_SCF: {
Scf *scf;
scf = mfread_scf(fp);
if (scf) {
read = scf2read(scf);
scf_deallocate(scf);
} else
read = NULLRead;
break;
}
#endif
#ifdef IOLIB_CTF
case TT_CTF:
read = mfread_ctf(fp);
break;
#endif
#ifdef IOLIB_ZTR
case TT_ZTR:
case TT_ZTR1:
case TT_ZTR2:
case TT_ZTR3: {
ztr_t *ztr;
if ((ztr = mfread_ztr(fp))) {
uncompress_ztr(ztr);
read = ztr2read(ztr);
delete_ztr(ztr);
} else {
read = NULLRead;
}
break;
}
#endif
#ifdef IOLIB_ABI
case TT_ABI:
read = mfread_abi(fp);
break;
#endif
#ifdef IOLIB_ALF
case TT_ALF:
read = mfread_alf(fp);
break;
#endif
#ifdef IOLIB_EXP
case TT_EXP: {
/* FIXME: we shouldn't redirect like this */
Exp_info *e = exp_mfread_info(fp);
read = e ? exp2read(e,fn) : NULLRead;
break;
}
#endif
#ifdef IOLIB_PLN
case TT_PLN:
read = mfread_pln(fp);
break;
#endif
default:
errout("Unknown format %d specified to read_reading()\n", format);
read = NULLRead;
}
if (read != NULLRead && (read->trace_name = (char *)xmalloc(strlen(fn)+1)))
strcpy(read->trace_name, fn);
if (newfp) mfclose(newfp);
return read;
}
